From 864b50ba094a1a785fe97abbe30578c37c7172d1 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Tue, 24 May 2022 14:39:39 +0100 Subject: [PATCH 01/84] New --strictly-novel option to downplay alleles which violate Mendelian inheritance but are not novel --- NEWS | 5 ++++ plugins/trio-dnm2.c | 50 +++++++++++++++++++++------------ test/test.pl | 2 ++ test/trio-dnm/trio-dnm.11.1.out | 2 ++ test/trio-dnm/trio-dnm.11.2.out | 2 ++ test/trio-dnm/trio-dnm.11.vcf | 11 ++++++++ 6 files changed, 54 insertions(+), 18 deletions(-) create mode 100644 test/trio-dnm/trio-dnm.11.1.out create mode 100644 test/trio-dnm/trio-dnm.11.2.out create mode 100644 test/trio-dnm/trio-dnm.11.vcf diff --git a/NEWS b/NEWS index 44352f609..e12f69448 100644 --- a/NEWS +++ b/NEWS @@ -11,6 +11,11 @@ - Suppress the output of MQSBZ and FS annotations in absence of alternate allele +* bcftools +trio-dnm2 + + - New -n, --strictly-novel option to downplay alleles which violate Mendelian + inheritance but are not novel + ## Release 1.15.1 (7th April 2022) diff --git a/plugins/trio-dnm2.c b/plugins/trio-dnm2.c index a23bc01ca..33ccf954c 100644 --- a/plugins/trio-dnm2.c +++ b/plugins/trio-dnm2.c @@ -1,19 +1,19 @@ /* The MIT License - Copyright (c) 2018-2021 Genome Research Ltd. + Copyright (c) 2018-2022 Genome Research Ltd. Author: Petr Danecek - + Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: - + The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. - + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE @@ -117,6 +117,7 @@ typedef struct int with_ppl, with_pad; // --with-pPL or --with-pAD int use_dng_priors; // --dng-priors int need_QS; + int strictly_novel; priors_t priors, priors_X, priors_XX; } args_t; @@ -130,7 +131,7 @@ const char *about(void) static const char *usage_text(void) { - return + return "\n" "About: Screen variants for possible de-novo mutations in trios\n" "Usage: bcftools +trio-dnm2 [OPTIONS]\n" @@ -168,6 +169,7 @@ static const char *usage_text(void) " --mrate NUM Mutation rate [1e-8]\n" " --pn FRAC[,NUM] Tolerance to parental noise or mosaicity, given as fraction of QS or number of reads [0.005,0]\n" " --pns FRAC[,NUM] Same as --pn but is not applied to alleles observed in both parents (fewer FPs, more FNs) [0.045,0]\n" + " -n, --strictly-novel When Mendelian inheritance is violiated, score highly only novel alleles (e.g. in LoH regions)\n" " --use-DNG The original DeNovoGear model, implies --dng-priors\n" " --use-NAIVE A naive calling model which uses only FMT/GT to determine DNMs\n" " --with-pAD Do not use FMT/QS but parental FMT/AD\n" @@ -365,7 +367,7 @@ static double init_mf_priors(args_t *args, int fi, int mi) gt_prior = p_poly / 57.; else if ( nref_mf==4 ) // 0 ALTs; 00,00 gt_prior = p_homref; - else if ( nref_mf==3 ) // this and all remaining have 1 unique ALT allele; 00,0x + else if ( nref_mf==3 ) // this and all remaining have 1 unique ALT allele; 00,0x gt_prior = p_nonref * (4.0/15.0) * (1.0/3.0); else if ( nref_mf==2 && ma==mb ) // hom alt; 00,xx gt_prior = p_nonref * (2.0/15.0) * (1.0/3.0); @@ -466,7 +468,7 @@ static void init_DNG_tprob_mprob(args_t *args, int fi, int mi, int ci, double *t } else { - if ( ca!=fa && ca!=fb && ca!=ma && ca!=mb && + if ( ca!=fa && ca!=fb && ca!=ma && ca!=mb && cb!=fa && cb!=fb && cb!=ma && cb!=mb ) *mprob = args->mrate * args->mrate; // two mutations else *mprob = args->mrate; @@ -502,7 +504,17 @@ static void init_tprob_mprob(args_t *args, int fi, int mi, int ci, double *tprob // tprob .. genotype transmission probability L(GC|GM,GF), 0 if not compatible with Mendelian inheritance // mprob .. probability of mutation - if ( ((ca==fa||ca==fb) && (cb==ma||cb==mb)) || ((ca==ma||ca==mb) && (cb==fa||cb==fb)) ) + int is_novel; + if ( args->strictly_novel ) // account for LoH sites, see chr1:10000057 in trio-dnm.11.vcf + { + is_novel = ( (ca!=fa && ca!=fb && ca!=ma && ca!=mb) || (cb!=fa && cb!=fb && cb!=ma && cb!=mb) ) ? 1 : 0; + } + else + { + is_novel = ( ((ca==fa||ca==fb) && (cb==ma||cb==mb)) || ((ca==ma||ca==mb) && (cb==fa||cb==fb)) ) ? 0 : 1; + } + + if ( !is_novel ) { if ( fa==fb && ma==mb ) *tprob = 1; else if ( fa==fb || ma==mb ) *tprob = 0.5; @@ -590,7 +602,7 @@ static void init_priors(args_t *args, priors_t *priors, init_priors_t type) if ( args->use_dng_priors ) init_DNG_tprob_mprob(args,fi,mi,ci,&tprob,&mprob,&allele); - else if ( type==autosomal ) + else if ( type==autosomal || args->strictly_novel ) init_tprob_mprob(args,fi,mi,ci,&tprob,&mprob,&allele); else if ( type==chrX ) init_tprob_mprob_chrX(args,mi,ci,&tprob,&mprob,&allele); @@ -849,7 +861,7 @@ static double process_trio_ACM(args_t *args, priors_t *priors, int nals, double else if ( fa==fb ) fpl += qs[iFATHER][i]; } - } + } int mi = 0; for (ma=0; madenovo[fi][mi][ci],fi,mi,ci,mpl,fpl,cpl,priors->pprob[fi][mi][ci], val,sum,(priors->denovo[fi][mi][ci] && max < val)?'*':'-'); #endif @@ -927,7 +939,7 @@ static double process_trio_DNG(args_t *args, priors_t *priors, int nals, double val = pl[iCHILD][ci] + pl[iFATHER][fi] + pl[iMOTHER][mi] + priors->pprob[fi][mi][ci]; sum = sum_log(val,sum); #if DEBUG - if(val!=-HUGE_VAL) + if(val!=-HUGE_VAL) fprintf(stderr,"m,f,c: %d%d+%d%d=%d%d dn=%d (%d,%d,%d) mpl,fpl,cpl: %+e %+e %+e \t prior:%+e \t pval=%+e sum=%+e %c\n", mb,ma,fb,fa,cb,ca,priors->denovo[fi][mi][ci],fi,mi,ci,pl[iMOTHER][mi],pl[iFATHER][fi],pl[iCHILD][ci],priors->pprob[fi][mi][ci], val,sum,(priors->denovo[fi][mi][ci] && max < val)?'*':'-'); #endif @@ -1029,7 +1041,7 @@ static void many_alts_trim(args_t *args, int *_nals, double *pl[3], int *_npl, d for (i=2; i1 && arr[idx[j]] < arr[idx[j-1]]; j--) tmp = idx[j], idx[j] = idx[j-1], idx[j-1] = tmp; - + for (i=0; i<3; i++) { for (j=0; j<4; j++) args->alt_tmp[j] = qs[i][args->alt_idx[j]]; @@ -1140,12 +1152,12 @@ static void set_trio_QS_noisy(args_t *args, trio_t *trio, double *pqs[3], int nq double tmp = qs[k]; if ( max_qs < tmp ) max_qs = tmp; } - for (k=0; kntrio; i++) { if ( args->filter && !args->trio[i].pass ) continue; - + int ignore_father = 0; // father is irrelevant for male proband on chrX and can have missing GT priors_t *priors; if ( !is_chrX ) priors = &args->priors; @@ -1541,6 +1553,7 @@ int run(int argc, char **argv) {"with-pad",no_argument,0,13}, {"chrX",required_argument,0,'X'}, {"min-score",required_argument,0,'m'}, + {"strictly-novel",no_argument,0,'n'}, {"include",required_argument,0,'i'}, {"exclude",required_argument,0,'e'}, {"output",required_argument,NULL,'o'}, @@ -1557,9 +1570,9 @@ int run(int argc, char **argv) }; int c; char *tmp; - while ((c = getopt_long(argc, argv, "p:P:o:O:s:i:e:r:R:t:T:m:au:X:",loptions,NULL)) >= 0) + while ((c = getopt_long(argc, argv, "p:P:o:O:s:i:e:r:R:t:T:m:au:X:n",loptions,NULL)) >= 0) { - switch (c) + switch (c) { case 1 : args->force_ad = 1; break; case 2 : free(args->dnm_score_tag); args->dnm_score_tag = strdup(optarg); break; @@ -1636,6 +1649,7 @@ int run(int argc, char **argv) case 'm': args->min_score = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: -M, --min-score %s\n", optarg); break; + case 'n': args->strictly_novel = 1; break; case 'h': case '?': default: error("%s", usage_text()); break; diff --git a/test/test.pl b/test/test.pl index 6fb1c66c4..1b15f69de 100755 --- a/test/test.pl +++ b/test/test.pl @@ -583,6 +583,8 @@ test_vcf_plugin($opts,in=>'trio-dnm/trio-dnm.9',out=>'trio-dnm/trio-dnm.9.1.out',cmd=>'+trio-dnm2',args=>"-p 1X:proband,father,mother --use-NAIVE | $$opts{bin}/bcftools query -f'[\\t%DNM]\\n'"); test_vcf_plugin($opts,in=>'trio-dnm/trio-dnm.9',out=>'trio-dnm/trio-dnm.9.2.out',cmd=>'+trio-dnm2',args=>"-p 2X:proband,father,mother --use-NAIVE | $$opts{bin}/bcftools query -f'[\\t%DNM]\\n'"); test_vcf_plugin($opts,in=>'trio-dnm/trio-dnm.10',out=>'trio-dnm/trio-dnm.10.1.out',cmd=>'+trio-dnm2',args=>"-p proband,father,mother --with-pAD | $$opts{bin}/bcftools query -f'[\\t%DNM][\\t%VAF]\\n'"); +test_vcf_plugin($opts,in=>'trio-dnm/trio-dnm.11',out=>'trio-dnm/trio-dnm.11.1.out',cmd=>'+trio-dnm2',args=>"-p proband,father,mother | $$opts{bin}/bcftools query -f'[\\t%DNM][\\t%VAF]\\n'"); +test_vcf_plugin($opts,in=>'trio-dnm/trio-dnm.11',out=>'trio-dnm/trio-dnm.11.2.out',cmd=>'+trio-dnm2',args=>"-p 1X:proband,father,mother --strictly-novel | $$opts{bin}/bcftools query -f'[\\t%DNM][\\t%VAF]\\n'"); test_vcf_plugin($opts,in=>'gvcfz',out=>'gvcfz.1.out',cmd=>'+gvcfz',args=>qq[-g 'PASS:GT!="alt"' -a | $$opts{bin}/bcftools query -f'%POS\\t%REF\\t%ALT\\t%END[\\t%GT][\\t%DP][\\t%GQ][\\t%RGQ]\\n']); test_vcf_plugin($opts,in=>'gvcfz',out=>'gvcfz.2.out',cmd=>'+gvcfz',args=>qq[-g 'PASS:GQ>10; FLT:-' -a | $$opts{bin}/bcftools query -f'%POS\\t%REF\\t%ALT\\t%FILTER\\t%END[\\t%GT][\\t%DP][\\t%GQ][\\t%RGQ]\\n']); test_vcf_plugin($opts,in=>'gvcfz.2',out=>'gvcfz.2.1.out',cmd=>'+gvcfz',args=>qq[-g 'PASS:GT!="alt"' -a | $$opts{bin}/bcftools query -f'%POS\\t%REF\\t%ALT\\t%FILTER\\t%END[\\t%GT][\\t%DP]\\n']); diff --git a/test/trio-dnm/trio-dnm.11.1.out b/test/trio-dnm/trio-dnm.11.1.out new file mode 100644 index 000000000..9a4d3078f --- /dev/null +++ b/test/trio-dnm/trio-dnm.11.1.out @@ -0,0 +1,2 @@ + -0.0953102 . . 100 100 0 + -20.5943 . . 79 56 0 diff --git a/test/trio-dnm/trio-dnm.11.2.out b/test/trio-dnm/trio-dnm.11.2.out new file mode 100644 index 000000000..04abbf9ee --- /dev/null +++ b/test/trio-dnm/trio-dnm.11.2.out @@ -0,0 +1,2 @@ + -inf . . 0 0 100 + -inf . . 79 56 0 diff --git a/test/trio-dnm/trio-dnm.11.vcf b/test/trio-dnm/trio-dnm.11.vcf new file mode 100644 index 000000000..bdaacabba --- /dev/null +++ b/test/trio-dnm/trio-dnm.11.vcf @@ -0,0 +1,11 @@ +##fileformat=VCFv4.2 +##reference=file:///lustre/scratch118/humgen/resources/ref/Homo_sapiens/GRCh38_15/Homo_sapiens.GRCh38_15.fa +##contig= +##contig= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT proband father mother +chr1 10000057 . C T . . . GT:PL:AD:QS 1/1:255,90,0:0,30:0,1116 1/1:255,78,0:0,26:0,921 0/0:0,114,255:38,0:1364,0 +chrX 10000804 . C G . . . GT:PL:AD:QS 0/1:255,0,85:5,19:174,671 0/1:202,0,157:7,9:255,323 0/0:0,30,227:10,0:370,0 From 5eaab694f70b16e6b58e6980c459153aa30c566c Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Mon, 30 May 2022 15:08:17 +0100 Subject: [PATCH 02/84] Set --pn/--pns separately for SNVs and indels, make the indel default strict (0) --- plugins/trio-dnm2.c | 126 ++++++++++++++++++++++++++++++++------------ 1 file changed, 92 insertions(+), 34 deletions(-) diff --git a/plugins/trio-dnm2.c b/plugins/trio-dnm2.c index 33ccf954c..ee4e13014 100644 --- a/plugins/trio-dnm2.c +++ b/plugins/trio-dnm2.c @@ -82,6 +82,13 @@ typedef struct } priors_t; +typedef struct +{ + double abs, frac; + double abs1, frac1; // applied only if allele observed in a single parent, but not when observed in both +} +pnoise_t; + typedef struct { int argc, filter_logic, regions_is_file, targets_is_file, output_type, record_cmd_line, clevel; @@ -112,8 +119,7 @@ typedef struct *dnm_allele_tag; int dnm_score_type; // given by e.g. --dnm-tag DNM:log double mrate; // --mrate, mutation rate - double pn_abs,pn_frac; // --pn - double pns_abs,pns_frac; // --pns + pnoise_t pn_snv, pn_indel; // --pn and --pns for SNVs and indels int with_ppl, with_pad; // --with-pPL or --with-pAD int use_dng_priors; // --dng-priors int need_QS; @@ -167,8 +173,9 @@ static const char *usage_text(void) "Model options:\n" " --dng-priors Use the original DeNovoGear priors (including bugs in prior assignment, but with chrX bugs fixed)\n" " --mrate NUM Mutation rate [1e-8]\n" - " --pn FRAC[,NUM] Tolerance to parental noise or mosaicity, given as fraction of QS or number of reads [0.005,0]\n" - " --pns FRAC[,NUM] Same as --pn but is not applied to alleles observed in both parents (fewer FPs, more FNs) [0.045,0]\n" + " --pn FRAC[,NUM][:type] Tolerance to parental noise or mosaicity, given as fraction of QS or number of reads. The type is\n" + " 'snv', 'indel' or 'both' [--pn 0.005,0:snv --pn 0,0:indel]\n" + " --pns FRAC[,NUM][:type] Same as --pn but applied for alleles observed in a single parent [--pns 0.045,0:snv --pns 0,0:indel]\n" " -n, --strictly-novel When Mendelian inheritance is violiated, score highly only novel alleles (e.g. in LoH regions)\n" " --use-DNG The original DeNovoGear model, implies --dng-priors\n" " --use-NAIVE A naive calling model which uses only FMT/GT to determine DNMs\n" @@ -1088,11 +1095,11 @@ static void set_trio_QS(args_t *args, trio_t *trio, double *pqs[3], int nqs1) for (k=0; kpn_abs && !args->pns_abs && !args->pns_frac ) n_ad = 0; // AD is not required + if ( n_ad && !pnoise->abs && !pnoise->abs1 && !pnoise->frac1 ) n_ad = 0; // AD is not required if ( n_ad ) { // Noise tolerance will be applied only for alleles observed in a single parent (a possible mosaic @@ -1109,18 +1116,18 @@ static void set_trio_QS_noisy(args_t *args, trio_t *trio, double *pqs[3], int nq pqs[j] = args->qs3 + j*nqs1; double pn = 0, pns = 0; double sum_qs = 0, sum_ad = 0; - if ( (args->pn_frac || args->pns_frac) && j!=iCHILD ) + if ( (pnoise->frac || pnoise->frac1) && j!=iCHILD ) { for (k=0; kpn_frac; - pns = sum_qs * args->pns_frac; + pn = sum_qs * pnoise->frac; + pns = sum_qs * pnoise->frac1; if ( n_ad ) { // "absolute" threshold: find the average QS per read from AD and use that // if bigger than the relative threshold for (k=0; kpn_abs * sum_qs / sum_ad ) pn = args->pn_abs * sum_qs / sum_ad; - if ( pns < args->pns_abs * sum_qs / sum_ad ) pns = args->pns_abs * sum_qs / sum_ad; + if ( pn < pnoise->abs * sum_qs / sum_ad ) pn = pnoise->abs * sum_qs / sum_ad; + if ( pns < pnoise->abs1 * sum_qs / sum_ad ) pns = pnoise->abs1 * sum_qs / sum_ad; } } // Reduce QS for all alleles to account for noise @@ -1359,6 +1366,8 @@ static void process_record(args_t *args, bcf1_t *rec) hts_expand(double,3*nqs1,args->mqs3,args->qs3); } + pnoise_t *pnoise = (bcf_get_variant_types(rec) & VCF_INDEL) ? &args->pn_indel : &args->pn_snv; + int is_chrX = 0; if ( regidx_overlap(args->chrX_idx,bcf_seqname(args->hdr,rec),rec->pos,rec->pos+rec->rlen,NULL) ) is_chrX = 1; @@ -1378,7 +1387,7 @@ static void process_record(args_t *args, bcf1_t *rec) double *pqs[3]; if ( args->use_model==USE_ACM ) - set_trio_QS_noisy(args,&args->trio[i],pqs,nqs1,n_ad); + set_trio_QS_noisy(args,&args->trio[i],pqs,nqs1,n_ad,pnoise); else if ( rec->n_allele > 4 ) // DNG does not use QS, but QS is needed when trimming ALTs set_trio_QS(args,&args->trio[i],pqs,nqs1); @@ -1471,26 +1480,34 @@ static void set_option(args_t *args, char *optarg) else if ( !strcasecmp(opt,"pn") || !strcasecmp(opt,"pnoise") ) { if ( !val ) error("Error: expected value with -u %s, e.g. -u %s=0.05\n",opt,opt); - args->pn_frac = strtod(val,&tmp); + double pn_frac,pn_abs = 0; + pn_frac = strtod(val,&tmp); if ( *tmp && *tmp==',' ) { - args->pn_abs = strtod(tmp+1,&tmp); + pn_abs = strtod(tmp+1,&tmp); if ( *tmp ) error("Could not parse: -u %s\n", optarg); } - if ( args->pn_frac<0 || args->pn_frac>1 ) error("Error: expected value from the interval [0,1] for -u %s\n", optarg); - if ( args->pn_abs<0 ) error("Error: expected positive value for -u %s\n", optarg); + if ( pn_frac<0 || pn_frac>1 ) error("Error: expected value from the interval [0,1] for -u %s\n", optarg); + if ( pn_abs<0 ) error("Error: expected positive value for -u %s\n", optarg); + args->pn_snv.frac = pn_frac; + args->pn_snv.abs = pn_abs; + args->pn_indel = args->pn_snv; } else if ( !strcasecmp(opt,"pns") ) { if ( !val ) error("Error: expected value with -u %s, e.g. -u %s=0.05\n",opt,opt); - args->pns_frac = strtod(val,&tmp); + double pn_frac,pn_abs = 0; + pn_frac = strtod(val,&tmp); if ( *tmp && *tmp==',' ) { - args->pns_abs = strtod(tmp+1,&tmp); + pn_abs = strtod(tmp+1,&tmp); if ( *tmp ) error("Could not parse: -u %s\n", optarg); } - if ( args->pns_frac<0 || args->pn_frac>1 ) error("Error: expected value from the interval [0,1] for -u %s\n", optarg); - if ( args->pns_abs<0 ) error("Error: expected positive value for -u %s\n", optarg); + if ( pn_frac<0 || pn_frac>1 ) error("Error: expected value from the interval [0,1] for -u %s\n", optarg); + if ( pn_abs<0 ) error("Error: expected positive value for -u %s\n", optarg); + args->pn_snv.frac1 = pn_frac; + args->pn_snv.abs1 = pn_abs; + args->pn_indel = args->pn_snv; } else if ( !strcasecmp(opt,"DNG") ) { args->use_model = USE_DNG; args->use_dng_priors = 1; } else if ( !strcasecmp(opt,"dng-priors") ) args->use_dng_priors = 1; @@ -1524,10 +1541,10 @@ int run(int argc, char **argv) args->dnm_vaf_tag = strdup("VAF"); args->dnm_allele_tag = strdup("VA"); args->mrate = 1e-8; - args->pn_frac = 0.005; - args->pn_abs = 0; - args->pns_frac = 0.045; - args->pns_abs = 0; + args->pn_snv.frac = 0.005; + args->pn_snv.frac1 = 0.045; + args->pn_snv.abs = 0; + args->pn_snv.abs1 = 0; args->record_cmd_line = 1; args->regions_overlap = 1; args->targets_overlap = 0; @@ -1570,6 +1587,7 @@ int run(int argc, char **argv) }; int c; char *tmp; + double pn_abs, pn_frac; while ((c = getopt_long(argc, argv, "p:P:o:O:s:i:e:r:R:t:T:m:au:X:n",loptions,NULL)) >= 0) { switch (c) @@ -1581,24 +1599,64 @@ int run(int argc, char **argv) case 5 : args->use_dng_priors = 1; break; case 6 : args->mrate = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: --mrate %s\n", optarg); break; case 7 : - args->pn_frac = strtod(optarg,&tmp); + pn_frac = strtod(optarg,&tmp); + pn_abs = 0; if ( *tmp && *tmp==',' ) { - args->pn_abs = strtod(tmp+1,&tmp); - if ( *tmp ) error("Could not parse: --pn %s\n", optarg); + pn_abs = strtod(tmp+1,&tmp); + if ( *tmp ) + { + if ( *tmp!=':' ) error("Could not parse: --pn %s\n", optarg); + if ( !strcasecmp("snv",tmp+1) ) { args->pn_snv.frac = pn_frac; args->pn_snv.abs = pn_abs; } + else if ( !strcasecmp("indel",tmp+1) ) { args->pn_indel.frac = pn_frac; args->pn_indel.abs = pn_abs; } + else error("Could not parse: --pn %s\n", optarg); + } + else + { + args->pn_snv.frac = pn_frac; + args->pn_snv.abs = pn_abs; + args->pn_indel.frac = pn_frac; + args->pn_indel.abs = pn_abs; + } } - if ( args->pn_frac<0 || args->pn_frac>1 ) error("Error: expected value from the interval [0,1] for --pn %s\n", optarg); - if ( args->pn_abs<0 ) error("Error: expected positive value for --pn %s\n", optarg); + else if ( *tmp ) error("Could not parse: --pn %s\n", optarg); + else + { + args->pn_snv.frac = pn_frac; + args->pn_indel.frac = pn_frac; + } + if ( pn_frac<0 || pn_frac>1 ) error("Error: expected value from the interval [0,1] for --pn %s\n", optarg); + if ( pn_abs<0 ) error("Error: expected positive value for --pn %s\n", optarg); break; case 8 : - args->pns_frac = strtod(optarg,&tmp); + pn_frac = strtod(optarg,&tmp); + pn_abs = 0; if ( *tmp && *tmp==',' ) { - args->pns_abs = strtod(tmp+1,&tmp); - if ( *tmp ) error("Could not parse: --pns %s\n", optarg); + pn_abs = strtod(tmp+1,&tmp); + if ( *tmp ) + { + if ( *tmp!=':' ) error("Could not parse: --pns %s\n", optarg); + if ( !strcasecmp("snv",tmp+1) ) { args->pn_snv.frac1 = pn_frac; args->pn_snv.abs1 = pn_abs; } + else if ( !strcasecmp("indel",tmp+1) ) { args->pn_indel.frac1 = pn_frac; args->pn_indel.abs1 = pn_abs; } + else error("Could not parse: --pns %s\n", optarg); + } + else + { + args->pn_snv.frac1 = pn_frac; + args->pn_snv.abs1 = pn_abs; + args->pn_indel.frac1 = pn_frac; + args->pn_indel.abs1 = pn_abs; + } + } + else if ( *tmp ) error("Could not parse: --pns %s\n", optarg); + else + { + args->pn_snv.frac1 = pn_frac; + args->pn_indel.frac1 = pn_frac; } - if ( args->pns_frac<0 || args->pns_frac>1 ) error("Error: expected value from the interval [0,1] for --pns %s\n", optarg); - if ( args->pns_abs<0 ) error("Error: expected positive value for --pns %s\n", optarg); + if ( pn_frac<0 || pn_frac>1 ) error("Error: expected value from the interval [0,1] for --pns %s\n", optarg); + if ( pn_abs<0 ) error("Error: expected positive value for --pns %s\n", optarg); break; case 9 : args->use_model = USE_DNG; args->use_dng_priors = 1; break; case 10 : args->with_ppl = 1; break; From cbd547022ea76d6848185a0c55b17b957332ee4e Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Wed, 29 Jun 2022 10:53:43 +0100 Subject: [PATCH 03/84] Skeleton for new mpileup indels, for now accessible with --indels-2.0 This is just an initial commit so that we can make incremental changes --- Makefile | 3 ++- bam2bcf.c | 2 ++ bam2bcf.h | 2 ++ mpileup.c | 36 +++++++++++++++++++++++------------- 4 files changed, 29 insertions(+), 14 deletions(-) diff --git a/Makefile b/Makefile index ad87f022b..9629abd55 100644 --- a/Makefile +++ b/Makefile @@ -40,7 +40,7 @@ OBJS = main.o vcfindex.o tabix.o \ vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o \ vcfcnv.o vcfhead.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o \ regidx.o smpl_ilist.o csq.o vcfbuf.o \ - mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o \ + mpileup.o bam2bcf.o bam2bcf_indel.o bam2bcf_iaux.o bam_sample.o \ vcfsort.o cols.o extsort.o dist.o abuf.o \ ccall.o em.o prob1.o kmin.o str_finder.o PLUGIN_OBJS = vcfplugin.o @@ -279,6 +279,7 @@ consensus.o: consensus.c $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_synced_bcf mpileup.o: mpileup.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) $(htslib_hts_os_h) regidx.h $(bcftools_h) $(bam2bcf_h) $(bam_sample_h) $(gvcf_h) bam2bcf.o: bam2bcf.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h) mw.h bam2bcf_indel.o: bam2bcf_indel.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_str2int_h) $(bam2bcf_h) $(htslib_ksort_h) str_finder.h +bam2bcf_iaux.o: bam2bcf_iaux.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_str2int_h) $(bam2bcf_h) $(htslib_ksort_h) str_finder.h bam_sample.o: bam_sample.c $(htslib_hts_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) $(khash_str2str_h) $(bam_sample_h) $(bcftools_h) version.o: version.h version.c hclust.o: hclust.c $(htslib_hts_h) $(htslib_kstring_h) $(bcftools_h) hclust.h diff --git a/bam2bcf.c b/bam2bcf.c index d373e99cb..a8a5e5753 100644 --- a/bam2bcf.c +++ b/bam2bcf.c @@ -72,9 +72,11 @@ bcf_callaux_t *bcf_call_init(double theta, int min_baseQ, int max_baseQ, return bca; } +void bcf_iaux_destroy(bcf_callaux_t *bca); void bcf_call_destroy(bcf_callaux_t *bca) { if (bca == 0) return; + bcf_iaux_destroy(bca); errmod_destroy(bca->e); if (bca->npos) { free(bca->ref_pos); free(bca->alt_pos); diff --git a/bam2bcf.h b/bam2bcf.h index c256b2696..9e915a9a8 100644 --- a/bam2bcf.h +++ b/bam2bcf.h @@ -104,6 +104,7 @@ typedef struct __bcf_callaux_t { void *rghash; float indel_bias; // adjusts indel score threshold; lower => call more. int32_t *ref_nm, *alt_nm; // pointers to bcf_call_t.{ref_nm,alt_nm} + void *iaux; // auxiliary structure for --indels-2.0 calling } bcf_callaux_t; // per-sample values @@ -162,6 +163,7 @@ extern "C" { int bcf_call2bcf(bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int fmt_flag, const bcf_callaux_t *bca, const char *ref); int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref); + int bcf_iaux_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref); void bcf_callaux_clean(bcf_callaux_t *bca, bcf_call_t *call); #ifdef __cplusplus diff --git a/mpileup.c b/mpileup.c index fc4f4b130..d0609d59f 100644 --- a/mpileup.c +++ b/mpileup.c @@ -97,6 +97,7 @@ typedef struct { bcf1_t *bcf_rec; htsFile *bcf_fp; bcf_hdr_t *bcf_hdr; + int indels_v20; int argc; char **argv; } mplp_conf_t; @@ -553,8 +554,7 @@ static int mpileup_reg(mplp_conf_t *conf, uint32_t beg, uint32_t end) } int has_ref = mplp_get_ref(conf->mplp_data[0], tid, &ref, &ref_len); if (has_ref && (conf->flag & MPLP_REALN)) - mplp_realn(conf->nfiles, conf->n_plp, conf->plp, conf->flag, - conf->max_read_len, ref, ref_len, pos); + mplp_realn(conf->nfiles, conf->n_plp, conf->plp, conf->flag, conf->max_read_len, ref, ref_len, pos); int total_depth, _ref0, ref16; for (i = total_depth = 0; i < conf->nfiles; ++i) total_depth += conf->n_plp[i]; @@ -567,23 +567,29 @@ static int mpileup_reg(mplp_conf_t *conf, uint32_t beg, uint32_t end) conf->bc.tid = tid; conf->bc.pos = pos; bcf_call_combine(conf->gplp->n, conf->bcr, conf->bca, ref16, &conf->bc); bcf_clear1(conf->bcf_rec); - bcf_call2bcf(&conf->bc, conf->bcf_rec, conf->bcr, conf->fmt_flag, - conf->bca, 0); + bcf_call2bcf(&conf->bc, conf->bcf_rec, conf->bcr, conf->fmt_flag, conf->bca, 0); flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, conf->bcf_rec); // call indels; todo: subsampling with total_depth>max_indel_depth instead of ignoring? // check me: rghash in bcf_call_gap_prep() should have no effect, reads mplp_func already excludes them - if (!(conf->flag&MPLP_NO_INDEL) && total_depth < conf->max_indel_depth - && (bcf_callaux_clean(conf->bca, &conf->bc), - bcf_call_gap_prep(conf->gplp->n, conf->gplp->n_plp, conf->gplp->plp, pos, conf->bca, ref) >= 0)) + if ( !(conf->flag&MPLP_NO_INDEL) && total_depth < conf->max_indel_depth ) { - for (i = 0; i < conf->gplp->n; ++i) - bcf_call_glfgen(conf->gplp->n_plp[i], conf->gplp->plp[i], -1, conf->bca, conf->bcr + i); - if (bcf_call_combine(conf->gplp->n, conf->bcr, conf->bca, -1, &conf->bc) >= 0) + bcf_callaux_clean(conf->bca, &conf->bc); + int iret; + if ( conf->indels_v20 ) + iret = bcf_iaux_gap_prep(conf->gplp->n, conf->gplp->n_plp, conf->gplp->plp, pos, conf->bca, ref); + else + iret = bcf_call_gap_prep(conf->gplp->n, conf->gplp->n_plp, conf->gplp->plp, pos, conf->bca, ref); + if ( iret>=0 ) { - bcf_clear1(conf->bcf_rec); - bcf_call2bcf(&conf->bc, conf->bcf_rec, conf->bcr, conf->fmt_flag, conf->bca, ref); - flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, conf->bcf_rec); + for (i = 0; i < conf->gplp->n; ++i) + bcf_call_glfgen(conf->gplp->n_plp[i], conf->gplp->plp[i], -1, conf->bca, conf->bcr + i); + if (bcf_call_combine(conf->gplp->n, conf->bcr, conf->bca, -1, &conf->bc) >= 0) + { + bcf_clear1(conf->bcf_rec); + bcf_call2bcf(&conf->bc, conf->bcf_rec, conf->bcr, conf->fmt_flag, conf->bca, ref); + flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, conf->bcf_rec); + } } } } @@ -1194,6 +1200,8 @@ static void print_usage(FILE *fp, const mplp_conf_t *mplp) " --indel-bias FLOAT Raise to favour recall over precision [%.2f]\n", mplp->indel_bias); fprintf(fp, " --indel-size INT Approximate maximum indel size considered [%d]\n", mplp->indel_win_size); + fprintf(fp, + " --indels-2.0 New indel calling model (diploid reference consensus)\n"); fprintf(fp,"\n"); fprintf(fp, "Configuration profiles activated with -X, --config:\n" @@ -1302,6 +1310,7 @@ int main_mpileup(int argc, char *argv[]) {"gap-frac", required_argument, NULL, 'F'}, {"indel-bias", required_argument, NULL, 10}, {"indel-size", required_argument, NULL, 15}, + {"indels-2.0", no_argument, NULL, 20}, {"tandem-qual", required_argument, NULL, 'h'}, {"skip-indels", no_argument, NULL, 'I'}, {"max-idepth", required_argument, NULL, 'L'}, @@ -1436,6 +1445,7 @@ int main_mpileup(int argc, char *argv[]) } } break; + case 20: mplp.indels_v20 = 1; break; case 'A': use_orphan = 1; break; case 'F': mplp.min_frac = atof(optarg); break; case 'm': mplp.min_support = atoi(optarg); break; From a828884e5d46afc39d34f99e929f7deb22837ec5 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Thu, 30 Jun 2022 15:17:26 +0100 Subject: [PATCH 04/84] Pileup client data and indel type finding - proper struct for pileup client data - flesh out the indel type finding routine. This is identical to the original code, the only difference is caching qlen in pileup client data --- bam2bcf.c | 2 +- bam2bcf.h | 26 +++- bam2bcf_iaux.c | 342 +++++++++++++++++++++++++++++++++++++++++++++++++ mpileup.c | 31 +++-- 4 files changed, 382 insertions(+), 19 deletions(-) create mode 100644 bam2bcf_iaux.c diff --git a/bam2bcf.c b/bam2bcf.c index a8a5e5753..7aaa51c96 100644 --- a/bam2bcf.c +++ b/bam2bcf.c @@ -256,7 +256,7 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t for (i = n = 0; i < _n; ++i) { const bam_pileup1_t *p = pl + i; int q, b, mapQ, baseQ, is_diff, min_dist, seqQ; - if ( bca->fmt_flag&(B2B_INFO_SCR|B2B_FMT_SCR) && PLP_HAS_SOFT_CLIP(p->cd.i) ) r->SCR++; + if ( bca->fmt_flag&(B2B_INFO_SCR|B2B_FMT_SCR) && PLP_HAS_SOFT_CLIP(&p->cd) ) r->SCR++; if (p->is_refskip || (p->b->core.flag&BAM_FUNMAP)) continue; if (p->is_del && !is_indel) continue; ++ori_depth; diff --git a/bam2bcf.h b/bam2bcf.h index 9e915a9a8..d654c9dfd 100644 --- a/bam2bcf.h +++ b/bam2bcf.h @@ -72,13 +72,25 @@ DEALINGS IN THE SOFTWARE. */ #define B2B_INC_AD 1 #define B2B_INC_AD0 2 -#define PLP_HAS_SOFT_CLIP(i) ((i)&1) -#define PLP_HAS_INDEL(i) ((i)&2) -#define PLP_SAMPLE_ID(i) ((i)>>2) -#define PLP_SET_SOFT_CLIP(i) ((i)|=1) -#define PLP_SET_INDEL(i) ((i)|=2) -#define PLP_SET_SAMPLE_ID(i,n) ((i)|=(n)<<2) +// Pileup "client data" for each read to cache per-read information +#define PLP_CD(x) ((plp_cd_t*)((x)->p)) +#define PLP_HAS_SOFT_CLIP(cd) (PLP_CD(cd)->i & 1) +#define PLP_HAS_INDEL(cd) (PLP_CD(cd)->i & 2) +#define PLP_SAMPLE_ID(cd) (PLP_CD(cd)->i >> 2) +#define PLP_QLEN(cd) (PLP_CD(cd)->qlen) + +#define PLP_SET_SOFT_CLIP(cd) (PLP_CD(cd)->i |= 1) +#define PLP_SET_INDEL(cd) (PLP_CD(cd)->i |= 2) +#define PLP_SET_SAMPLE_ID(cd,n) (PLP_CD(cd)->i |= (n)<<2) + +typedef struct +{ + int64_t i; // used to store sample id and flags for presence of soft-clip and indel + uint32_t qlen; // cached output of bam_cigar2qlen(), 0 if unset +} +plp_cd_t; + typedef struct __bcf_callaux_t { int fmt_flag, ambig_reads; @@ -105,6 +117,7 @@ typedef struct __bcf_callaux_t { float indel_bias; // adjusts indel score threshold; lower => call more. int32_t *ref_nm, *alt_nm; // pointers to bcf_call_t.{ref_nm,alt_nm} void *iaux; // auxiliary structure for --indels-2.0 calling + char *chr; // current chromosome } bcf_callaux_t; // per-sample values @@ -151,6 +164,7 @@ typedef struct { kstring_t tmp; } bcf_call_t; + #ifdef __cplusplus extern "C" { #endif diff --git a/bam2bcf_iaux.c b/bam2bcf_iaux.c new file mode 100644 index 000000000..9c1ed3e2d --- /dev/null +++ b/bam2bcf_iaux.c @@ -0,0 +1,342 @@ +/* bam2bcf_iaux.c -- modified indel caller + + Copyright (C) 2022 Genome Research Ltd. + + Author: pd3@sanger, jkb + + Permission is hereby granted, free of charge, to any person obtaining a copy + of this software and associated documentation files (the "Software"), to deal + in the Software without restriction, including without limitation the rights + to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + copies of the Software, and to permit persons to whom the Software is + furnished to do so, subject to the following conditions: + + The above copyright notice and this permission notice shall be included in + all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL + THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + DEALINGS IN THE SOFTWARE +*/ + +#include +#include +#include +#include +#include +#include +#include +#include "bam2bcf.h" + +#include +KSORT_INIT_STATIC_GENERIC(uint32_t) + + +#define MAX_TYPES 64 + +typedef struct +{ + int pos; // current position + char *chr; // current chromosome + int nsmpl; // number of samples + int *nplp; // per-sample number of reads + bam_pileup1_t **plp; // per-sample reads + bcf_callaux_t *bca; // auxiliary bam2bcf structure + const char *ref; // reference genome (ASCII) + uint32_t *uitmp; // temporary unsigned int array + uint32_t *inscns; // insertions consensus [itype*max_ins_len+i] + int muitmp, minscns; // size of uitmp, inscns + int iref_type, ntypes, types[MAX_TYPES]; // indel types + int max_ins_len; +} +indel_aux_t; + +static void _print_types(indel_aux_t *iaux) +{ + int i,j; + fprintf(stderr,"types at %s:%d ... ",iaux->chr,iaux->pos+1); + for (i=0; intypes; i++) + { + if ( iaux->types[i]<=0 ) + { + if ( i==iaux->iref_type ) fprintf(stderr," %d",iaux->types[i]); + continue; + } + fprintf(stderr," "); + uint32_t *cns = &iaux->inscns[i*iaux->max_ins_len]; + for (j=0; jtypes[i]; j++) fprintf(stderr,"%c","ACGTN"[cns[j]]); + } + fprintf(stderr,"\n"); +} + +static int _have_indel_reads(indel_aux_t *iaux) +{ + int i,j; + for (i=0; insmpl; i++) + { + for (j=0; jnplp[i]; j++) + if ( iaux->plp[i][j].indel ) return 1; + } + return 0; +} + +static int iaux_init_ins_types(indel_aux_t *iaux) +{ + if ( !iaux->max_ins_len ) return 0; + + uint32_t *aux; + int naux = 5 * iaux->ntypes * iaux->max_ins_len; + if ( iaux->muitmp < naux ) + { + aux = (uint32_t*) realloc(iaux->uitmp,naux*sizeof(*aux)); + if ( !aux ) return -1; + iaux->uitmp = aux; + iaux->muitmp = naux; + } + else aux = iaux->uitmp; + memset(aux,0,naux*sizeof(*aux)); + + // count the number of occurrences of each base at each position for each type of insertion + int t,s,i,j; + for (t=0; tntypes; t++) + { + if ( iaux->types[t] <= 0) continue; + for (s=0; snsmpl; s++) + { + for (i=0; inplp[s]; i++) + { + bam_pileup1_t *plp = iaux->plp[s] + i; + if ( plp->indel != iaux->types[t] ) continue; + uint8_t *seq = bam_get_seq(plp->b); + for (j=0; jindel; j++) + { + int c = seq_nt16_int[bam_seqi(seq, plp->qpos+j+1)]; + assert(c<5); + aux[5*(t*iaux->max_ins_len+j) + c]++; + } + } + } + } + + uint32_t *cns; + int ncns = iaux->ntypes * iaux->max_ins_len; + if ( iaux->minscns < ncns ) + { + cns = (uint32_t*) realloc(iaux->inscns,naux*sizeof(*aux)); + if ( !cns ) return -1; + iaux->inscns = cns; + iaux->minscns = ncns; + } + else cns = iaux->inscns; + memset(aux,0,ncns*sizeof(*cns)); + + // use the majority rule to construct the consensus + for (t=0; tntypes; t++) + { + for (i=0; itypes[t]; i++) + { + uint32_t *tmp = &aux[5*(t*iaux->max_ins_len+i)], max = tmp[0], max_j = 0; + for (j=1; j<5; j++) + if ( max < tmp[j] ) max = tmp[j], max_j = j; + cns[t*iaux->max_ins_len + i] = max ? max_j : 4; + if ( max_j==4 ) { iaux->types[t] = 0; break; } // discard insertions which contain N's + } + } + return 0; +} + +#define MINUS_CONST 0x10000000 +static int iaux_init_types(indel_aux_t *iaux) +{ + if ( !_have_indel_reads(iaux) ) return -1; + + iaux->bca->max_support = 0; + + int i,j, nreads = 0; + for (i=0; insmpl; i++) nreads += iaux->nplp[i]; + + uint32_t *aux; + if ( iaux->muitmp < nreads+1 ) + { + aux = (uint32_t*) realloc(iaux->uitmp,(nreads+1)*sizeof(*iaux->uitmp)); + if ( !aux ) return -1; + iaux->uitmp = aux; + iaux->muitmp = nreads+1; + } + else aux = iaux->uitmp; + memset(aux,0,(nreads+1)*sizeof(*aux)); + + int naux = 0, indel_support_ok = 0, n_alt = 0, n_tot = 0; + int max_rd_len = 0; // max sequence length that includes ref+del bases + + // Fill out aux[] array with all the non-zero indel sizes. + aux[naux++] = MINUS_CONST; // zero indel is always a type (REF) + for (i=0; insmpl; i++) + { + int nalt = naux, ntot = 0; // per sample values + for (j=0; jnplp[i]; j++) + { + const bam_pileup1_t *plp = iaux->plp[i] + j; + ntot++; + if ( plp->indel ) aux[naux++] = MINUS_CONST + plp->indel; + if ( !PLP_QLEN(&plp->cd) ) PLP_QLEN(&plp->cd) = bam_cigar2qlen(plp->b->core.n_cigar, bam_get_cigar(plp->b)); + if ( PLP_QLEN(&plp->cd) > max_rd_len ) max_rd_len = PLP_QLEN(&plp->cd); + } + nalt = naux - nalt; + if ( iaux->bca->per_sample_flt ) + { + double frac = (double)nalt/naux; + if ( nalt >= iaux->bca->min_support && frac >= iaux->bca->min_frac ) indel_support_ok = 1; + if ( nalt > iaux->bca->max_support && frac > 0 ) iaux->bca->max_support = nalt, iaux->bca->max_frac = frac; + } + else + { + n_alt += nalt; + n_tot += ntot; + } + } + + // Check if the minimum required number of indel reads has been observed + if ( !iaux->bca->per_sample_flt && n_alt >= iaux->bca->min_support && (double)n_alt/n_tot >= iaux->bca->min_frac ) indel_support_ok = 1; + if ( naux==1 || !indel_support_ok ) return -1; + + // To prevent long stretches of N's to be mistaken for indels (sometimes thousands of bases), check the number of N's in the + // sequence and skip places where half or more reference bases in the sequence that follows pos are Ns + int nN = 0, i_end = iaux->pos + (iaux->bca->indel_win_size < max_rd_len ? iaux->bca->indel_win_size : max_rd_len); + for (i=iaux->pos; iref[i]; i++) + if ( iaux->ref[i] == 'N' ) nN++; + if ( 2*nN > i - iaux->pos ) return -1; + + // Sort aux[] and dedup + int n_types = 1; + ks_introsort(uint32_t, naux, aux); + for (i=1; i= MAX_TYPES ) + { + static int warned = 0; + if ( !warned ) + { + fprintf(stderr, "Warning: excessive number of INDEL alleles at %s:%d, skipping. (This warning is printed only once)\n",iaux->chr,iaux->pos+1); + warned = 1; + } + return -1; + } + + // Finally fill out the types[] array detailing the size of insertion or deletion. + iaux->ntypes = 0; + iaux->max_ins_len = 0; + for (i=0; iiref_type = iaux->ntypes; + } + else + { + if ( j-i >= iaux->bca->min_support ) is_ok = 1; + if ( !iaux->bca->per_sample_flt && (double)(j-i) / n_tot < iaux->bca->min_frac ) is_ok = 0; + } + if ( is_ok ) + { + iaux->types[iaux->ntypes++] = isize; + if ( isize > 0 && isize > iaux->max_ins_len ) iaux->max_ins_len = isize; + } + i = j-1; + } + if ( iaux->ntypes <= 1 ) return -1; + + // Init insertion types + if ( iaux_init_ins_types(iaux) < 0 ) return -1; + + _print_types(iaux); + + return iaux->ntypes; +} +#undef MINUS_CONST + +static int iaux_set_consensus(indel_aux_t *iaux, int ismpl) +{ + return -1; +} +static int iaux_score_reads(indel_aux_t *iaux, int ismpl, int itype) +{ + return -1; +} +static int iaux_compute_quality(indel_aux_t *iaux) +{ + return -1; +} + +/* +FIXME: with high number of samples, do we handle IMF correctly? Is it +fraction of indels across entire data set, or just fraction for this +specific sample? Needs to check bca->per_sample_flt (--per-sample-mF) opt. + */ + +/* + notes: + - n .. number of samples + - the routine sets bam_pileup1_t.aux of each read as follows: + - 6: unused + - 6: the call; index to bcf_callaux_t.indel_types .. (aux>>16)&0x3f + - 8: estimated sequence quality .. (aux>>8)&0xff + - 8: indel quality .. aux&0xff + */ +int bcf_iaux_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref) +{ +assert(!(ref == 0 || bca == 0)); // can this ever happen? when? + if (ref == 0 || bca == 0) return -1; + + if ( !bca->iaux ) bca->iaux = calloc(1,sizeof(indel_aux_t)); + indel_aux_t *iaux = bca->iaux; + iaux->nsmpl = n; + iaux->nplp = n_plp; + iaux->plp = plp; + iaux->bca = bca; + iaux->ref = ref; + iaux->pos = pos; + iaux->chr = bca->chr; + + // Check if there is an indel at this position and if yes, find all indel types and determine + // window boundaries. todo: We want this information cached so that for long reads we don't keep + // redoing the whole analysis again and again + int ntypes = iaux_init_types(iaux); + if ( !ntypes ) return -1; + + + // Create two template consensus sequences for each sample (assuming max diploid organism). + // Then apply each indel type on top of the templates, realign every read and remember score + int i,j; + for (i=0; insmpl; i++) + { + iaux_set_consensus(iaux, i); + for (j=0; j 0 ? 0 : -1; +} +void bcf_iaux_destroy(bcf_callaux_t *bca) +{ + if ( !bca->iaux ) return; + indel_aux_t *iaux = (indel_aux_t*)bca->iaux; + free(iaux->uitmp); + free(iaux->inscns); + free(iaux); +} + + diff --git a/mpileup.c b/mpileup.c index d0609d59f..79c0c7a0e 100644 --- a/mpileup.c +++ b/mpileup.c @@ -295,24 +295,21 @@ static int mplp_func(void *data, bam1_t *b) // We cache sample information here so we don't have to keep recomputing this // on each and every pileup column. If FMT/SCR annotation is requested, a flag // is set to indicate the presence of a soft clip. -// -// Cd is an arbitrary block of data we can write into, which ends up in -// the pileup structures. We stash the sample ID there: -// has_soft_clip .. cd->i & 1 -// sample_id .. cd->i >> 1 static int pileup_constructor(void *data, const bam1_t *b, bam_pileup_cd *cd) { + cd->p = calloc(1,sizeof(plp_cd_t)); + mplp_aux_t *ma = (mplp_aux_t *)data; int n = bam_smpl_get_sample_id(ma->conf->bsmpl, ma->bam_id, (bam1_t *)b); - cd->i = 0; - PLP_SET_SAMPLE_ID(cd->i, n); + PLP_SET_SAMPLE_ID(cd, n); + // Whether read has a soft-clip is used in mplp_realn's heuristics. // TODO: consider whether clip length is beneficial to use? int i; for (i=0; icore.n_cigar; i++) { int cig = bam_get_cigar(b)[i] & BAM_CIGAR_MASK; if (cig == BAM_CSOFT_CLIP) { - PLP_SET_SOFT_CLIP(cd->i); + PLP_SET_SOFT_CLIP(cd); break; } } @@ -331,7 +328,7 @@ static int pileup_constructor(void *data, const bam1_t *b, bam_pileup_cd *cd) // Possible further optimsation, check tot_ins==1 later // (and remove break) so we can detect single bp indels. // We may want to focus BAQ on more complex regions only. - PLP_SET_INDEL(cd->i); + PLP_SET_INDEL(cd); break; } @@ -346,6 +343,11 @@ static int pileup_constructor(void *data, const bam1_t *b, bam_pileup_cd *cd) return 0; } +static int pileup_destructor(void *data, const bam1_t *b, bam_pileup_cd *cd) +{ + free(cd->p); + return 0; +} static void group_smpl(mplp_pileup_t *m, bam_smpl_t *bsmpl, int n, int *n_plp, const bam_pileup1_t **plp) { @@ -356,7 +358,7 @@ static void group_smpl(mplp_pileup_t *m, bam_smpl_t *bsmpl, int n, int *n_plp, c for (j = 0; j < n_plp[i]; ++j) // iterate over all reads available at this position { const bam_pileup1_t *p = plp[i] + j; - int id = PLP_SAMPLE_ID(p->cd.i); + int id = PLP_SAMPLE_ID(&(p->cd)); if (m->n_plp[id] == m->m_plp[id]) { m->m_plp[id] = m->m_plp[id]? m->m_plp[id]<<1 : 8; @@ -419,11 +421,11 @@ static void mplp_realn(int n, int *n_plp, const bam_pileup1_t **plp, nt += n_plp[i]; for (j = 0; j < n_plp[i]; j++) { // iterate over reads bam_pileup1_t *p = (bam_pileup1_t *)plp[i] + j; - has_indel += (PLP_HAS_INDEL(p->cd.i) || p->indel) ? 1 : 0; + has_indel += (PLP_HAS_INDEL(&p->cd) || p->indel) ? 1 : 0; // Has_clip is almost always true for very long reads // (eg PacBio CCS), but these rarely matter as the clip // is likely a long way from this indel. - has_clip += (PLP_HAS_SOFT_CLIP(p->cd.i)) ? 1 : 0; + has_clip += (PLP_HAS_SOFT_CLIP(&p->cd)) ? 1 : 0; if (max_indel < p->indel) max_indel = p->indel; if (min_indel > p->indel) @@ -438,6 +440,8 @@ static void mplp_realn(int n, int *n_plp, const bam_pileup1_t **plp, return; } +static int reminded = 0; +if ( !reminded ) { fprintf(stderr,"todo: use plp_cd_t to avoid the read-only limitation of p->cd.i\n"); reminded = 1; } // Realign for (i = 0; i < n; i++) { // iterate over bams for (j = 0; j < n_plp[i]; j++) { // iterate over reads @@ -575,6 +579,7 @@ static int mpileup_reg(mplp_conf_t *conf, uint32_t beg, uint32_t end) if ( !(conf->flag&MPLP_NO_INDEL) && total_depth < conf->max_indel_depth ) { bcf_callaux_clean(conf->bca, &conf->bc); + conf->bca->chr = tid>=0 ? hdr->target_name[tid] : NULL; int iret; if ( conf->indels_v20 ) iret = bcf_iaux_gap_prep(conf->gplp->n, conf->gplp->n_plp, conf->gplp->plp, pos, conf->bca, ref); @@ -908,6 +913,8 @@ static int mpileup(mplp_conf_t *conf) conf->max_indel_depth = conf->max_indel_depth * nsmpl; conf->bcf_rec = bcf_init1(); bam_mplp_constructor(conf->iter, pileup_constructor); + bam_mplp_destructor(conf->iter, pileup_destructor); + // Run mpileup for multiple regions if ( nregs ) From 6b8eb04dcd484286bc1abe7c0ccf025ab4d1f2d0 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Tue, 5 Jul 2022 11:13:10 +0100 Subject: [PATCH 05/84] Outline for read consensus creation --- Makefile | 5 +- bam2bcf.h | 2 + bam2bcf_iaux.c | 47 +++++++-- bam2bcf_indel.c | 2 +- read_consensus.c | 253 +++++++++++++++++++++++++++++++++++++++++++++++ read_consensus.h | 49 +++++++++ 6 files changed, 347 insertions(+), 11 deletions(-) create mode 100644 read_consensus.c create mode 100644 read_consensus.h diff --git a/Makefile b/Makefile index 9629abd55..de1ee9dde 100644 --- a/Makefile +++ b/Makefile @@ -40,7 +40,7 @@ OBJS = main.o vcfindex.o tabix.o \ vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o \ vcfcnv.o vcfhead.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o \ regidx.o smpl_ilist.o csq.o vcfbuf.o \ - mpileup.o bam2bcf.o bam2bcf_indel.o bam2bcf_iaux.o bam_sample.o \ + mpileup.o bam2bcf.o bam2bcf_indel.o bam2bcf_iaux.o read_consensus.o bam_sample.o \ vcfsort.o cols.o extsort.o dist.o abuf.o \ ccall.o em.o prob1.o kmin.o str_finder.o PLUGIN_OBJS = vcfplugin.o @@ -279,7 +279,8 @@ consensus.o: consensus.c $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_synced_bcf mpileup.o: mpileup.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) $(htslib_hts_os_h) regidx.h $(bcftools_h) $(bam2bcf_h) $(bam_sample_h) $(gvcf_h) bam2bcf.o: bam2bcf.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h) mw.h bam2bcf_indel.o: bam2bcf_indel.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_str2int_h) $(bam2bcf_h) $(htslib_ksort_h) str_finder.h -bam2bcf_iaux.o: bam2bcf_iaux.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_str2int_h) $(bam2bcf_h) $(htslib_ksort_h) str_finder.h +bam2bcf_iaux.o: bam2bcf_iaux.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_str2int_h) $(bam2bcf_h) $(htslib_ksort_h) str_finder.h read_consensus.h +read_consensus.o: read_consensus.c read_consensus.h $(htslib_hts_h) $(htslib_sam_h) bam_sample.o: bam_sample.c $(htslib_hts_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) $(khash_str2str_h) $(bam_sample_h) $(bcftools_h) version.o: version.h version.c hclust.o: hclust.c $(htslib_hts_h) $(htslib_kstring_h) $(bcftools_h) hclust.h diff --git a/bam2bcf.h b/bam2bcf.h index d654c9dfd..9e64917fb 100644 --- a/bam2bcf.h +++ b/bam2bcf.h @@ -180,6 +180,8 @@ extern "C" { int bcf_iaux_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref); void bcf_callaux_clean(bcf_callaux_t *bca, bcf_call_t *call); + int bcf_cgp_l_run(const char *ref, int pos); + #ifdef __cplusplus } #endif diff --git a/bam2bcf_iaux.c b/bam2bcf_iaux.c index 9c1ed3e2d..a45876906 100644 --- a/bam2bcf_iaux.c +++ b/bam2bcf_iaux.c @@ -31,6 +31,7 @@ #include #include #include "bam2bcf.h" +#include "read_consensus.h" #include KSORT_INIT_STATIC_GENERIC(uint32_t) @@ -51,7 +52,11 @@ typedef struct uint32_t *inscns; // insertions consensus [itype*max_ins_len+i] int muitmp, minscns; // size of uitmp, inscns int iref_type, ntypes, types[MAX_TYPES]; // indel types - int max_ins_len; + int max_ins_len; // largest insertion + int left, right; // consensus sequence boundaries + read_cns_t *rcns; // read consensus + const char **cns_seq; // array of consensus sequences + int *cns_pos; // array of relative pos indexes within cns_seq sequences } indel_aux_t; @@ -73,6 +78,26 @@ static void _print_types(indel_aux_t *iaux) fprintf(stderr,"\n"); } +static void iaux_init_sequence_context(indel_aux_t *iaux) +{ + // Calculate left and right boundary. The array types is sorted in ascending order, the first + // element is the largest deletion (if a deletion present) + iaux->left = iaux->pos > iaux->bca->indel_win_size ? iaux->pos - iaux->bca->indel_win_size : 0; + iaux->right = iaux->pos + iaux->bca->indel_win_size; + if ( iaux->types[0] < 0 ) iaux->right -= iaux->types[0]; // extend by the largest deletion length + + // In case the alignments stand out the reference + int i; + for (i=iaux->pos; iright; i++) + if ( !iaux->ref[i] ) break; + iaux->right = i; + + // The length of the homopolymer run around the current position +// iaux->l_run = bcf_cgp_l_run(iaux->ref, iaux->pos); +//int l_run_base = seq_nt16_table[(uint8_t)ref[pos+1]]; +//int l_run_ins = 0; +} + static int _have_indel_reads(indel_aux_t *iaux) { int i,j; @@ -137,7 +162,7 @@ static int iaux_init_ins_types(indel_aux_t *iaux) // use the majority rule to construct the consensus for (t=0; tntypes; t++) { - for (i=0; itypes[t]; i++) + for (i=0; itypes[t]; i++) // this naturally includes only insertions { uint32_t *tmp = &aux[5*(t*iaux->max_ins_len+i)], max = tmp[0], max_j = 0; for (j=1; j<5; j++) @@ -263,6 +288,8 @@ static int iaux_init_types(indel_aux_t *iaux) // Init insertion types if ( iaux_init_ins_types(iaux) < 0 ) return -1; + iaux_init_sequence_context(iaux); + _print_types(iaux); return iaux->ntypes; @@ -271,6 +298,15 @@ static int iaux_init_types(indel_aux_t *iaux) static int iaux_set_consensus(indel_aux_t *iaux, int ismpl) { + if ( !iaux->rcns ) + iaux->rcns = rcns_init(iaux->pos, iaux->left, iaux->right); + else + rcns_reset(iaux->rcns, iaux->pos, iaux->left, iaux->right); + + rcns_set_reads(iaux->rcns, iaux->plp[ismpl], iaux->nplp[ismpl]); + + iaux->cns_seq = rcns_get_consensus(iaux->rcns, iaux->ref + iaux->left, &iaux->cns_pos); + return -1; } static int iaux_score_reads(indel_aux_t *iaux, int ismpl, int itype) @@ -282,12 +318,6 @@ static int iaux_compute_quality(indel_aux_t *iaux) return -1; } -/* -FIXME: with high number of samples, do we handle IMF correctly? Is it -fraction of indels across entire data set, or just fraction for this -specific sample? Needs to check bca->per_sample_flt (--per-sample-mF) opt. - */ - /* notes: - n .. number of samples @@ -336,6 +366,7 @@ void bcf_iaux_destroy(bcf_callaux_t *bca) indel_aux_t *iaux = (indel_aux_t*)bca->iaux; free(iaux->uitmp); free(iaux->inscns); + rcns_destroy(iaux->rcns); free(iaux); } diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c index 108d50557..7166a9b9e 100644 --- a/bam2bcf_indel.c +++ b/bam2bcf_indel.c @@ -408,7 +408,7 @@ static char **bcf_cgp_ref_sample(int n, int *n_plp, bam_pileup1_t **plp, } // The length of the homopolymer run around the current position -static int bcf_cgp_l_run(const char *ref, int pos) { +int bcf_cgp_l_run(const char *ref, int pos) { int i, l_run; int c = seq_nt16_table[(int)ref[pos + 1]]; diff --git a/read_consensus.c b/read_consensus.c new file mode 100644 index 000000000..d2fa79592 --- /dev/null +++ b/read_consensus.c @@ -0,0 +1,253 @@ +/* read_consensus.c -- create and maintain consensus of reads + + Copyright (C) 2022 Genome Research Ltd. + + Author: pd3@sanger + + Permission is hereby granted, free of charge, to any person obtaining a copy + of this software and associated documentation files (the "Software"), to deal + in the Software without restriction, including without limitation the rights + to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + copies of the Software, and to permit persons to whom the Software is + furnished to do so, subject to the following conditions: + + The above copyright notice and this permission notice shall be included in + all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL + THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + DEALINGS IN THE SOFTWARE. */ + +#include +#include + +#define NI 10 // number of alternative insertion sequences at one position in a single sample +typedef struct +{ + char *str[NI]; + int len[NI]; + int freq[NI]; +} +ins_freq_t; + +typedef struct +{ + int len[NI]; + int freq[NI]; +} +del_freq_t; + +typedef struct +{ + int base[5]; // frequencies of A,C,G,T,N +} +base_freq_t; + +struct _read_cns_t +{ + int pos, beg, end; + int band; // maximum absolute deviation from the diagonal, used for BAQ alignment + base_freq_t *base_freq; + ins_freq_t *ins_freq; + del_freq_t *del_freq; + char *stmp; + int mstmp, mfreq; // allocated size of stmp and *_freq arrays +}; + +void rcns_destroy(read_cns_t *rcns) +{ + int i,j; + for (i=0; imfreq; i++) + { + ins_freq_t *ifrq = &rcns->ins_freq[i]; + for (j=0; jstr[j]; j++) free(ifrq->str[j]); + } + free(rcns->ins_freq); + free(rcns->del_freq); + free(rcns->base_freq); + free(rcns->stmp); + free(rcns); +} +int _rcns_init_arrays(read_cns_t *rcns) +{ + int i,j,n = rcns->end - rcns->beg + 1; + if ( n > rcns->mfreq ) + { + ins_freq_t *ifrq = (ins_freq_t*) realloc(rcns->ins_freq,sizeof(*rcns->ins_freq)*n); + if ( !ifrq ) return -1; + rcns->ins_freq = ifrq; + memset(ifrq+rcns->mfreq,0,sizeof(*rcns->ins_freq)*(n-rcns->mfreq)); + + del_freq_t *dfrq = (del_freq_t*) realloc(rcns->del_freq,sizeof(*rcns->del_freq)*n); + if ( !dfrq ) return -1; + rcns->del_freq = dfrq; + memset(dfrq+rcns->mfreq,0,sizeof(*rcns->del_freq)*(n-rcns->mfreq)); + + base_freq_t *bfrq = (base_freq_t*) realloc(rcns->base_freq,sizeof(*rcns->base_freq)*n); + if ( !bfrq ) return -1; + rcns->base_freq = bfrq; + memset(bfrq+rcns->mfreq,0,sizeof(*rcns->base_freq)*(n-rcns->mfreq)); + + rcns->mfreq = n; + } + memset(rcns->base_freq,0,sizeof(*rcns->base_freq)*n); + memset(rcns->del_freq,0,sizeof(*rcns->del_freq)*n); + for (i=0; iins_freq[i]; + for (j=0; jstr[j]; j++) free(ifrq->str[j]); + } + memset(rcns->ins_freq,0,sizeof(*rcns->ins_freq)*n); + return 0; +} +int rcns_reset(read_cns_t *rcns, int pos, int beg, int end) +{ + rcns->band = 0; + rcns->pos = pos; + rcns->beg = beg; + rcns->end = end; + return _rcns_init_arrays(rcns); +} + +static inline void _rcns_add_base(read_cns_t *rcns, int ref_pos, int nt16) +{ + int i = ref_pos - rcns->beg; + rcns->base_freq[i].base[seq_nt16_int[nt16]]++; +} +static void _rcns_add_ins(read_cns_t *rcns, int ref_pos, uint8_t *nt16_seq, int len) +{ + int i = ref_pos - rcns->beg; + ins_freq_t *ifrq = &rcns->ins_freq[i]; + + char *str; + if ( rcns->mstmp < len ) + { + str = realloc(rcns->stmp,len*sizeof(*str)); + if ( !str ) return; + rcns->mstmp = len; + rcns->stmp = str; + } + else + str = rcns->stmp; + for (i=0; istr[i]; i++) + if ( ifrq->len[i]==len && !memcmp(ifrq->str[i],str,len) ) break; + + assert( i=NI ) return; // too many choices; discard + + if ( !ifrq->str[i] ) // new insertion + { + if ( !(ifrq->str[i]=malloc(len)) ) return; + memcpy(ifrq->str[i], str, len); + ifrq->len[i] = len; + } + ifrq->freq[i]++; +} +static void _rcns_add_del(read_cns_t *rcns, int ref_pos, int len) +{ + int i = ref_pos - rcns->beg; + del_freq_t *dfrq = &rcns->del_freq[i]; + + for (i=0; ilen[i]; i++) + if ( dfrq->len[i]==len ) break; + + assert( i=NI ) return; // too many choices; discard + + if ( !dfrq->len[i] ) dfrq->len[i] = len; // new deletion + dfrq->freq[i]++; +} + +read_cns_t *rcns_init(int pos, int beg, int end) +{ + read_cns_t *rcns = (read_cns_t*) calloc(1,sizeof(read_cns_t)); + rcns->pos = pos; + rcns->beg = beg; + rcns->end = end; + if ( _rcns_init_arrays(rcns)!=0 ) + { + rcns_destroy(rcns); + return NULL; + } + return rcns; +} + +int rcns_set_reads(read_cns_t *rcns, bam_pileup1_t *plp, int nplp) +{ + // fill consensus arrays + int i,j,k, local_band_max = 0; // maximum absolute deviation from diagonal + for (i=0; ib; + int x = b->core.pos; // ref coordinate + int y = 0; // seq coordinate + uint32_t *cigar = bam_get_cigar(b); + uint8_t *seq = bam_get_seq(b); + + int local_band = 0; // current deviation from diagonal + for (k = 0; k < b->core.n_cigar; ++k) + { + int op = cigar[k] & BAM_CIGAR_MASK; + int len = cigar[k] >> BAM_CIGAR_SHIFT; + if ( op==BAM_CSOFT_CLIP ) y += len; + else if ( op==BAM_CMATCH || op==BAM_CEQUAL || op==BAM_CDIFF ) + { + int j_end = rcns->end < x + len - 1 ? rcns->end - x : len - 1; + int j_beg = rcns->beg > x ? rcns->beg - x : 0; + x += j_beg; // ref pos + y += j_beg; // seq pos + for (j=j_beg; j<=j_end; j++, x++, y++) _rcns_add_base(rcns,x,bam_seqi(seq,y)); + } + else if ( op==BAM_CINS ) + { + if ( x>=rcns->beg && xend ) + { + local_band += p->indel; + _rcns_add_ins(rcns,x,seq,len); + } + } + else if ( op==BAM_CDEL ) + { + if ( x>=rcns->beg && x+len-1<=rcns->end ) + { + local_band += -p->indel; + _rcns_add_del(rcns,x,len); + } + } + if ( local_band_max < local_band ) local_band_max = local_band; + } + + // Track the biggest deviation +/- from diagonal, used in BAQ alignment step. + if ( rcns->band < local_band_max ) rcns->band = local_band_max; + } + + return 0; +} + +// The algorithm: +// 1. Identify variant positions +// 2. Sort variants by abs(variant_allele_freq-0.5) in descending order +// 3. Take the top sorted variants (up to 8 to fit in uint8_t) and count the number of +// corresponding reads to create frequency spectrum +// 4. Correct errors, collapse to the requested number of haplotypes (consensus sequences) +// using majority vote for the distribution tail +const char **rcns_get_consensus(read_cns_t *rcns, const char *ref, int **npos) +{ + int i,j,n = rcns->end - rcns->beg + 1; + for (i=0; ibeg+i+1); + for (j=0; j<5; j++) + fprintf(stderr,"\t%d",rcns->base_freq[i].base[j]); + fprintf(stderr,"\n"); + } + return NULL; +} + diff --git a/read_consensus.h b/read_consensus.h new file mode 100644 index 000000000..4ee908583 --- /dev/null +++ b/read_consensus.h @@ -0,0 +1,49 @@ +/* read_consensus.h -- create and maintain consensus of reads + + Copyright (C) 2022 Genome Research Ltd. + + Author: pd3@sanger + + Permission is hereby granted, free of charge, to any person obtaining a copy + of this software and associated documentation files (the "Software"), to deal + in the Software without restriction, including without limitation the rights + to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + copies of the Software, and to permit persons to whom the Software is + furnished to do so, subject to the following conditions: + + The above copyright notice and this permission notice shall be included in + all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL + THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + DEALINGS IN THE SOFTWARE. */ + +#ifndef READ_CONSENSUS_H +#define READ_CONSENSUS_H + +#include +#include +#include + +typedef struct _read_cns_t read_cns_t; + +// Init and destroy read consensus +read_cns_t *rcns_init(int pos, int beg, int end); +void rcns_destroy(read_cns_t *rcns); + +// Reset the structures for new sample and/or position +int rcns_reset(read_cns_t *rcns, int pos, int beg, int end); + +// Add reads to consensus. Can be called once or multiple times, eg for creating +// a shared consensus for multiple samples (note ploidy might be an issue) +int rcns_set_reads(read_cns_t *rcns, bam_pileup1_t *plp, int nplp); + +// Generate up to two consensus sequences, the npos[] array holds the pos index +// relative to the returned sequence (0-based) +const char **rcns_get_consensus(read_cns_t *rcns, const char *ref, int **npos); + +#endif From 1e06536f8e8975a821a3e4e0d7f11ecb5122dbb1 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Thu, 28 Jul 2022 09:44:34 +0100 Subject: [PATCH 06/84] First draft of read consensus creation functional --- Makefile | 2 +- bam2bcf_iaux.c | 15 +- cigar_state.h | 113 +++++++++++ read_consensus.c | 477 +++++++++++++++++++++++++++++++++++++++++++---- read_consensus.h | 24 ++- 5 files changed, 580 insertions(+), 51 deletions(-) create mode 100644 cigar_state.h diff --git a/Makefile b/Makefile index de1ee9dde..9b52cf8b4 100644 --- a/Makefile +++ b/Makefile @@ -279,7 +279,7 @@ consensus.o: consensus.c $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_synced_bcf mpileup.o: mpileup.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) $(htslib_hts_os_h) regidx.h $(bcftools_h) $(bam2bcf_h) $(bam_sample_h) $(gvcf_h) bam2bcf.o: bam2bcf.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h) mw.h bam2bcf_indel.o: bam2bcf_indel.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_str2int_h) $(bam2bcf_h) $(htslib_ksort_h) str_finder.h -bam2bcf_iaux.o: bam2bcf_iaux.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_str2int_h) $(bam2bcf_h) $(htslib_ksort_h) str_finder.h read_consensus.h +bam2bcf_iaux.o: bam2bcf_iaux.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_str2int_h) $(bam2bcf_h) $(htslib_ksort_h) str_finder.h read_consensus.h cigar_state.h read_consensus.o: read_consensus.c read_consensus.h $(htslib_hts_h) $(htslib_sam_h) bam_sample.o: bam_sample.c $(htslib_hts_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) $(khash_str2str_h) $(bam_sample_h) $(bcftools_h) version.o: version.h version.c diff --git a/bam2bcf_iaux.c b/bam2bcf_iaux.c index a45876906..2c515b61b 100644 --- a/bam2bcf_iaux.c +++ b/bam2bcf_iaux.c @@ -55,12 +55,12 @@ typedef struct int max_ins_len; // largest insertion int left, right; // consensus sequence boundaries read_cns_t *rcns; // read consensus - const char **cns_seq; // array of consensus sequences + cns_seq_t *cns_seq; // array of consensus sequences int *cns_pos; // array of relative pos indexes within cns_seq sequences } indel_aux_t; -static void _print_types(indel_aux_t *iaux) +static void debug_print_types(indel_aux_t *iaux) { int i,j; fprintf(stderr,"types at %s:%d ... ",iaux->chr,iaux->pos+1); @@ -68,7 +68,7 @@ static void _print_types(indel_aux_t *iaux) { if ( iaux->types[i]<=0 ) { - if ( i==iaux->iref_type ) fprintf(stderr," %d",iaux->types[i]); + if ( i==iaux->iref_type ) fprintf(stderr," ref=%d",iaux->types[i]); continue; } fprintf(stderr," "); @@ -290,7 +290,7 @@ static int iaux_init_types(indel_aux_t *iaux) iaux_init_sequence_context(iaux); - _print_types(iaux); + debug_print_types(iaux); return iaux->ntypes; } @@ -305,7 +305,12 @@ static int iaux_set_consensus(indel_aux_t *iaux, int ismpl) rcns_set_reads(iaux->rcns, iaux->plp[ismpl], iaux->nplp[ismpl]); - iaux->cns_seq = rcns_get_consensus(iaux->rcns, iaux->ref + iaux->left, &iaux->cns_pos); + iaux->cns_seq = rcns_get_consensus(iaux->rcns, iaux->ref + iaux->left); + +// todo: +// rcns should also collect localized number of mismatches as a substitute +// for uninformative MQ. This would not affect calling but would help with +// filtering return -1; } diff --git a/cigar_state.h b/cigar_state.h new file mode 100644 index 000000000..f29adadb4 --- /dev/null +++ b/cigar_state.h @@ -0,0 +1,113 @@ +/* cigar_state.h -- API for efficient parsing of CIGAR strings + + Copyright (C) 2022 Genome Research Ltd. + + Author: pd3@sanger + + Permission is hereby granted, free of charge, to any person obtaining a copy + of this software and associated documentation files (the "Software"), to deal + in the Software without restriction, including without limitation the rights + to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + copies of the Software, and to permit persons to whom the Software is + furnished to do so, subject to the following conditions: + + The above copyright notice and this permission notice shall be included in + all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL + THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + DEALINGS IN THE SOFTWARE. */ + +#ifndef CIGAR_STATE_H +#define CIGAR_STATE_H + +#include +#include +#include + +typedef struct +{ + bam1_t *bam; + uint32_t *cigar; + uint8_t *seq; + int ncig; + int icig; // position in the cigar string + int iseq; // the cigar[icigar] operation refers to seq[iseq+1] + hts_pos_t ref_pos; // reference coordinate, corresponds to iseq +} +cigar_state_t; + +inline void cstate_init(cigar_state_t *cs, bam1_t *bam) +{ + cs->bam = bam; + cs->cigar = bam_get_cigar(bam); + cs->seq = bam_get_seq(bam); + cs->ncig = bam->core.n_cigar; + cs->icig = 0; + cs->iseq = 0; + cs->ref_pos = bam->core.pos; + int op = cs->cigar[0] & BAM_CIGAR_MASK; + int len = cs->cigar[0] >> BAM_CIGAR_SHIFT; + if ( op==BAM_CINS || op==BAM_CSOFT_CLIP ) cs->ref_pos -= len; +} + +// Move in the cigar forward to find query index that matches the +// seek operator and the reference position. +// +// Returns the index to the query sequence cs->seq +// on success; -1 when there is no such matching position but the cigar +// is still not entirely consumed (e.g. a deletion or a soft-clip); -2 +// when there is no overlap (i.e. the read ends before the position). +inline int cstate_seek_fwd(cigar_state_t *cs, hts_pos_t pos, int seek_op, int *oplen) +{ + while ( cs->ref_pos <= pos ) + { + if ( cs->icig >= cs->ncig ) return -2; + + int op = cs->cigar[cs->icig] & BAM_CIGAR_MASK; + int len = cs->cigar[cs->icig] >> BAM_CIGAR_SHIFT; + if ( op==BAM_CMATCH || op==BAM_CEQUAL || op==BAM_CDIFF ) + { + if ( cs->ref_pos + len <= pos ) + { + cs->ref_pos += len; + cs->iseq += len; + cs->icig++; + continue; + } + if ( seek_op==BAM_CMATCH ) return pos - cs->ref_pos + cs->iseq; + return -1; + } + if ( op==BAM_CINS || op==BAM_CSOFT_CLIP ) + { + if ( cs->ref_pos == pos + 1 && seek_op==op ) + { + if ( oplen ) *oplen = len; + return cs->iseq; + } + if ( cs->ref_pos >= pos ) return -1; + cs->iseq += len; + cs->icig++; + continue; + } + if ( op==BAM_CDEL || op==BAM_CREF_SKIP ) + { + if ( cs->ref_pos == pos && seek_op==op ) + { + if ( oplen ) *oplen = len; + return cs->iseq; + } + if ( cs->ref_pos >= pos ) return -1; + cs->ref_pos += len; + cs->icig++; + continue; + } + } + return cs->icig < cs->ncig ? -1 : -2; +} + +#endif diff --git a/read_consensus.c b/read_consensus.c index d2fa79592..576feb420 100644 --- a/read_consensus.c +++ b/read_consensus.c @@ -22,13 +22,20 @@ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -#include #include +#include +#include "read_consensus.h" +#include "cigar_state.h" +#include "kheap.h" +// #define DEBUG_RCNS 1 + + +// Frequency arrays for each variant type #define NI 10 // number of alternative insertion sequences at one position in a single sample typedef struct { - char *str[NI]; + char *nt16_seq[NI]; int len[NI]; int freq[NI]; } @@ -47,15 +54,46 @@ typedef struct } base_freq_t; + +// Candidate variants for each interesting position to build consensus haplotypes +enum variant_type { snv, ins, del, done }; +typedef struct +{ + enum variant_type vtype; + hts_pos_t pos; // variant position (reference sequence coordinates), indels follow VCF convention + int idx; // temporary 0-based index to rcns.cvar + int which, // base/ins/del in rcns.[base|ins|del]_freq array + depth; // coverage at the position + float af, af_dev; // variant allele frequency (just for debugging printout) and absolute af deviation from 0.5 +} +candidate_var_t; +static inline int cvar_not_preferred(candidate_var_t *a, candidate_var_t *b) +{ + if ( a->af_dev == b->af_dev ) return a->depth < b->depth ? 1 : 0; + return a->af_dev > b->af_dev ? 1 : 0; +} +KHEAP_INIT(cvh, candidate_var_t, cvar_not_preferred); +typedef khp_cvh_t cvar_heap_t; + +#define MAX_NCVAR 8 // This results in alloc() of 2^MAX_NCVAR possible haplotypes +#define NHAP (1<mfreq; i++) { ins_freq_t *ifrq = &rcns->ins_freq[i]; - for (j=0; jstr[j]; j++) free(ifrq->str[j]); + for (j=0; jnt16_seq[j]; j++) free(ifrq->nt16_seq[j]); } + for (i=0; i<2; i++) + free(rcns->cns[i].seq); free(rcns->ins_freq); free(rcns->del_freq); free(rcns->base_freq); free(rcns->stmp); + khp_destroy(cvh,rcns->cv_heap); free(rcns); } -int _rcns_init_arrays(read_cns_t *rcns) +int init_arrays(read_cns_t *rcns) { int i,j,n = rcns->end - rcns->beg + 1; if ( n > rcns->mfreq ) @@ -92,6 +133,13 @@ int _rcns_init_arrays(read_cns_t *rcns) rcns->base_freq = bfrq; memset(bfrq+rcns->mfreq,0,sizeof(*rcns->base_freq)*(n-rcns->mfreq)); + for (i=0; i<2; i++) + { + char *seq = (char*) realloc(rcns->cns[i].seq,sizeof(char)*n); + if ( !seq ) return -1; + rcns->cns[i].seq = seq; + } + rcns->mfreq = n; } memset(rcns->base_freq,0,sizeof(*rcns->base_freq)*n); @@ -99,30 +147,34 @@ int _rcns_init_arrays(read_cns_t *rcns) for (i=0; iins_freq[i]; - for (j=0; jstr[j]; j++) free(ifrq->str[j]); + for (j=0; jnt16_seq[j]; j++) free(ifrq->nt16_seq[j]); } memset(rcns->ins_freq,0,sizeof(*rcns->ins_freq)*n); return 0; } -int rcns_reset(read_cns_t *rcns, int pos, int beg, int end) +int rcns_reset(read_cns_t *rcns, hts_pos_t pos, hts_pos_t beg, hts_pos_t end) { +fprintf(stderr,"init: pos=%"PRIhts_pos" beg,end=%"PRIhts_pos",%"PRIhts_pos"\n",pos,beg,end); rcns->band = 0; rcns->pos = pos; rcns->beg = beg; rcns->end = end; - return _rcns_init_arrays(rcns); + int i; + for (i=0; i<2; i++) rcns->cns[i].nseq = rcns->cns[i].ipos = 0; + // this should not be necessary if the caller did run all steps + while (rcns->cv_heap->ndat) khp_delete(cvh, rcns->cv_heap); + return init_arrays(rcns); } -static inline void _rcns_add_base(read_cns_t *rcns, int ref_pos, int nt16) +static inline void add_base(read_cns_t *rcns, int ref_pos, int nt16) { int i = ref_pos - rcns->beg; rcns->base_freq[i].base[seq_nt16_int[nt16]]++; } -static void _rcns_add_ins(read_cns_t *rcns, int ref_pos, uint8_t *nt16_seq, int len) +static void add_ins(read_cns_t *rcns, int ref_pos, int seq_pos, uint8_t *raw_seq, int len) { int i = ref_pos - rcns->beg; ins_freq_t *ifrq = &rcns->ins_freq[i]; - char *str; if ( rcns->mstmp < len ) { @@ -133,23 +185,23 @@ static void _rcns_add_ins(read_cns_t *rcns, int ref_pos, uint8_t *nt16_seq, int } else str = rcns->stmp; - for (i=0; istr[i]; i++) - if ( ifrq->len[i]==len && !memcmp(ifrq->str[i],str,len) ) break; + for (i=0; int16_seq[i]; i++) + if ( ifrq->len[i]==len && !memcmp(ifrq->nt16_seq[i],str,len) ) break; - assert( i=NI ) return; // too many choices; discard - if ( !ifrq->str[i] ) // new insertion + if ( !ifrq->nt16_seq[i] ) // new insertion { - if ( !(ifrq->str[i]=malloc(len)) ) return; - memcpy(ifrq->str[i], str, len); + if ( !(ifrq->nt16_seq[i]=malloc(len)) ) return; + memcpy(ifrq->nt16_seq[i], str, len); ifrq->len[i] = len; } ifrq->freq[i]++; } -static void _rcns_add_del(read_cns_t *rcns, int ref_pos, int len) +static void add_del(read_cns_t *rcns, int ref_pos, int len) { int i = ref_pos - rcns->beg; del_freq_t *dfrq = &rcns->del_freq[i]; @@ -157,20 +209,22 @@ static void _rcns_add_del(read_cns_t *rcns, int ref_pos, int len) for (i=0; ilen[i]; i++) if ( dfrq->len[i]==len ) break; - assert( i=NI ) return; // too many choices; discard if ( !dfrq->len[i] ) dfrq->len[i] = len; // new deletion dfrq->freq[i]++; } -read_cns_t *rcns_init(int pos, int beg, int end) +read_cns_t *rcns_init(hts_pos_t pos, hts_pos_t beg, hts_pos_t end) { +fprintf(stderr,"init: pos=%"PRIhts_pos" beg,end=%"PRIhts_pos",%"PRIhts_pos"\n",pos,beg,end); read_cns_t *rcns = (read_cns_t*) calloc(1,sizeof(read_cns_t)); rcns->pos = pos; rcns->beg = beg; rcns->end = end; - if ( _rcns_init_arrays(rcns)!=0 ) + rcns->cv_heap = khp_init(cvh); + if ( init_arrays(rcns)!=0 ) { rcns_destroy(rcns); return NULL; @@ -180,6 +234,10 @@ read_cns_t *rcns_init(int pos, int beg, int end) int rcns_set_reads(read_cns_t *rcns, bam_pileup1_t *plp, int nplp) { + // save the reads for phasing, this can be called multiple times + rcns->plp = plp; + rcns->nplp = nplp; + // fill consensus arrays int i,j,k, local_band_max = 0; // maximum absolute deviation from diagonal for (i=0; ibeg > x ? rcns->beg - x : 0; x += j_beg; // ref pos y += j_beg; // seq pos - for (j=j_beg; j<=j_end; j++, x++, y++) _rcns_add_base(rcns,x,bam_seqi(seq,y)); + for (j=j_beg; j<=j_end; j++, x++, y++) add_base(rcns,x,bam_seqi(seq,y)); } else if ( op==BAM_CINS ) { if ( x>=rcns->beg && xend ) { local_band += p->indel; - _rcns_add_ins(rcns,x,seq,len); + add_ins(rcns,x-1,y,seq,len); // x-1: one base before as in VCF + y += len; } } else if ( op==BAM_CDEL ) @@ -218,7 +277,8 @@ int rcns_set_reads(read_cns_t *rcns, bam_pileup1_t *plp, int nplp) if ( x>=rcns->beg && x+len-1<=rcns->end ) { local_band += -p->indel; - _rcns_add_del(rcns,x,len); + add_del(rcns,x-1,len); // x-1: one base before as in VCF + x += len; } } if ( local_band_max < local_band ) local_band_max = local_band; @@ -231,23 +291,364 @@ int rcns_set_reads(read_cns_t *rcns, bam_pileup1_t *plp, int nplp) return 0; } +#if DEBUG_RCNS +static void debug_print_base_freqs(read_cns_t *rcns, const char *ref) +{ + int i,j,k,n = rcns->end - rcns->beg + 1; + base_freq_t *bfreq = rcns->base_freq; + ins_freq_t *ifreq = rcns->ins_freq; + del_freq_t *dfreq = rcns->del_freq; + for (i=0; ibeg+i+1,ref[i]); + for (j=0; j<5; j++) + fprintf(stderr,"\t%d%s",bfreq[i].base[j],ref[i]=="ACGTN"[j]?"*":""); + fprintf(stderr,"\t"); + for (j=0; jncvar; i++) + { + candidate_var_t *var = &rcns->cvar[i]; + fprintf(stderr,"\tvar%d pos=%"PRIhts_pos" idx=%d vtype=%d which=%d depth=%d af=%f af_dev=%f\n", + i,var->pos+1,var->idx,var->vtype,var->which,var->depth,var->af,var->af_dev); + } +} +static void debug_print_haplotype_frequency_spectrum(read_cns_t *rcns) +{ + int i,j; + fprintf(stderr,"Haplotype frequencies:\n"); + for (i=0; ihap_freq[i] ) continue; + fprintf(stderr,"\t%d: ",i); + for (j=0; jncvar; j++) + fprintf(stderr,"%d", i&(1<hap_freq[i]); + } +} +static void debug_print_consensus(read_cns_t *rcns) +{ + int i,j; + for (i=0; i<2; i++) + { + if ( !rcns->cns[i].nseq ) break; + fprintf(stderr,"Consensus%d: ",i); + for (j=0; jcns[i].ipos; j++) + fprintf(stderr,"%c",seq_nt16_str[(int)rcns->cns[i].seq[j]]); + fprintf(stderr,"#"); + for (; jcns[i].nseq; j++) + fprintf(stderr,"%c",seq_nt16_str[(int)rcns->cns[i].seq[j]]); + fprintf(stderr,"\n"); + } +} +#else +#define debug_print_base_freqs(rcns,ref) +#define debug_print_candidate_variants(rcns) +#define debug_print_haplotype_frequency_spectrum(rcns) +#define debug_print_consensus(rcns) +#endif + +static int cvar_pos_cmp(const void *aptr, const void *bptr) +{ + candidate_var_t *a = (candidate_var_t*)aptr; + candidate_var_t *b = (candidate_var_t*)bptr; + if ( a->pos < b->pos ) return -1; + if ( a->pos > b->pos ) return 1; + if ( a->vtype < b->vtype ) return -1; + if ( a->vtype > b->vtype ) return 1; + if ( a->which < b->which ) return -1; + if ( a->which > b->which ) return 1; + return 0; +} +static void register_variant(read_cns_t *rcns, enum variant_type vtype, int cns_pos, int which, int depth, float freq) +{ + cvar_heap_t *cv_heap = rcns->cv_heap; + if ( vtype==done ) + { + rcns->ncvar = 0; + while (cv_heap->ndat) + { + rcns->cvar[rcns->ncvar++] = cv_heap->dat[0]; + khp_delete(cvh,cv_heap); + } + // sort the variants by pos,type,which to make determination of haplotypes from reads faster + if ( rcns->ncvar ) + qsort(rcns->cvar, rcns->ncvar, sizeof(*rcns->cvar), cvar_pos_cmp); + return; + } + + candidate_var_t var; + var.pos = cns_pos + rcns->beg; + var.which = which; + var.vtype = vtype; + var.depth = depth; + var.af_dev = fabs(0.5-freq); + var.af = freq; + + int free_slot; + + // keep the number of variants small, maximum MAX_NCVAR + if ( rcns->ncvar==MAX_NCVAR ) + { + if ( cvar_not_preferred(&var,&cv_heap->dat[0]) ) return; // no need to add, the new variant is worse than the heap's worst one + free_slot = cv_heap->dat[0].idx; + khp_delete(cvh,cv_heap); + } + else + free_slot = rcns->ncvar++; + var.idx = free_slot; + rcns->cvar[free_slot] = var; + khp_insert(cvh,cv_heap,&var); +} + +// Identify candidate variant positions. (Note that homozygous variants are not considered +// as those will be added trivially by taking the consensus base.) The detection limit is +// for now hard-wired. This has only indirect effect on sensitivity, it just will not +// contribute to the consensus template for realigning. +static int select_candidate_variants(read_cns_t *rcns, const char *ref) +{ + //const float af_th = 0.1; +const float af_th = 0.05;// just for debugging + int i,j, n = rcns->end - rcns->beg + 1; + base_freq_t *bfreq = rcns->base_freq; + ins_freq_t *ifreq = rcns->ins_freq; + del_freq_t *dfreq = rcns->del_freq; + for (i=0; ipos - rcns->beg ) continue; // creating consensus from everything but the variants at the current position + int dp = 0; + for (j=0; j<4; j++) dp += bfreq[i].base[j]; + for (j=0; jaf_th && af<(1-af_th) ) register_variant(rcns,snv,i,j,dp,af); + } + for (j=0; jaf_th && af<(1-af_th) ) register_variant(rcns,del,i,j,dp,af); + } + for (j=0; jaf_th && af<(1-af_th) ) register_variant(rcns,ins,i,j,dp,af); + } + } + register_variant(rcns,done,0,0,0,0); // finalize + return 0; +} +static int create_haplotype_frequency_spectrum(read_cns_t *rcns) +{ + memset(rcns->hap_freq,0,sizeof(rcns->hap_freq)); + + int i; + for (i=0; inplp; i++) // for each read... + { + const bam_pileup1_t *p = rcns->plp + i; + cigar_state_t cigar; + cstate_init(&cigar,p->b); + + int j,k,hap = 0; + for (j=0; jncvar; j++) + { + candidate_var_t *cvar = &rcns->cvar[j]; + if ( cvar->vtype==snv ) + { + int iseq = cstate_seek_fwd(&cigar, cvar->pos, BAM_CMATCH, NULL); + if ( iseq==-2 ) break; + if ( iseq==-1 ) continue; + int nt16 = bam_seqi(cigar.seq, iseq); + if ( seq_nt16_int[nt16]==cvar->which ) hap |= 1<vtype==ins ) + { + int len; + ins_freq_t *ifrq = &rcns->ins_freq[cvar->pos - rcns->beg]; + int iseq = cstate_seek_fwd(&cigar, cvar->pos, BAM_CINS, &len); + if ( iseq==-2 ) break; + if ( iseq==-1 ) continue; + if ( len!=ifrq->len[cvar->which] ) continue; + for (k=0; klen[cvar->which]; k++) + if ( bam_seqi(cigar.seq,iseq+k)!=ifrq->nt16_seq[cvar->which][k] ) break; + if ( k==ifrq->len[cvar->which] ) hap |= 1<vtype==del ) + { + int len; + del_freq_t *dfrq = &rcns->del_freq[cvar->pos - rcns->beg]; + int ret = cstate_seek_fwd(&cigar, cvar->pos, BAM_CDEL, &len); + if ( ret==-2 ) break; + if ( ret==-1 ) continue; + if ( len!=dfrq->len[cvar->which] ) continue; + hap |= 1<hap_freq[hap]++; + } + return 0; +} + +typedef struct +{ + int idx, count; +} +ii_t; + +static int ii_cmp(const void *a, const void *b) +{ + if ( ((ii_t*)a)->count > ((ii_t*)b)->count ) return -1; + if ( ((ii_t*)a)->count < ((ii_t*)b)->count ) return 1; + return 0; +} + +static int correct_haplotype_errors(read_cns_t *rcns) +{ + int i,j, tot = 0; + ii_t freq[NHAP]; + for (i=0; ihap_freq[i]; + tot += rcns->hap_freq[i]; + } + qsort(freq, NHAP, sizeof(ii_t), ii_cmp); + for (i=NHAP-1; i>=0; i--) + { + //if ( freq[1].count > tot - freq[0].count ) break; // the top2 hapotypes cannot change anymore + if ( !freq[i].count ) continue; + + // Find a similar haplotype with the highest frequency. Assuming errors go in 0->1 + // direction only and considering one error only. + int count = freq[i].count, max_hap = 0; + for (j=0; j=0 && haphap_freq[hap] ) count = rcns->hap_freq[hap], max_hap = hap; + } + if ( count == freq[i].count ) continue; + + // Update frequency and sort the two modified elements + count = freq[i].count; + freq[i].count = 0; + rcns->hap_freq[freq[i].idx] = 0; + rcns->hap_freq[max_hap] += count; + for (j=i+1; j=0; j--) + { + if ( freq[j].idx==max_hap ) freq[j].count += count; // update the best matching haplotype + if ( freq[j].count < freq[j+1].count ) + { + ii_t tmp = freq[j]; freq[j] = freq[j+1]; freq[j+1] = tmp; + } + } + } + rcns->cns_hap[0] = freq[0].idx; + rcns->cns_hap[1] = freq[1].idx; + + // Use only one consensus if the next best haplotype is populated by less than 10% of reads + rcns->ncns = (freq[1].count / (freq[0].count + freq[1].count) < 0.1) ? 1 : 2; +rcns->ncns = 2; + + return 0; +} + +void create_consensus(read_cns_t *rcns, const char *ref, int ith) +{ + int n = rcns->end - rcns->beg + 1; + cns_seq_t *cns = &rcns->cns[ith]; + int j,k, ivar = 0; + for (j=0; jbeg + j; + if ( rcns->pos == ref_pos ) cns->ipos = j; + + while ( ivar < rcns->ncvar && rcns->cvar[ivar].pos < ref_pos ) ivar++; + + if ( ivar >= rcns->ncvar || rcns->cvar[ivar].pos != ref_pos || !(rcns->cns_hap[ith] & (1U<seq[cns->nseq++] = seq_nt16_table[(int)ref[ref_pos]]; + continue; + } + int which = rcns->cvar[ivar].which; + if ( rcns->cvar[ivar].vtype == snv ) + { + cns->seq[cns->nseq++] = 1<cvar[ivar].vtype == ins ) + { + cns->seq[cns->nseq++] = ref[ref_pos]; + int len = rcns->ins_freq[j].len[which]; + char *seq = rcns->ins_freq[j].nt16_seq[which]; + for (k=0; kseq[cns->nseq++] = seq[k]; + } + if ( rcns->cvar[ivar].vtype == del ) + { + cns->seq[cns->nseq++] = ref[ref_pos]; + j += rcns->del_freq[j].len[which]; + continue; + } + } +} + // The algorithm: -// 1. Identify variant positions +// 1. Identify heterozygous variant positions // 2. Sort variants by abs(variant_allele_freq-0.5) in descending order // 3. Take the top sorted variants (up to 8 to fit in uint8_t) and count the number of // corresponding reads to create frequency spectrum // 4. Correct errors, collapse to the requested number of haplotypes (consensus sequences) // using majority vote for the distribution tail -const char **rcns_get_consensus(read_cns_t *rcns, const char *ref, int **npos) +cns_seq_t *rcns_get_consensus(read_cns_t *rcns, const char *ref) { - int i,j,n = rcns->end - rcns->beg + 1; - for (i=0; incvar ) { - fprintf(stderr,"%d\t",rcns->beg+i+1); - for (j=0; j<5; j++) - fprintf(stderr,"\t%d",rcns->base_freq[i].base[j]); - fprintf(stderr,"\n"); + create_haplotype_frequency_spectrum(rcns); + debug_print_haplotype_frequency_spectrum(rcns); + + correct_haplotype_errors(rcns); + debug_print_haplotype_frequency_spectrum(rcns); + } + else + { + rcns->cns_hap[0] = 0; + rcns->ncns = 1; } - return NULL; + + // create consensus + int i; + for (i=0; incns; i++) create_consensus(rcns,ref,i); + debug_print_consensus(rcns); + + return rcns->cns; } diff --git a/read_consensus.h b/read_consensus.h index 4ee908583..91fcc1586 100644 --- a/read_consensus.h +++ b/read_consensus.h @@ -29,21 +29,31 @@ #include #include +typedef struct +{ + char *seq; // nt16 sequence + int nseq, ipos; // the sequence length and the `pos` index relative to seq +} +cns_seq_t; + typedef struct _read_cns_t read_cns_t; // Init and destroy read consensus -read_cns_t *rcns_init(int pos, int beg, int end); +read_cns_t *rcns_init(hts_pos_t pos, hts_pos_t beg, hts_pos_t end); void rcns_destroy(read_cns_t *rcns); // Reset the structures for new sample and/or position -int rcns_reset(read_cns_t *rcns, int pos, int beg, int end); +int rcns_reset(read_cns_t *rcns, hts_pos_t pos, hts_pos_t beg, hts_pos_t end); -// Add reads to consensus. Can be called once or multiple times, eg for creating -// a shared consensus for multiple samples (note ploidy might be an issue) +// Add reads to consensus. The provided structures must continue to exist +// until rcns_get_consensus() is called. +// +// Todo (easy): allow it to be called once or multiple times, eg for +// creating a shared consensus for multiple samples int rcns_set_reads(read_cns_t *rcns, bam_pileup1_t *plp, int nplp); -// Generate up to two consensus sequences, the npos[] array holds the pos index -// relative to the returned sequence (0-based) -const char **rcns_get_consensus(read_cns_t *rcns, const char *ref, int **npos); +// Generate up to two consensus sequences, cns_seq[1].nseq is 0 when only +// the first is set +cns_seq_t *rcns_get_consensus(read_cns_t *rcns, const char *ref); #endif From 2240ff38aabb6d00ca9dab600dfeefde91311cc8 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Thu, 11 Aug 2022 15:13:15 +0100 Subject: [PATCH 07/84] Functional --indels-2.0 prototype This version is able to make simple calls, correctly creates up to two reference consensus templates. The code is based on the original indel calling but does not contain the heuristics introduced later by jkb. --- bam2bcf.h | 1 + bam2bcf_iaux.c | 311 ++++++++++++++++++++++++++++++++++++++++++----- bam2bcf_indel.c | 4 +- read_consensus.c | 165 +++++++++++++++++++------ read_consensus.h | 7 +- 5 files changed, 417 insertions(+), 71 deletions(-) diff --git a/bam2bcf.h b/bam2bcf.h index 9e64917fb..53d565758 100644 --- a/bam2bcf.h +++ b/bam2bcf.h @@ -181,6 +181,7 @@ extern "C" { void bcf_callaux_clean(bcf_callaux_t *bca, bcf_call_t *call); int bcf_cgp_l_run(const char *ref, int pos); + int est_indelreg(int pos, const char *ref, int l, char *ins4); #ifdef __cplusplus } diff --git a/bam2bcf_iaux.c b/bam2bcf_iaux.c index 2c515b61b..6013bdcfa 100644 --- a/bam2bcf_iaux.c +++ b/bam2bcf_iaux.c @@ -36,6 +36,7 @@ #include KSORT_INIT_STATIC_GENERIC(uint32_t) +#define DEBUG_ALN 0 #define MAX_TYPES 64 @@ -49,7 +50,7 @@ typedef struct bcf_callaux_t *bca; // auxiliary bam2bcf structure const char *ref; // reference genome (ASCII) uint32_t *uitmp; // temporary unsigned int array - uint32_t *inscns; // insertions consensus [itype*max_ins_len+i] + char *inscns; // insertions consensus "ACGTN"[itype*max_ins_len+i] int muitmp, minscns; // size of uitmp, inscns int iref_type, ntypes, types[MAX_TYPES]; // indel types int max_ins_len; // largest insertion @@ -57,9 +58,18 @@ typedef struct read_cns_t *rcns; // read consensus cns_seq_t *cns_seq; // array of consensus sequences int *cns_pos; // array of relative pos indexes within cns_seq sequences + uint8_t *ref_seq, *qry_seq; // reference and query sequence to align + int nref_seq, nqry_seq; // the allocated size of ref_seq and qry_seq + uint8_t *qual; + int nqual; + int *read_scores, // read scores for each indel type [ntypes*iread+itype] + mread_scores, + ref_qual[MAX_TYPES], // refseq quality at pos for each indel type in the context of homopolymer runs + sum_qual[MAX_TYPES]; // qual contributions to each indel type from all reads } indel_aux_t; +#if DEBUG_ALN static void debug_print_types(indel_aux_t *iaux) { int i,j; @@ -72,11 +82,28 @@ static void debug_print_types(indel_aux_t *iaux) continue; } fprintf(stderr," "); - uint32_t *cns = &iaux->inscns[i*iaux->max_ins_len]; - for (j=0; jtypes[i]; j++) fprintf(stderr,"%c","ACGTN"[cns[j]]); + char *cns = &iaux->inscns[i*iaux->max_ins_len]; + for (j=0; jtypes[i]; j++) fprintf(stderr,"%c","ACGTN"[(int)cns[j]]); } fprintf(stderr,"\n"); } +#else +#define debug_print_types(iaux) +#endif + +void bcf_iaux_destroy(bcf_callaux_t *bca) +{ + if ( !bca->iaux ) return; + indel_aux_t *iaux = (indel_aux_t*)bca->iaux; + free(iaux->uitmp); + free(iaux->inscns); + free(iaux->ref_seq); + free(iaux->qry_seq); + free(iaux->qual); + free(iaux->read_scores); + rcns_destroy(iaux->rcns); + free(iaux); +} static void iaux_init_sequence_context(indel_aux_t *iaux) { @@ -92,10 +119,46 @@ static void iaux_init_sequence_context(indel_aux_t *iaux) if ( !iaux->ref[i] ) break; iaux->right = i; - // The length of the homopolymer run around the current position -// iaux->l_run = bcf_cgp_l_run(iaux->ref, iaux->pos); -//int l_run_base = seq_nt16_table[(uint8_t)ref[pos+1]]; -//int l_run_ins = 0; + // Sequence quality in the context of homopolymers for each indel type + int l_run = bcf_cgp_l_run(iaux->ref, iaux->pos); // The length of the homopolymer run around the current position + for (i=0; intypes; i++) + { + int l = iaux->types[i]; + + // This is the original est_seqQ() code. FIXME: check if the inserted sequence is consistent with the homopolymer run + int q = iaux->bca->openQ + iaux->bca->extQ * (abs(l) - 1); + int qh = l_run >= 3? (int)(iaux->bca->tandemQ * (double)abs(l) / l_run + .499) : 1000; + if ( q > qh ) q = qh; + + iaux->ref_qual[i] = q < 255 ? q : 255; + } + + // Determine the indel region, this makes the difference between e.g. T>TA vs TA>TAA + iaux->bca->indelreg = 0; + for (i=0; intypes; i++) + { + if ( !iaux->types[i] ) continue; + int ireg; + if ( iaux->types[i] > 0 ) + ireg = est_indelreg(iaux->pos, iaux->ref, iaux->types[i], &iaux->inscns[i*iaux->max_ins_len]); + else + ireg = est_indelreg(iaux->pos, iaux->ref, -iaux->types[i], 0); + if ( ireg > iaux->bca->indelreg ) iaux->bca->indelreg = ireg; + } +} + +static int iaux_init_scores(indel_aux_t *iaux, int ismpl) +{ + int n = iaux->nplp[ismpl] * iaux->ntypes; + if ( iaux->mread_scores < n ) + { + int *tmp = (int*) realloc(iaux->read_scores,n*sizeof(int)); + if ( !tmp ) return -1; + iaux->mread_scores = n; + iaux->read_scores = tmp; + } + memset(iaux->read_scores,0,n); + return 0; } static int _have_indel_reads(indel_aux_t *iaux) @@ -109,6 +172,9 @@ static int _have_indel_reads(indel_aux_t *iaux) return 0; } +// For insertions only their sizes were collected so far. Now go through the reads and +// create consensus sequence for each insert, therefore note that there can be only one +// sequence per insertion length static int iaux_init_ins_types(indel_aux_t *iaux) { if ( !iaux->max_ins_len ) return 0; @@ -147,11 +213,11 @@ static int iaux_init_ins_types(indel_aux_t *iaux) } } - uint32_t *cns; + char *cns; int ncns = iaux->ntypes * iaux->max_ins_len; if ( iaux->minscns < ncns ) { - cns = (uint32_t*) realloc(iaux->inscns,naux*sizeof(*aux)); + cns = (char*) realloc(iaux->inscns,naux*sizeof(*aux)); if ( !cns ) return -1; iaux->inscns = cns; iaux->minscns = ncns; @@ -177,9 +243,10 @@ static int iaux_init_ins_types(indel_aux_t *iaux) #define MINUS_CONST 0x10000000 static int iaux_init_types(indel_aux_t *iaux) { - if ( !_have_indel_reads(iaux) ) return -1; + if ( !_have_indel_reads(iaux) ) return 0; iaux->bca->max_support = 0; + memset(iaux->sum_qual,0,MAX_TYPES*sizeof(*iaux->sum_qual)); int i,j, nreads = 0; for (i=0; insmpl; i++) nreads += iaux->nplp[i]; @@ -198,7 +265,8 @@ static int iaux_init_types(indel_aux_t *iaux) int naux = 0, indel_support_ok = 0, n_alt = 0, n_tot = 0; int max_rd_len = 0; // max sequence length that includes ref+del bases - // Fill out aux[] array with all the non-zero indel sizes. + // Fill out aux[] array with all the non-zero indel sizes. This is an unsorted list with as many + // entries as there are reads aux[naux++] = MINUS_CONST; // zero indel is always a type (REF) for (i=0; insmpl; i++) { @@ -227,7 +295,7 @@ static int iaux_init_types(indel_aux_t *iaux) // Check if the minimum required number of indel reads has been observed if ( !iaux->bca->per_sample_flt && n_alt >= iaux->bca->min_support && (double)n_alt/n_tot >= iaux->bca->min_frac ) indel_support_ok = 1; - if ( naux==1 || !indel_support_ok ) return -1; + if ( naux==1 || !indel_support_ok ) return 0; // To prevent long stretches of N's to be mistaken for indels (sometimes thousands of bases), check the number of N's in the // sequence and skip places where half or more reference bases in the sequence that follows pos are Ns @@ -236,7 +304,7 @@ static int iaux_init_types(indel_aux_t *iaux) if ( iaux->ref[i] == 'N' ) nN++; if ( 2*nN > i - iaux->pos ) return -1; - // Sort aux[] and dedup + // Sort aux[] and dedup indel types int n_types = 1; ks_introsort(uint32_t, naux, aux); for (i=1; intypes = 0; iaux->max_ins_len = 0; for (i=0; intypes <= 1 ) return -1; + if ( iaux->ntypes <= 1 ) return 0; - // Init insertion types + // Init insertion types, including their sequence if ( iaux_init_ins_types(iaux) < 0 ) return -1; iaux_init_sequence_context(iaux); - debug_print_types(iaux); - return iaux->ntypes; } #undef MINUS_CONST @@ -312,15 +378,201 @@ static int iaux_set_consensus(indel_aux_t *iaux, int ismpl) // for uninformative MQ. This would not affect calling but would help with // filtering - return -1; + return 0; +} + +static int iaux_align_read(indel_aux_t *iaux, bam1_t *bam, uint8_t *ref, int nref) +{ + if ( bam->core.flag & BAM_FUNMAP ) return 1; // skip unmapped reads + +// BAM_CREF_SKIP check: save in plp aux data? +// uint32_t *cigar = bam_get_cigar(bam); + + // prepare query sequence + int i, qbeg = 0, qend = bam->core.l_qseq; + if ( iaux->nqry_seq < qend - qbeg ) + { + uint8_t *tmp = (uint8_t*) calloc(qend - qbeg, 1); + if ( !tmp ) return -1; // critical error + iaux->qry_seq = tmp; + iaux->nqry_seq = qend - qbeg; + } + uint8_t *seq = bam_get_seq(bam); + for (i=qbeg; iqry_seq[i-qbeg] = seq_nt16_int[bam_seqi(seq,i)]; + + // prepare qualities, either BQ or BAQ qualities (ZQ) + if ( iaux->nqual < qend - qbeg ) + { + uint8_t *tmp = (uint8_t*) calloc(qend - qbeg, 1); + if ( !tmp ) return -1; // critical error + iaux->qual = tmp; + iaux->nqual = qend - qbeg; + } + uint8_t *qual = iaux->qual; + const uint8_t *qq = bam_get_qual(bam); + const uint8_t *bq = (uint8_t*)bam_aux_get(bam, "ZQ"); + if ( bq ) bq++; // skip type + for (i=qbeg; i 30 ) qual[i-qbeg] = 30; + if ( qual[i-qbeg] < 7 ) qual[i-qbeg] = 7; + } + +// Illumina +probaln_par_t apf = { 1e-4, 1e-2, 10 }; + + // align + int score = probaln_glocal(ref, nref, iaux->qry_seq, qend - qbeg, qual, &apf, 0, 0); + int adj_score = (int)(100. * score / (qend - qbeg) + .499) * iaux->bca->indel_bias; + +#if DEBUG_ALN + fprintf(stderr,"aln: %d/%d\t%s\n\tref: ",score,adj_score,bam_get_qname(bam)); + for (i=0; iqry_seq[i]]); + fprintf(stderr,"\n\tqual: "); + for (i=0; i 255 ) adj_score = 255; + return score<<8 | adj_score; } + +// Score all reads for this sample and indel type using the up to two consensus sequence templates. +// On output sets iaux->read_scores[iread*ntypes+itype] = (raw_score<<8 | length_adjusted_score) static int iaux_score_reads(indel_aux_t *iaux, int ismpl, int itype) { - return -1; + int i; + cns_seq_t *cns = iaux->cns_seq; + while ( cns->nseq ) + { + // resize buffers if necessary + int ref_len = cns->nseq + iaux->types[itype]; + if ( iaux->nref_seq < ref_len ) + { + uint8_t *buf = (uint8_t*) realloc(iaux->ref_seq,sizeof(uint8_t)*ref_len); + if ( !buf ) return -1; + iaux->ref_seq = buf; + iaux->nref_seq = ref_len; + } + + // apply the indel + memcpy(iaux->ref_seq,cns->seq,cns->ipos+1); + if ( iaux->types[itype] < 0 ) // deletion + memcpy(iaux->ref_seq + cns->ipos + 1, cns->seq + cns->ipos + 1 - iaux->types[itype], cns->nseq - cns->ipos - 1 + iaux->types[itype]); + else + { + char *ins = &iaux->inscns[itype*iaux->max_ins_len]; + for (i=0; itypes[itype]; i++) iaux->ref_seq[cns->ipos+1+i] = ins[i]; + memcpy(iaux->ref_seq + cns->ipos + 1 + iaux->types[itype], cns->seq + 1 + cns->ipos, cns->nseq - cns->ipos - 1); + } + + // score reads + for (i=0; inplp[ismpl]; i++) + { + const bam_pileup1_t *plp = iaux->plp[ismpl] + i; + int aln_score = iaux_align_read(iaux, plp->b, iaux->ref_seq, ref_len); + int *score = &iaux->read_scores[i*iaux->ntypes+itype]; + if ( cns==iaux->cns_seq || *score > aln_score ) *score = aln_score; + } + cns++; + } + return 0; } -static int iaux_compute_quality(indel_aux_t *iaux) + +// Determines indel quality for each read and populates 22 bits of pileup aux field with +// three integers as follows +// plp->aux = indel_type << 16 | seqQ << 8 | indelQ +static int iaux_eval_scored_reads(indel_aux_t *iaux, int ismpl) { - return -1; + int i,j; + for (i=0; inplp[ismpl]; i++) + { + bam_pileup1_t *plp = iaux->plp[ismpl] + i; + + // Find the best indel type and the ref type, their scores difference is the indel quality + int *score = &iaux->read_scores[i*iaux->ntypes]; + int alt_score = INT_MAX, alt_j = 0; + for (j=0; jiref_type; j++) + if ( alt_score > score[j] ) alt_score = score[j], alt_j = j; + for (j=iaux->iref_type+1; jntypes; j++) + if ( alt_score > score[j] ) alt_score = score[j], alt_j = j; + int ref_score = score[iaux->iref_type]; + int sc0, sc1, j0; + if ( alt_score < ref_score ) sc0 = alt_score, sc1 = ref_score, j0 = alt_j; + else sc0 = ref_score, sc1 = alt_score, j0 = iaux->iref_type; + + int indelQ = (sc1>>8) - (sc0>>8); // low=bad, high=good + int seqQ = iaux->ref_qual[alt_j]; + +#if DEBUG_ALN + fprintf(stderr,"indelQ: %d (ref=%d alt=%d) j0=%d\t%s\n",indelQ,ref_score,alt_score,j0,bam_get_qname(plp->b)); +#endif + + // Reduce indelQ. High length-normalized alignment scores (i.e. bad alignments) + // lower the quality more (e.g. gnuplot> plot [0:111] (1-x/111.)*255) + int adj_score = sc0 & 0xff; + indelQ = adj_score > 111 ? 0 : (int)((1. - adj_score/111.) * indelQ + .499); + + if ( indelQ > seqQ ) indelQ = seqQ; // seqQ already capped at 255 + plp->aux = j0<<16 | seqQ<<8 | indelQ; // use 22 bits in total + iaux->sum_qual[j0] += indelQ; + } + return 0; +} + +// Find the best indel types, include the ref type plus maximum three alternate indel alleles. +static int iaux_eval_best_indels(indel_aux_t *iaux) +{ + bcf_callaux_t *bca = iaux->bca; + bca->maxins = iaux->max_ins_len; + bca->inscns = (char*) realloc(bca->inscns, bca->maxins * 4); + if ( bca->maxins && !bca->inscns ) return -1; + + // insertion sort, descending, high-quality indels come first + int i,j,t, tmp, *sumq = iaux->sum_qual, ntypes = iaux->ntypes; + for (t=0; t0 && sumq[j] > sumq[j-1]; j--) + tmp = sumq[j], sumq[j] = sumq[j-1], sumq[j-1] = tmp; + for (t=0; tiref_type ) break; + if ( t ) + { + // move the reference type to the first + tmp = sumq[t]; + for (; t>0; t--) sumq[t] = sumq[t-1]; + sumq[0] = tmp; + } + + // Initialize bca's structures and create a mapping between old and new types + int old2new_type[MAX_TYPES]; + for (t=0; tntypes; t++) + { + int itype = sumq[t] & 0x3f; + old2new_type[itype] = t; + if ( t>=4 ) continue; + bca->indel_types[t] = iaux->types[itype]; + if ( bca->indel_types[t] <= 0 ) continue; + memcpy(&bca->inscns[t*bca->maxins], &iaux->inscns[itype*iaux->max_ins_len], bca->maxins); + } + + // Update indel type in plp->aux for all reads + int ismpl, n_alt = 0; + for (ismpl=0; ismplnsmpl; ismpl++) + { + for (i=0; inplp[ismpl]; i++) + { + bam_pileup1_t *plp = iaux->plp[ismpl] + i; + int itype_old = (plp->aux >> 16) & 0x3f; + int itype_new = old2new_type[itype_old]; + plp->aux = itype_new<<16 | (itype_new>=4 ? 0 : (plp->aux & 0xffff)); + if ( itype_new>0 ) n_alt++; + } + } + return n_alt; } /* @@ -353,6 +605,7 @@ assert(!(ref == 0 || bca == 0)); // can this ever happen? when? int ntypes = iaux_init_types(iaux); if ( !ntypes ) return -1; + debug_print_types(iaux); // Create two template consensus sequences for each sample (assuming max diploid organism). // Then apply each indel type on top of the templates, realign every read and remember score @@ -360,19 +613,11 @@ assert(!(ref == 0 || bca == 0)); // can this ever happen? when? for (i=0; insmpl; i++) { iaux_set_consensus(iaux, i); + iaux_init_scores(iaux, i); for (j=0; j 0 ? 0 : -1; } -void bcf_iaux_destroy(bcf_callaux_t *bca) -{ - if ( !bca->iaux ) return; - indel_aux_t *iaux = (indel_aux_t*)bca->iaux; - free(iaux->uitmp); - free(iaux->inscns); - rcns_destroy(iaux->rcns); - free(iaux); -} - diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c index 7166a9b9e..faedc3fef 100644 --- a/bam2bcf_indel.c +++ b/bam2bcf_indel.c @@ -84,7 +84,7 @@ static inline int est_seqQ(const bcf_callaux_t *bca, int l, int l_run) return q < qh? q : qh; } -static inline int est_indelreg(int pos, const char *ref, int l, char *ins4) +inline int est_indelreg(int pos, const char *ref, int l, char *ins4) { int i, j, max = 0, max_i = pos, score = 0; l = abs(l); @@ -922,7 +922,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, fprintf(stderr, "pos=%d type=%d read=%d:%d name=%s " "qbeg=%d tbeg=%d score=%d\n", pos, types[t], s, i, bam_get_qname(p->b), - qbeg, tbeg, sc); + qbeg, tbeg, score[K*n_types + t]); #endif } } diff --git a/read_consensus.c b/read_consensus.c index 576feb420..9f2d2221a 100644 --- a/read_consensus.c +++ b/read_consensus.c @@ -28,8 +28,6 @@ #include "cigar_state.h" #include "kheap.h" -// #define DEBUG_RCNS 1 - // Frequency arrays for each variant type #define NI 10 // number of alternative insertion sequences at one position in a single sample @@ -50,7 +48,7 @@ del_freq_t; typedef struct { - int base[5]; // frequencies of A,C,G,T,N + int base[6]; // frequencies of A,C,G,T,N,deletion } base_freq_t; @@ -80,7 +78,8 @@ typedef khp_cvh_t cvar_heap_t; struct _read_cns_t { hts_pos_t pos, beg, end; // current position and window boundaries (0-based, inclusive, ref seq coordinates) - int band; // maximum absolute deviation from the diagonal, used for BAQ alignment + int band, // maximum absolute deviation from the diagonal, used for BAQ alignment + max_del; // maximum deletion lentgth starting at the tested position base_freq_t *base_freq; // frequency of each variant type: base, ins, del ins_freq_t *ins_freq; del_freq_t *del_freq; @@ -93,7 +92,8 @@ struct _read_cns_t bam_pileup1_t *plp; // reads to construct consensus from int nplp; // number of reads in the pileup int cns_hap[2], ncns; // the top two consensus haplotypes and the number of haplotypes to use - cns_seq_t cns[2]; // the consensus sequences to fill + int mcns; // the allocated size of cns.seq and cns.pos buffers + cns_seq_t cns[3]; // the consensus sequences to fill }; void rcns_destroy(read_cns_t *rcns) @@ -105,7 +105,10 @@ void rcns_destroy(read_cns_t *rcns) for (j=0; jnt16_seq[j]; j++) free(ifrq->nt16_seq[j]); } for (i=0; i<2; i++) + { free(rcns->cns[i].seq); + free(rcns->cns[i].pos); + } free(rcns->ins_freq); free(rcns->del_freq); free(rcns->base_freq); @@ -133,13 +136,6 @@ int init_arrays(read_cns_t *rcns) rcns->base_freq = bfrq; memset(bfrq+rcns->mfreq,0,sizeof(*rcns->base_freq)*(n-rcns->mfreq)); - for (i=0; i<2; i++) - { - char *seq = (char*) realloc(rcns->cns[i].seq,sizeof(char)*n); - if ( !seq ) return -1; - rcns->cns[i].seq = seq; - } - rcns->mfreq = n; } memset(rcns->base_freq,0,sizeof(*rcns->base_freq)*n); @@ -154,7 +150,6 @@ int init_arrays(read_cns_t *rcns) } int rcns_reset(read_cns_t *rcns, hts_pos_t pos, hts_pos_t beg, hts_pos_t end) { -fprintf(stderr,"init: pos=%"PRIhts_pos" beg,end=%"PRIhts_pos",%"PRIhts_pos"\n",pos,beg,end); rcns->band = 0; rcns->pos = pos; rcns->beg = beg; @@ -204,8 +199,12 @@ static void add_ins(read_cns_t *rcns, int ref_pos, int seq_pos, uint8_t *raw_seq static void add_del(read_cns_t *rcns, int ref_pos, int len) { int i = ref_pos - rcns->beg; - del_freq_t *dfrq = &rcns->del_freq[i]; + int j,n = rcns->end - rcns->beg + 1; + if ( i + len + 1 < n ) n = i + len + 1; + for (j=i+1; jbase_freq[j].base[5]++; + del_freq_t *dfrq = &rcns->del_freq[i]; for (i=0; ilen[i]; i++) if ( dfrq->len[i]==len ) break; @@ -218,7 +217,6 @@ static void add_del(read_cns_t *rcns, int ref_pos, int len) read_cns_t *rcns_init(hts_pos_t pos, hts_pos_t beg, hts_pos_t end) { -fprintf(stderr,"init: pos=%"PRIhts_pos" beg,end=%"PRIhts_pos",%"PRIhts_pos"\n",pos,beg,end); read_cns_t *rcns = (read_cns_t*) calloc(1,sizeof(read_cns_t)); rcns->pos = pos; rcns->beg = beg; @@ -301,8 +299,8 @@ static void debug_print_base_freqs(read_cns_t *rcns, const char *ref) for (i=0; ibeg+i+1,ref[i]); - for (j=0; j<5; j++) - fprintf(stderr,"\t%d%s",bfreq[i].base[j],ref[i]=="ACGTN"[j]?"*":""); + for (j=0; j<6; j++) + fprintf(stderr,"\t%d%s",bfreq[i].base[j],ref[i]=="ACGTNi"[j]?"*":""); fprintf(stderr,"\t"); for (j=0; jcns[i].nseq ) break; fprintf(stderr,"Consensus%d: ",i); for (j=0; jcns[i].ipos; j++) - fprintf(stderr,"%c",seq_nt16_str[(int)rcns->cns[i].seq[j]]); + fprintf(stderr,"%c","ACGTN"[(int)rcns->cns[i].seq[j]]); fprintf(stderr,"#"); for (; jcns[i].nseq; j++) - fprintf(stderr,"%c",seq_nt16_str[(int)rcns->cns[i].seq[j]]); + fprintf(stderr,"%c","ACGTN"[(int)rcns->cns[i].seq[j]]); fprintf(stderr,"\n"); } } @@ -417,19 +415,23 @@ static void register_variant(read_cns_t *rcns, enum variant_type vtype, int cns_ // Identify candidate variant positions. (Note that homozygous variants are not considered // as those will be added trivially by taking the consensus base.) The detection limit is -// for now hard-wired. This has only indirect effect on sensitivity, it just will not -// contribute to the consensus template for realigning. +// for now hard-wired. This has only indirect effect on sensitivity, will just not contribute +// to the consensus template when realigning. static int select_candidate_variants(read_cns_t *rcns, const char *ref) { //const float af_th = 0.1; const float af_th = 0.05;// just for debugging int i,j, n = rcns->end - rcns->beg + 1; + int max_ins_len = 0; // maximum total length of all insertions applied to allocate big enough buffers base_freq_t *bfreq = rcns->base_freq; ins_freq_t *ifreq = rcns->ins_freq; del_freq_t *dfreq = rcns->del_freq; for (i=0; ipos - rcns->beg ) continue; // creating consensus from everything but the variants at the current position + int dp = 0; for (j=0; j<4; j++) dp += bfreq[i].base[j]; for (j=0; jmcns < n + max_ins_len ) + { + n += max_ins_len; + for (i=0; i<2; i++) + { + char *seq = (char*) realloc(rcns->cns[i].seq,sizeof(char)*n); + if ( !seq ) return -1; + rcns->cns[i].seq = seq; + + hts_pos_t *pos = (hts_pos_t*) realloc(rcns->cns[i].pos,sizeof(hts_pos_t)*n); + if ( !pos ) return -1; + rcns->cns[i].pos = pos; + } + rcns->mcns = n; + } + + // Find the longest deletion at the query position + i = rcns->pos - rcns->beg; + rcns->max_del = 0; + for (j=0; jmax_del < -dfreq[i].len[j] ) rcns->max_del = -dfreq[i].len[j]; + } + return 0; } static int create_haplotype_frequency_spectrum(read_cns_t *rcns) @@ -571,7 +599,7 @@ static int correct_haplotype_errors(read_cns_t *rcns) // Use only one consensus if the next best haplotype is populated by less than 10% of reads rcns->ncns = (freq[1].count / (freq[0].count + freq[1].count) < 0.1) ? 1 : 2; -rcns->ncns = 2; +if (freq[1].count) rcns->ncns = 2; return 0; } @@ -580,6 +608,9 @@ void create_consensus(read_cns_t *rcns, const char *ref, int ith) { int n = rcns->end - rcns->beg + 1; cns_seq_t *cns = &rcns->cns[ith]; + base_freq_t *bfreq = rcns->base_freq; + ins_freq_t *ifreq = rcns->ins_freq; + del_freq_t *dfreq = rcns->del_freq; int j,k, ivar = 0; for (j=0; jncvar && rcns->cvar[ivar].pos < ref_pos ) ivar++; - if ( ivar >= rcns->ncvar || rcns->cvar[ivar].pos != ref_pos || !(rcns->cns_hap[ith] & (1U<= rcns->ncvar || rcns->cvar[ivar].pos != ref_pos ) { - // the haplotype does not have a variant at this position - cns->seq[cns->nseq++] = seq_nt16_table[(int)ref[ref_pos]]; + // This position is not recognised as a het variant so take the most frequent base, including + // a deletion if that is most frequent. However, for deleted bases make sure they are not part + // of the deletion that is being tested at this positions + int max_freq = 0, kmax = seq_nt16_int[seq_nt16_table[(int)ref[ref_pos]]]; + int nk = ( ref_pos < rcns->pos || ref_pos > rcns->pos + rcns->max_del ) ? 6 : 5; + for (k=0; kpos[cns->nseq] = ref_pos; + cns->seq[cns->nseq++] = kmax; + } + if ( rcns->pos == ref_pos ) continue; // do not apply insertions that are being tested + + // Also check how frequent are insertions adjacent to this position. Note that reads with + // an insertion usually increment also bfreq counts at this position, but not necessarily so, + // therefore the counts are approximate + int nreads = 0; + for (k=0; k<5; k++) nreads += bfreq[j].base[k]; + max_freq = 0, kmax = 0; + for (k=0; k max_freq*2 ) continue; // the most frequent insertion is less than half of the reads + + int len = ifreq[j].len[kmax]; + char *seq = ifreq[j].nt16_seq[kmax]; + for (k=0; kpos[cns->nseq] = ref_pos; + cns->seq[cns->nseq++] = seq_nt16_int[(int)seq[k]]; + } + continue; + } + if ( !(rcns->cns_hap[ith] & (1U<cvar[ivar].vtype==snv && rcns->cvar[ivar].which==k ) continue; + if ( max_freq < bfreq[j].base[k] ) max_freq = bfreq[j].base[k], kmax = k; + } + if ( kmax!=5 && (!cns->nseq || cns->pos[cns->nseq-1] != ref_pos) ) + { + cns->pos[cns->nseq] = ref_pos; + cns->seq[cns->nseq++] = kmax; + } continue; } int which = rcns->cvar[ivar].which; if ( rcns->cvar[ivar].vtype == snv ) { - cns->seq[cns->nseq++] = 1<pos[cns->nseq] = ref_pos; + cns->seq[cns->nseq++] = which; continue; } - if ( rcns->cvar[ivar].vtype == ins ) + + // There be multiple variants at this position, for example snv+ins. SNVs come first + // thanks to cvar_pos_cmp(), make sure the base has not been added already. + if ( !cns->nseq || cns->pos[cns->nseq-1] != ref_pos ) { - cns->seq[cns->nseq++] = ref[ref_pos]; - int len = rcns->ins_freq[j].len[which]; - char *seq = rcns->ins_freq[j].nt16_seq[which]; - for (k=0; kseq[cns->nseq++] = seq[k]; + int max_freq = 0, kmax = seq_nt16_int[seq_nt16_table[(int)ref[ref_pos]]]; + for (k=0; k<6; k++) + { + if ( rcns->cvar[ivar].vtype==snv && rcns->cvar[ivar].which==k ) continue; + if ( max_freq < bfreq[j].base[k] ) max_freq = bfreq[j].base[k], kmax = k; + } + if ( kmax!=5 ) + { + cns->pos[cns->nseq] = ref_pos; + cns->seq[cns->nseq++] = kmax; + } } - if ( rcns->cvar[ivar].vtype == del ) + if ( rcns->cvar[ivar].vtype == ins ) { - cns->seq[cns->nseq++] = ref[ref_pos]; - j += rcns->del_freq[j].len[which]; - continue; + int len = ifreq[j].len[which]; + char *seq = ifreq[j].nt16_seq[which]; + for (k=0; kpos[cns->nseq] = ref_pos; + cns->seq[cns->nseq++] = seq_nt16_int[(int)seq[k]]; + } } + else if ( rcns->cvar[ivar].vtype == del ) j += dfreq[j].len[which]; } } diff --git a/read_consensus.h b/read_consensus.h index 91fcc1586..f90e518f0 100644 --- a/read_consensus.h +++ b/read_consensus.h @@ -29,10 +29,15 @@ #include #include +#ifndef DEBUG_RCNS +#define DEBUG_RCNS 0 +#endif + typedef struct { - char *seq; // nt16 sequence + char *seq; // nt5 sequence: "ACGTN"[(int)seq[i]] int nseq, ipos; // the sequence length and the `pos` index relative to seq + hts_pos_t *pos; // corresponding refseq coordinates, inserted bases appear as a block of equal positions } cns_seq_t; From cef69be8aa00ccd341d347aa3c30bf8882502a16 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Thu, 18 Aug 2022 15:14:51 +0100 Subject: [PATCH 08/84] Long reads with --indels-2.0 It is now possible to call from long reads. To do: consider allowing smaller than 2*110bp window for trimming ref and qry sequences in realignment. Currently it is possible to increase --indel-size but it is not possible to decrease it --- bam2bcf_iaux.c | 116 ++++++++++++++++++++++++--------- cigar_state.h | 88 ++++++++++++++++++++++--- read_consensus.c | 164 ++++++++++++++++++++++++++++++++--------------- 3 files changed, 276 insertions(+), 92 deletions(-) diff --git a/bam2bcf_iaux.c b/bam2bcf_iaux.c index 6013bdcfa..3bf0fa265 100644 --- a/bam2bcf_iaux.c +++ b/bam2bcf_iaux.c @@ -30,8 +30,10 @@ #include #include #include +#include "bcftools.h" #include "bam2bcf.h" #include "read_consensus.h" +#include "cigar_state.h" #include KSORT_INIT_STATIC_GENERIC(uint32_t) @@ -54,11 +56,12 @@ typedef struct int muitmp, minscns; // size of uitmp, inscns int iref_type, ntypes, types[MAX_TYPES]; // indel types int max_ins_len; // largest insertion - int left, right; // consensus sequence boundaries + int left, right; // consensus sequence boundaries, 0-based fa ref coordinates read_cns_t *rcns; // read consensus cns_seq_t *cns_seq; // array of consensus sequences int *cns_pos; // array of relative pos indexes within cns_seq sequences uint8_t *ref_seq, *qry_seq; // reference and query sequence to align + hts_pos_t *pos_seq; // ref_seq consensus template positions in reference sequence (see also cns_seq_t.pos) int nref_seq, nqry_seq; // the allocated size of ref_seq and qry_seq uint8_t *qual; int nqual; @@ -73,12 +76,13 @@ indel_aux_t; static void debug_print_types(indel_aux_t *iaux) { int i,j; - fprintf(stderr,"types at %s:%d ... ",iaux->chr,iaux->pos+1); + fprintf(stderr,"types at %s:%d n=%d... ",iaux->chr,iaux->pos+1,iaux->ntypes); for (i=0; intypes; i++) { if ( iaux->types[i]<=0 ) { if ( i==iaux->iref_type ) fprintf(stderr," ref=%d",iaux->types[i]); + else fprintf(stderr," %d",iaux->types[i]); continue; } fprintf(stderr," "); @@ -99,6 +103,7 @@ void bcf_iaux_destroy(bcf_callaux_t *bca) free(iaux->inscns); free(iaux->ref_seq); free(iaux->qry_seq); + free(iaux->pos_seq); free(iaux->qual); free(iaux->read_scores); rcns_destroy(iaux->rcns); @@ -381,58 +386,86 @@ static int iaux_set_consensus(indel_aux_t *iaux, int ismpl) return 0; } -static int iaux_align_read(indel_aux_t *iaux, bam1_t *bam, uint8_t *ref, int nref) +// Finds the smallest index in the seq_pos array holding value equal to pos, or if there is no +// such value, the largest index with value smaller than pos. Starts at initial guess ioff. +// This could use a binary search but the assumption is that the initial guess is indel-size close +// to the actuall coordinate. +static int find_ref_offset(hts_pos_t pos, hts_pos_t *seq_pos, int nseq_pos, int ioff) +{ + if ( ioff<0 ) ioff = 0; + else if ( ioff >= nseq_pos ) ioff = nseq_pos - 1; + if ( seq_pos[ioff] < pos ) + { + while ( ioff+1 < nseq_pos && seq_pos[ioff] < pos ) ioff++; + if ( seq_pos[ioff] > pos ) ioff--; + return ioff; + } + while ( ioff > 0 && seq_pos[ioff-1] >= pos ) ioff--; + return ioff; +} + +static int iaux_align_read(indel_aux_t *iaux, bam1_t *bam, uint8_t *ref_seq, hts_pos_t *pos_seq, int nref_seq) { if ( bam->core.flag & BAM_FUNMAP ) return 1; // skip unmapped reads -// BAM_CREF_SKIP check: save in plp aux data? -// uint32_t *cigar = bam_get_cigar(bam); + // Trim both ref and qry to the window of interest + hts_pos_t ref_beg = iaux->left; + hts_pos_t ref_end = iaux->right; + cigar_state_t cigar; + cstate_init(&cigar,bam); + int qry_off1 = cstate_seek_fwd(&cigar, &ref_beg, 1); // trim qry from left + int qry_off2 = cstate_seek_fwd(&cigar, &ref_end, 0); // trim qry from right + assert( qry_off1>=0 && qry_off2>=0 ); + + int ref_off1 = find_ref_offset(ref_beg, pos_seq, nref_seq, ref_beg - iaux->left); // trim ref from left + int ref_off2 = find_ref_offset(ref_end, pos_seq, nref_seq, ref_end - iaux->left); // trim ref from right // prepare query sequence - int i, qbeg = 0, qend = bam->core.l_qseq; - if ( iaux->nqry_seq < qend - qbeg ) + int i, qlen = qry_off2 - qry_off1 + 1, rlen = ref_off2 - ref_off1 + 1; + if ( iaux->nqry_seq < qlen ) { - uint8_t *tmp = (uint8_t*) calloc(qend - qbeg, 1); + uint8_t *tmp = (uint8_t*) realloc(iaux->qry_seq, qlen); if ( !tmp ) return -1; // critical error iaux->qry_seq = tmp; - iaux->nqry_seq = qend - qbeg; + iaux->nqry_seq = qlen; } uint8_t *seq = bam_get_seq(bam); - for (i=qbeg; iqry_seq[i-qbeg] = seq_nt16_int[bam_seqi(seq,i)]; + for (i=qry_off1; i<=qry_off2; i++) iaux->qry_seq[i-qry_off1] = seq_nt16_int[bam_seqi(seq,i)]; // prepare qualities, either BQ or BAQ qualities (ZQ) - if ( iaux->nqual < qend - qbeg ) + if ( iaux->nqual < qlen ) { - uint8_t *tmp = (uint8_t*) calloc(qend - qbeg, 1); + uint8_t *tmp = (uint8_t*) realloc(iaux->qual, qlen); if ( !tmp ) return -1; // critical error iaux->qual = tmp; - iaux->nqual = qend - qbeg; + iaux->nqual = qlen; } uint8_t *qual = iaux->qual; const uint8_t *qq = bam_get_qual(bam); const uint8_t *bq = (uint8_t*)bam_aux_get(bam, "ZQ"); if ( bq ) bq++; // skip type - for (i=qbeg; i 30 ) qual[i-qbeg] = 30; - if ( qual[i-qbeg] < 7 ) qual[i-qbeg] = 7; + int j = i - qry_off1; + qual[j] = bq ? qq[i] + (bq[i] - 64) : qq[i]; + if ( qual[j] > 30 ) qual[j] = 30; + if ( qual[j] < 7 ) qual[j] = 7; } // Illumina probaln_par_t apf = { 1e-4, 1e-2, 10 }; // align - int score = probaln_glocal(ref, nref, iaux->qry_seq, qend - qbeg, qual, &apf, 0, 0); - int adj_score = (int)(100. * score / (qend - qbeg) + .499) * iaux->bca->indel_bias; + int score = probaln_glocal(ref_seq + ref_off1, rlen, iaux->qry_seq, qlen, qual, &apf, 0, 0); + int adj_score = (int)(100. * score / qlen + .499) * iaux->bca->indel_bias; #if DEBUG_ALN fprintf(stderr,"aln: %d/%d\t%s\n\tref: ",score,adj_score,bam_get_qname(bam)); - for (i=0; iqry_seq[i]]); + for (i=0; iqry_seq[i]]); fprintf(stderr,"\n\tqual: "); - for (i=0; icns_seq; while ( cns->nseq ) { - // resize buffers if necessary + // Resize buffers if necessary int ref_len = cns->nseq + iaux->types[itype]; if ( iaux->nref_seq < ref_len ) { - uint8_t *buf = (uint8_t*) realloc(iaux->ref_seq,sizeof(uint8_t)*ref_len); - if ( !buf ) return -1; - iaux->ref_seq = buf; + uint8_t *ref_buf = (uint8_t*) realloc(iaux->ref_seq,sizeof(uint8_t)*ref_len); + if ( !ref_buf ) return -1; + iaux->ref_seq = ref_buf; + hts_pos_t *pos_buf = (hts_pos_t*) realloc(iaux->pos_seq,sizeof(hts_pos_t)*ref_len); + if ( !pos_buf ) return -1; + iaux->pos_seq = pos_buf; iaux->nref_seq = ref_len; } - // apply the indel - memcpy(iaux->ref_seq,cns->seq,cns->ipos+1); + // Apply the indel and create the template ref sequence... + memcpy(iaux->ref_seq,cns->seq,(cns->ipos+1)*sizeof(*iaux->ref_seq)); if ( iaux->types[itype] < 0 ) // deletion - memcpy(iaux->ref_seq + cns->ipos + 1, cns->seq + cns->ipos + 1 - iaux->types[itype], cns->nseq - cns->ipos - 1 + iaux->types[itype]); + memcpy(iaux->ref_seq + cns->ipos + 1, cns->seq + cns->ipos + 1 - iaux->types[itype], (cns->nseq - cns->ipos - 1 + iaux->types[itype])*sizeof(*iaux->ref_seq)); else { char *ins = &iaux->inscns[itype*iaux->max_ins_len]; for (i=0; itypes[itype]; i++) iaux->ref_seq[cns->ipos+1+i] = ins[i]; - memcpy(iaux->ref_seq + cns->ipos + 1 + iaux->types[itype], cns->seq + 1 + cns->ipos, cns->nseq - cns->ipos - 1); + memcpy(iaux->ref_seq + cns->ipos + 1 + iaux->types[itype], cns->seq + 1 + cns->ipos, (cns->nseq - cns->ipos - 1)*sizeof(*iaux->ref_seq)); } - // score reads + // ...and corresponding ref positions + memcpy(iaux->pos_seq,cns->pos,(cns->ipos+1)*sizeof(*iaux->pos_seq)); + if ( iaux->types[itype] < 0 ) // deletion + memcpy(iaux->pos_seq + cns->ipos + 1, cns->pos + cns->ipos + 1 - iaux->types[itype], (cns->nseq - cns->ipos - 1 + iaux->types[itype])*sizeof(*iaux->pos_seq)); + else + { + for (i=0; itypes[itype]; i++) iaux->pos_seq[cns->ipos+1+i] = cns->pos[cns->ipos]; + memcpy(iaux->pos_seq + cns->ipos + 1 + iaux->types[itype], cns->pos + 1 + cns->ipos, (cns->nseq - cns->ipos - 1)*sizeof(*iaux->pos_seq)); + } + +#if DEBUG_ALN + fprintf(stderr,"template %d, type %d, sample %d: ",cns==iaux->cns_seq?0:1,itype,ismpl); + for (i=0; iref_seq[i]]); + fprintf(stderr,"\n"); +#endif + + // Align and score reads for (i=0; inplp[ismpl]; i++) { const bam_pileup1_t *plp = iaux->plp[ismpl] + i; - int aln_score = iaux_align_read(iaux, plp->b, iaux->ref_seq, ref_len); + int aln_score = iaux_align_read(iaux, plp->b, iaux->ref_seq, iaux->pos_seq, ref_len); int *score = &iaux->read_scores[i*iaux->ntypes+itype]; if ( cns==iaux->cns_seq || *score > aln_score ) *score = aln_score; } diff --git a/cigar_state.h b/cigar_state.h index f29adadb4..c4763b255 100644 --- a/cigar_state.h +++ b/cigar_state.h @@ -36,8 +36,9 @@ typedef struct uint8_t *seq; int ncig; int icig; // position in the cigar string - int iseq; // the cigar[icigar] operation refers to seq[iseq+1] - hts_pos_t ref_pos; // reference coordinate, corresponds to iseq + int iseq; // the cigar[icigar] operation refers to &seq[iseq] + hts_pos_t ref_pos; // reference coordinate, corresponds to iseq; points to + // the first base after the read when consumed } cigar_state_t; @@ -55,14 +56,81 @@ inline void cstate_init(cigar_state_t *cs, bam1_t *bam) if ( op==BAM_CINS || op==BAM_CSOFT_CLIP ) cs->ref_pos -= len; } -// Move in the cigar forward to find query index that matches the -// seek operator and the reference position. -// -// Returns the index to the query sequence cs->seq -// on success; -1 when there is no such matching position but the cigar -// is still not entirely consumed (e.g. a deletion or a soft-clip); -2 -// when there is no overlap (i.e. the read ends before the position). -inline int cstate_seek_fwd(cigar_state_t *cs, hts_pos_t pos, int seek_op, int *oplen) +/** + * cstate_seek_fwd() - Move in the cigar forward to find query index that + * matches the reference position. + * + * When the position is not contained within the sequence, either because there + * is a deletion or there is no overlap, the behavior is controlled by the value + * of trim_left: + * - read starts after: qry_beg > pos && trim_left=1 .. returns 0 and sets pos to qry_beg + * - read starts after: qry_beg > pos && trim_left=0 .. returns -1 + * - read ends before: qry_end < pos && trim_left=1 .. returns -2 + * - read ends before: qry_end < pos && trim_left=0 .. returns qry_len-1 and sets pos to qry_end + * - pos inside a deletion && trim_left=1 .. returns position after the deletion + * - pos inside a deletion && trim_left=0 .. returns position before the deletion + */ +inline int cstate_seek_fwd(cigar_state_t *cs, hts_pos_t *pos_ptr, int trim_left) +{ + hts_pos_t pos = *pos_ptr; + while ( cs->ref_pos <= pos ) + { + if ( cs->icig >= cs->ncig ) // the read ends before pos + { + if ( trim_left ) return -2; + *pos_ptr = cs->ref_pos - 1; + return cs->iseq - 1; + } + + int op = cs->cigar[cs->icig] & BAM_CIGAR_MASK; + int len = cs->cigar[cs->icig] >> BAM_CIGAR_SHIFT; + if ( op==BAM_CMATCH || op==BAM_CEQUAL || op==BAM_CDIFF ) + { + if ( cs->ref_pos + len > pos ) return pos - cs->ref_pos + cs->iseq; // the cigar op overlaps pos + cs->ref_pos += len; + cs->iseq += len; + cs->icig++; + continue; + } + if ( op==BAM_CINS || op==BAM_CSOFT_CLIP ) + { + cs->iseq += len; + cs->icig++; + continue; + } + if ( op==BAM_CDEL || op==BAM_CREF_SKIP ) + { + if ( cs->ref_pos + len > pos ) + { + // The deletion overlaps the position. NB: assuming del is never the first or last op + *pos_ptr = trim_left ? cs->ref_pos + len : cs->ref_pos - 1; + return trim_left ? cs->iseq : cs->iseq - 1; + } + cs->ref_pos += len; + cs->icig++; + continue; + } + } + // the read starts after pos + if ( trim_left ) + { + *pos_ptr = cs->bam->core.pos; + return 0; + } + return -1; +} + + +/** + * cstate_seek_op_fwd() - Move in the cigar forward to find query index that + * matches the seek operator and the reference position. + * + * Returns the index to the query sequence cs->seq + * on success; -1 when there is no such matching position but the cigar + * is still not entirely consumed (e.g. a deletion or a soft-clip); -2 + * when there is no overlap (i.e. the read ends before the position). + */ +inline int cstate_seek_op_fwd(cigar_state_t *cs, hts_pos_t pos, int seek_op, int *oplen) { while ( cs->ref_pos <= pos ) { diff --git a/read_consensus.c b/read_consensus.c index 9f2d2221a..0197d4ed8 100644 --- a/read_consensus.c +++ b/read_consensus.c @@ -24,6 +24,7 @@ #include #include +#include "bcftools.h" #include "read_consensus.h" #include "cigar_state.h" #include "kheap.h" @@ -116,9 +117,10 @@ void rcns_destroy(read_cns_t *rcns) khp_destroy(cvh,rcns->cv_heap); free(rcns); } -int init_arrays(read_cns_t *rcns) +static int init_arrays(read_cns_t *rcns) { int i,j,n = rcns->end - rcns->beg + 1; +fprintf(stderr,"arrays: %d-%d n=%d\n",(int)rcns->beg+1,(int)rcns->end+1,n); if ( n > rcns->mfreq ) { ins_freq_t *ifrq = (ins_freq_t*) realloc(rcns->ins_freq,sizeof(*rcns->ins_freq)*n); @@ -164,11 +166,13 @@ int rcns_reset(read_cns_t *rcns, hts_pos_t pos, hts_pos_t beg, hts_pos_t end) static inline void add_base(read_cns_t *rcns, int ref_pos, int nt16) { int i = ref_pos - rcns->beg; +assert(i>=0); rcns->base_freq[i].base[seq_nt16_int[nt16]]++; } static void add_ins(read_cns_t *rcns, int ref_pos, int seq_pos, uint8_t *raw_seq, int len) { int i = ref_pos - rcns->beg; +assert(i>=0); ins_freq_t *ifrq = &rcns->ins_freq[i]; char *str; if ( rcns->mstmp < len ) @@ -199,6 +203,7 @@ static void add_ins(read_cns_t *rcns, int ref_pos, int seq_pos, uint8_t *raw_seq static void add_del(read_cns_t *rcns, int ref_pos, int len) { int i = ref_pos - rcns->beg; +assert(i>=0); int j,n = rcns->end - rcns->beg + 1; if ( i + len + 1 < n ) n = i + len + 1; for (j=i+1; jplp = plp; rcns->nplp = nplp; +fprintf(stderr,"rcns_beg1,end1,pos1=%d %d %d\n\n",(int)rcns->beg+1,(int)rcns->end+1,(int)rcns->pos+1); + // fill consensus arrays int i,j,k, local_band_max = 0; // maximum absolute deviation from diagonal for (i=0; iend < x + len - 1 ? rcns->end - x : len - 1; - int j_beg = rcns->beg > x ? rcns->beg - x : 0; - x += j_beg; // ref pos - y += j_beg; // seq pos - for (j=j_beg; j<=j_end; j++, x++, y++) add_base(rcns,x,bam_seqi(seq,y)); + if ( xend && x+len>rcns->beg ) + { + int j_beg = rcns->beg > x ? rcns->beg - x : 0; // how many bases to skip in the ref and qry + int j_end = rcns->end < x + len - 1 ? rcns->end - x : len - 1; + x += j_beg; + y += j_beg; + for (j=j_beg; j<=j_end; j++, x++, y++) add_base(rcns,x,bam_seqi(seq,y)); + } + else + { + x += len; + y += len; + } } else if ( op==BAM_CINS ) { - if ( x>=rcns->beg && xend ) + if ( x>rcns->beg && xend ) { local_band += p->indel; add_ins(rcns,x-1,y,seq,len); // x-1: one base before as in VCF - y += len; } + y += len; } else if ( op==BAM_CDEL ) { - if ( x>=rcns->beg && x+len-1<=rcns->end ) + if ( x>rcns->beg && x+len-1<=rcns->end ) { local_band += -p->indel; add_del(rcns,x-1,len); // x-1: one base before as in VCF - x += len; } + x += len; } + else error("rcns_set_reads todo: unknown cigar operator %d\n",op); if ( local_band_max < local_band ) local_band_max = local_band; } @@ -293,6 +309,7 @@ int rcns_set_reads(read_cns_t *rcns, bam_pileup1_t *plp, int nplp) static void debug_print_base_freqs(read_cns_t *rcns, const char *ref) { int i,j,k,n = rcns->end - rcns->beg + 1; + fprintf(stderr,"beg,end,pos=%d %d %d\n",(int)rcns->beg,(int)rcns->end,(int)rcns->pos); base_freq_t *bfreq = rcns->base_freq; ins_freq_t *ifreq = rcns->ins_freq; del_freq_t *dfreq = rcns->del_freq; @@ -351,6 +368,9 @@ static void debug_print_consensus(read_cns_t *rcns) for (; jcns[i].nseq; j++) fprintf(stderr,"%c","ACGTN"[(int)rcns->cns[i].seq[j]]); fprintf(stderr,"\n"); + for (j=0; jcns[i].nseq; j++) + fprintf(stderr," %d",(int)rcns->cns[i].pos[j]); + fprintf(stderr,"\n"); } } #else @@ -478,7 +498,7 @@ const float af_th = 0.05;// just for debugging rcns->max_del = 0; for (j=0; jmax_del < -dfreq[i].len[j] ) rcns->max_del = -dfreq[i].len[j]; + if ( rcns->max_del < dfreq[i].len[j] ) rcns->max_del = dfreq[i].len[j]; } return 0; @@ -500,7 +520,7 @@ static int create_haplotype_frequency_spectrum(read_cns_t *rcns) candidate_var_t *cvar = &rcns->cvar[j]; if ( cvar->vtype==snv ) { - int iseq = cstate_seek_fwd(&cigar, cvar->pos, BAM_CMATCH, NULL); + int iseq = cstate_seek_op_fwd(&cigar, cvar->pos, BAM_CMATCH, NULL); if ( iseq==-2 ) break; if ( iseq==-1 ) continue; int nt16 = bam_seqi(cigar.seq, iseq); @@ -510,7 +530,7 @@ static int create_haplotype_frequency_spectrum(read_cns_t *rcns) { int len; ins_freq_t *ifrq = &rcns->ins_freq[cvar->pos - rcns->beg]; - int iseq = cstate_seek_fwd(&cigar, cvar->pos, BAM_CINS, &len); + int iseq = cstate_seek_op_fwd(&cigar, cvar->pos, BAM_CINS, &len); if ( iseq==-2 ) break; if ( iseq==-1 ) continue; if ( len!=ifrq->len[cvar->which] ) continue; @@ -522,7 +542,7 @@ static int create_haplotype_frequency_spectrum(read_cns_t *rcns) { int len; del_freq_t *dfrq = &rcns->del_freq[cvar->pos - rcns->beg]; - int ret = cstate_seek_fwd(&cigar, cvar->pos, BAM_CDEL, &len); + int ret = cstate_seek_op_fwd(&cigar, cvar->pos, BAM_CDEL, &len); if ( ret==-2 ) break; if ( ret==-1 ) continue; if ( len!=dfrq->len[cvar->which] ) continue; @@ -536,7 +556,7 @@ static int create_haplotype_frequency_spectrum(read_cns_t *rcns) typedef struct { - int idx, count; + int haplotype, count; } ii_t; @@ -547,20 +567,22 @@ static int ii_cmp(const void *a, const void *b) return 0; } +// Select two most common haplotypes trying to account for 1bp errors. Haplotypes +// are represented as 8-bit numbers, each bit corresponds to one candidate variant. static int correct_haplotype_errors(read_cns_t *rcns) { int i,j, tot = 0; ii_t freq[NHAP]; for (i=0; ihap_freq[i]; tot += rcns->hap_freq[i]; } - qsort(freq, NHAP, sizeof(ii_t), ii_cmp); + qsort(freq, NHAP, sizeof(ii_t), ii_cmp); // sort haplotypes in descending order for (i=NHAP-1; i>=0; i--) { - //if ( freq[1].count > tot - freq[0].count ) break; // the top2 hapotypes cannot change anymore +//if ( freq[1].count > tot - freq[0].count ) break; // the top2 hapotypes cannot change anymore if ( !freq[i].count ) continue; // Find a similar haplotype with the highest frequency. Assuming errors go in 0->1 @@ -568,8 +590,8 @@ static int correct_haplotype_errors(read_cns_t *rcns) int count = freq[i].count, max_hap = 0; for (j=0; j=0 && haphap_freq[hap] ) count = rcns->hap_freq[hap], max_hap = hap; } @@ -578,7 +600,7 @@ static int correct_haplotype_errors(read_cns_t *rcns) // Update frequency and sort the two modified elements count = freq[i].count; freq[i].count = 0; - rcns->hap_freq[freq[i].idx] = 0; + rcns->hap_freq[freq[i].haplotype] = 0; rcns->hap_freq[max_hap] += count; for (j=i+1; j=0; j--) { - if ( freq[j].idx==max_hap ) freq[j].count += count; // update the best matching haplotype + if ( freq[j].haplotype==max_hap ) freq[j].count += count; // update the best matching haplotype if ( freq[j].count < freq[j+1].count ) { ii_t tmp = freq[j]; freq[j] = freq[j+1]; freq[j+1] = tmp; } } } - rcns->cns_hap[0] = freq[0].idx; - rcns->cns_hap[1] = freq[1].idx; // Use only one consensus if the next best haplotype is populated by less than 10% of reads rcns->ncns = (freq[1].count / (freq[0].count + freq[1].count) < 0.1) ? 1 : 2; if (freq[1].count) rcns->ncns = 2; + // Remove unused candidate variants from the top two haplotypes + int hap0 = freq[0].haplotype; + int hap1 = rcns->ncns==2 ? freq[1].haplotype : 0; + rcns->cns_hap[0] = 0; + rcns->cns_hap[1] = 0; + for (i=0,j=0; icvar[j] = rcns->cvar[i]; + if ( hap0 & (1U<cns_hap[0] |= 1U<cns_hap[1] |= 1U<ncvar = j; + +#if DEBUG_RCNS + // This only matters for debugging print + memset(rcns->hap_freq,0,NHAP*sizeof(*rcns->hap_freq)); + rcns->hap_freq[rcns->cns_hap[1]] = freq[1].count; // NB: the order matters when ncns==1 + rcns->hap_freq[rcns->cns_hap[0]] = freq[0].count; +#endif + return 0; } -void create_consensus(read_cns_t *rcns, const char *ref, int ith) + +// Check how frequent are insertions adjacent to the j-th position. Note that reads with an +// insertion usually increment also bfreq counts at this position, but not necessarily so, +// therefore the counts are approximate +static inline void apply_consensus_insertion(read_cns_t *rcns, cns_seq_t *cns, int j, int ivar) +{ + // Only apply consensus insertions that are not being tested by bam2bcf_iaux, i.e. not at the current pos + hts_pos_t ref_pos = rcns->beg + j; + if ( rcns->pos == ref_pos ) return; + + // Only apply when there is no insertion at this position registered as a variant + while ( ivar < rcns->ncvar && rcns->cvar[ivar].pos == ref_pos ) + { + if ( rcns->cvar[ivar].vtype == ins ) return; + ivar++; + } + + base_freq_t *bfreq = rcns->base_freq; + ins_freq_t *ifreq = rcns->ins_freq; + int k, nreads = 0; + for (k=0; k<5; k++) nreads += bfreq[j].base[k]; + int max_freq = 0, kmax = 0; + for (k=0; k max_freq*2 ) return; + + int len = ifreq[j].len[kmax]; + char *seq = ifreq[j].nt16_seq[kmax]; + for (k=0; kpos[cns->nseq] = ref_pos; + cns->seq[cns->nseq++] = seq_nt16_int[(int)seq[k]]; + } +} + +static void create_consensus(read_cns_t *rcns, const char *ref, int ith) { int n = rcns->end - rcns->beg + 1; cns_seq_t *cns = &rcns->cns[ith]; @@ -624,7 +703,7 @@ void create_consensus(read_cns_t *rcns, const char *ref, int ith) // This position is not recognised as a het variant so take the most frequent base, including // a deletion if that is most frequent. However, for deleted bases make sure they are not part // of the deletion that is being tested at this positions - int max_freq = 0, kmax = seq_nt16_int[seq_nt16_table[(int)ref[ref_pos]]]; + int max_freq = 0, kmax = seq_nt16_int[seq_nt16_table[(int)ref[j]]]; int nk = ( ref_pos < rcns->pos || ref_pos > rcns->pos + rcns->max_del ) ? 6 : 5; for (k=0; kpos[cns->nseq] = ref_pos; cns->seq[cns->nseq++] = kmax; } - if ( rcns->pos == ref_pos ) continue; // do not apply insertions that are being tested - - // Also check how frequent are insertions adjacent to this position. Note that reads with - // an insertion usually increment also bfreq counts at this position, but not necessarily so, - // therefore the counts are approximate - int nreads = 0; - for (k=0; k<5; k++) nreads += bfreq[j].base[k]; - max_freq = 0, kmax = 0; - for (k=0; k max_freq*2 ) continue; // the most frequent insertion is less than half of the reads - - int len = ifreq[j].len[kmax]; - char *seq = ifreq[j].nt16_seq[kmax]; - for (k=0; kpos[cns->nseq] = ref_pos; - cns->seq[cns->nseq++] = seq_nt16_int[(int)seq[k]]; - } + // Only apply consensus insertions that are not being tested by bam2bcf_iaux, i.e. not at the current pos + apply_consensus_insertion(rcns, cns, j, ivar); continue; } + int which = rcns->cvar[ivar].which; if ( !(rcns->cns_hap[ith] & (1U<cvar[ivar].vtype==snv && rcns->cvar[ivar].which==k ) continue; @@ -671,21 +733,22 @@ void create_consensus(read_cns_t *rcns, const char *ref, int ith) cns->pos[cns->nseq] = ref_pos; cns->seq[cns->nseq++] = kmax; } + apply_consensus_insertion(rcns, cns, j, ivar); continue; } - int which = rcns->cvar[ivar].which; if ( rcns->cvar[ivar].vtype == snv ) { cns->pos[cns->nseq] = ref_pos; cns->seq[cns->nseq++] = which; + apply_consensus_insertion(rcns, cns, j, ivar); continue; } - // There be multiple variants at this position, for example snv+ins. SNVs come first + // There can be multiple variants at this position, for example snv+ins. SNVs come first // thanks to cvar_pos_cmp(), make sure the base has not been added already. if ( !cns->nseq || cns->pos[cns->nseq-1] != ref_pos ) { - int max_freq = 0, kmax = seq_nt16_int[seq_nt16_table[(int)ref[ref_pos]]]; + int max_freq = 0, kmax = seq_nt16_int[seq_nt16_table[(int)ref[j]]]; for (k=0; k<6; k++) { if ( rcns->cvar[ivar].vtype==snv && rcns->cvar[ivar].which==k ) continue; @@ -731,6 +794,7 @@ cns_seq_t *rcns_get_consensus(read_cns_t *rcns, const char *ref) debug_print_haplotype_frequency_spectrum(rcns); correct_haplotype_errors(rcns); + debug_print_candidate_variants(rcns); debug_print_haplotype_frequency_spectrum(rcns); } else From 311486e486546fb07fdcf466c3edc5179f60be25 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Wed, 31 Aug 2022 17:26:46 +0200 Subject: [PATCH 09/84] Fix ref/qry sequence trimming for indel realignment Remove the heuristics introduced by e4e161068 which appears unnecessary and even harmful on documented test cases. --- bam2bcf.c | 28 ++++++++++----- bam2bcf.h | 2 +- bam2bcf_iaux.c | 90 +++++++++++++++++++++++++++++++++++++----------- mpileup.c | 1 + read_consensus.c | 14 ++++---- 5 files changed, 98 insertions(+), 37 deletions(-) diff --git a/bam2bcf.c b/bam2bcf.c index 7aaa51c96..cc7125123 100644 --- a/bam2bcf.c +++ b/bam2bcf.c @@ -275,16 +275,26 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t } continue; } - if (p->indel == 0 && (q < _n/2 || _n > 20)) { - // high quality indel calls without p->indel set aren't - // particularly indicative of being a good REF match either, - // at least not in low coverage. So require solid coverage - // before we start utilising such quals. - b = 0; - q = (int)bam_get_qual(p->b)[p->qpos]; - seqQ = (3*seqQ + 2*q)/8; + if ( !bca->indels_v20 ) + { + /* + This heuristics was introduced by e4e161068 and claims to fix #1446. However, we obtain + correct result on the provided test case even when this code is commented out, so this + may not be needed anymore. Leaving it in only for backward compatibility for now. + See mpileup-tests homdel-issue-1446 and CHM1_CHM13_2.45x-1-1701408 that work only when + this code is disabled. + */ + if (p->indel == 0 && (q < _n/2 || _n > 20)) { + // high quality indel calls without p->indel set aren't + // particularly indicative of being a good REF match either, + // at least not in low coverage. So require solid coverage + // before we start utilising such quals. + b = 0; + q = (int)bam_get_qual(p->b)[p->qpos]; + seqQ = (3*seqQ + 2*q)/8; + } + if (_n > 20 && seqQ > 40) seqQ = 40; } - if (_n > 20 && seqQ > 40) seqQ = 40; baseQ = p->aux>>8&0xff; is_diff = (b != 0); diff --git a/bam2bcf.h b/bam2bcf.h index 53d565758..095f271ab 100644 --- a/bam2bcf.h +++ b/bam2bcf.h @@ -107,7 +107,7 @@ typedef struct __bcf_callaux_t { // for internal uses int max_bases; int indel_types[4]; // indel lengths - int indel_win_size; + int indel_win_size, indels_v20; int maxins, indelreg; int read_len; char *inscns; diff --git a/bam2bcf_iaux.c b/bam2bcf_iaux.c index 3bf0fa265..1f2c35cba 100644 --- a/bam2bcf_iaux.c +++ b/bam2bcf_iaux.c @@ -38,7 +38,9 @@ #include KSORT_INIT_STATIC_GENERIC(uint32_t) +#ifndef DEBUG_ALN #define DEBUG_ALN 0 +#endif #define MAX_TYPES 64 @@ -76,16 +78,16 @@ indel_aux_t; static void debug_print_types(indel_aux_t *iaux) { int i,j; - fprintf(stderr,"types at %s:%d n=%d... ",iaux->chr,iaux->pos+1,iaux->ntypes); + fprintf(stderr,"types at %s:%d ntypes=%d... ",iaux->chr,iaux->pos+1,iaux->ntypes); for (i=0; intypes; i++) { + fprintf(stderr," type%d=",i); if ( iaux->types[i]<=0 ) { - if ( i==iaux->iref_type ) fprintf(stderr," ref=%d",iaux->types[i]); - else fprintf(stderr," %d",iaux->types[i]); + if ( i==iaux->iref_type ) fprintf(stderr,"%d(ref)",iaux->types[i]); + else fprintf(stderr,"%d",iaux->types[i]); continue; } - fprintf(stderr," "); char *cns = &iaux->inscns[i*iaux->max_ins_len]; for (j=0; jtypes[i]; j++) fprintf(stderr,"%c","ACGTN"[(int)cns[j]]); } @@ -390,6 +392,8 @@ static int iaux_set_consensus(indel_aux_t *iaux, int ismpl) // such value, the largest index with value smaller than pos. Starts at initial guess ioff. // This could use a binary search but the assumption is that the initial guess is indel-size close // to the actuall coordinate. +// +// TODO: remove this function and seq_pos from cns creation as it seems unnecessary static int find_ref_offset(hts_pos_t pos, hts_pos_t *seq_pos, int nseq_pos, int ioff) { if ( ioff<0 ) ioff = 0; @@ -409,16 +413,59 @@ static int iaux_align_read(indel_aux_t *iaux, bam1_t *bam, uint8_t *ref_seq, hts if ( bam->core.flag & BAM_FUNMAP ) return 1; // skip unmapped reads // Trim both ref and qry to the window of interest - hts_pos_t ref_beg = iaux->left; - hts_pos_t ref_end = iaux->right; + hts_pos_t ref_beg = iaux->left; // fa ref coordinates + hts_pos_t ref_end = iaux->right < ref_beg + nref_seq ? iaux->right : ref_beg + nref_seq - 1; + cigar_state_t cigar; cstate_init(&cigar,bam); - int qry_off1 = cstate_seek_fwd(&cigar, &ref_beg, 1); // trim qry from left - int qry_off2 = cstate_seek_fwd(&cigar, &ref_end, 0); // trim qry from right - assert( qry_off1>=0 && qry_off2>=0 ); + int qry_off1, qry_off2, ref_off1, ref_off2; + if ( ref_beg > bam->core.pos ) + { + // the read needs trimming from left + qry_off1 = cstate_seek_fwd(&cigar, &ref_beg, 1); + ref_off1 = ref_beg - iaux->left; - int ref_off1 = find_ref_offset(ref_beg, pos_seq, nref_seq, ref_beg - iaux->left); // trim ref from left - int ref_off2 = find_ref_offset(ref_end, pos_seq, nref_seq, ref_end - iaux->left); // trim ref from right + if ( ref_beg + (bam->core.l_qseq - qry_off1) > ref_end ) + { + // the read needs trimming from right + qry_off2 = ref_end - ref_beg + qry_off1; + ref_off2 = ref_end - iaux->left; + } + else + { + // the ref template needs trimming from right + qry_off2 = bam->core.l_qseq - 1; + ref_off2 = ref_off1 + qry_off2 - qry_off1; + } + } + else + { + // the ref template needs trimming from left + qry_off1 = 0; + ref_off1 = bam->core.pos - ref_beg; + + if ( bam->core.pos + bam->core.l_qseq - 1 > ref_end ) + { + // the read needs trimming from right + ref_off2 = ref_end - iaux->left; + qry_off2 = ref_off2 - ref_off1; + } + else + { + // the ref template needs trimming from right + qry_off2 = bam->core.l_qseq - 1; + ref_off2 = ref_off1 + qry_off2 - qry_off1; + } + } +//fprintf(stderr,"xtrim: %s .. left,right=%d,%d rbeg,end=%d,%d qpos=%d qlen=%d qoff=%d,%d roff=%d,%d rlen=%d\n",bam_get_qname(bam),iaux->left,iaux->right,(int)ref_beg,(int)ref_end,(int)bam->core.pos,bam->core.l_qseq, qry_off1,qry_off2,ref_off1,ref_off2,nref_seq); + + assert( qry_off1<=qry_off2 ); + assert( qry_off1>=0 && qry_off1core.l_qseq ); + assert( qry_off2>=0 && qry_off2core.l_qseq ); + + assert( ref_off1<=ref_off2 ); + assert( ref_off1>=0 && ref_off1=0 && ref_off2qry_seq[i]]); fprintf(stderr,"\n\tqual: "); for (i=0; i 255 ) adj_score = 255; @@ -519,6 +566,8 @@ static int iaux_score_reads(indel_aux_t *iaux, int ismpl, int itype) fprintf(stderr,"template %d, type %d, sample %d: ",cns==iaux->cns_seq?0:1,itype,ismpl); for (i=0; iref_seq[i]]); fprintf(stderr,"\n"); + for (i=0; ipos_seq[i-1]+1==iaux->pos_seq[i])?' ':'x',(int)iaux->pos_seq[i]); + fprintf(stderr,"\n"); #endif // Align and score reads @@ -559,18 +608,19 @@ static int iaux_eval_scored_reads(indel_aux_t *iaux, int ismpl) int indelQ = (sc1>>8) - (sc0>>8); // low=bad, high=good int seqQ = iaux->ref_qual[alt_j]; -#if DEBUG_ALN - fprintf(stderr,"indelQ: %d (ref=%d alt=%d) j0=%d\t%s\n",indelQ,ref_score,alt_score,j0,bam_get_qname(plp->b)); -#endif - // Reduce indelQ. High length-normalized alignment scores (i.e. bad alignments) // lower the quality more (e.g. gnuplot> plot [0:111] (1-x/111.)*255) int adj_score = sc0 & 0xff; - indelQ = adj_score > 111 ? 0 : (int)((1. - adj_score/111.) * indelQ + .499); + int adj_indelQ = adj_score > 111 ? 0 : (int)((1. - adj_score/111.) * indelQ + .499); + +#if DEBUG_ALN + fprintf(stderr,"indelQ: %d (raw_indelQ=%d adj_score=%d; ref=%d alt=%d) j0=%d\t%s\n",adj_indelQ,indelQ,adj_score,ref_score,alt_score,j0,bam_get_qname(plp->b)); +#endif + + if ( adj_indelQ > seqQ ) adj_indelQ = seqQ; // seqQ already capped at 255 + plp->aux = j0<<16 | seqQ<<8 | adj_indelQ; // use 22 bits in total + iaux->sum_qual[j0] += adj_indelQ; - if ( indelQ > seqQ ) indelQ = seqQ; // seqQ already capped at 255 - plp->aux = j0<<16 | seqQ<<8 | indelQ; // use 22 bits in total - iaux->sum_qual[j0] += indelQ; } return 0; } diff --git a/mpileup.c b/mpileup.c index 79c0c7a0e..97452b989 100644 --- a/mpileup.c +++ b/mpileup.c @@ -863,6 +863,7 @@ static int mpileup(mplp_conf_t *conf) conf->bca->fmt_flag = conf->fmt_flag; conf->bca->ambig_reads = conf->ambig_reads; conf->bca->indel_win_size = conf->indel_win_size; + conf->bca->indels_v20 = conf->indels_v20; conf->bc.bcf_hdr = conf->bcf_hdr; conf->bc.n = nsmpl; diff --git a/read_consensus.c b/read_consensus.c index 0197d4ed8..87792f21d 100644 --- a/read_consensus.c +++ b/read_consensus.c @@ -120,7 +120,7 @@ void rcns_destroy(read_cns_t *rcns) static int init_arrays(read_cns_t *rcns) { int i,j,n = rcns->end - rcns->beg + 1; -fprintf(stderr,"arrays: %d-%d n=%d\n",(int)rcns->beg+1,(int)rcns->end+1,n); +//fprintf(stderr,"arrays: %d-%d n=%d\n",(int)rcns->beg+1,(int)rcns->end+1,n); if ( n > rcns->mfreq ) { ins_freq_t *ifrq = (ins_freq_t*) realloc(rcns->ins_freq,sizeof(*rcns->ins_freq)*n); @@ -241,7 +241,7 @@ int rcns_set_reads(read_cns_t *rcns, bam_pileup1_t *plp, int nplp) rcns->plp = plp; rcns->nplp = nplp; -fprintf(stderr,"rcns_beg1,end1,pos1=%d %d %d\n\n",(int)rcns->beg+1,(int)rcns->end+1,(int)rcns->pos+1); +//fprintf(stderr,"rcns_beg1,end1,pos1=%d %d %d\n\n",(int)rcns->beg+1,(int)rcns->end+1,(int)rcns->pos+1); // fill consensus arrays int i,j,k, local_band_max = 0; // maximum absolute deviation from diagonal @@ -439,8 +439,8 @@ static void register_variant(read_cns_t *rcns, enum variant_type vtype, int cns_ // to the consensus template when realigning. static int select_candidate_variants(read_cns_t *rcns, const char *ref) { - //const float af_th = 0.1; -const float af_th = 0.05;// just for debugging + const float af_th = 0.1; +//const float af_th = 0.05;// just for debugging int i,j, n = rcns->end - rcns->beg + 1; int max_ins_len = 0; // maximum total length of all insertions applied to allocate big enough buffers base_freq_t *bfreq = rcns->base_freq; @@ -582,8 +582,8 @@ static int correct_haplotype_errors(read_cns_t *rcns) qsort(freq, NHAP, sizeof(ii_t), ii_cmp); // sort haplotypes in descending order for (i=NHAP-1; i>=0; i--) { -//if ( freq[1].count > tot - freq[0].count ) break; // the top2 hapotypes cannot change anymore - if ( !freq[i].count ) continue; + if ( freq[1].count > tot - freq[0].count ) break; // the top2 hapotypes cannot change anymore +//if ( !freq[i].count ) continue; // Find a similar haplotype with the highest frequency. Assuming errors go in 0->1 // direction only and considering one error only. @@ -619,7 +619,7 @@ static int correct_haplotype_errors(read_cns_t *rcns) // Use only one consensus if the next best haplotype is populated by less than 10% of reads rcns->ncns = (freq[1].count / (freq[0].count + freq[1].count) < 0.1) ? 1 : 2; -if (freq[1].count) rcns->ncns = 2; +//if (freq[1].count) rcns->ncns = 2; // Remove unused candidate variants from the top two haplotypes int hap0 = freq[0].haplotype; From 61691ab25c641263c72f7101eb5d8925e1f8283e Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Thu, 1 Sep 2022 10:00:23 +0100 Subject: [PATCH 10/84] Fix a bug, float arithmetics must be used, not int --- read_consensus.c | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/read_consensus.c b/read_consensus.c index 87792f21d..326c6e9bd 100644 --- a/read_consensus.c +++ b/read_consensus.c @@ -583,7 +583,6 @@ static int correct_haplotype_errors(read_cns_t *rcns) for (i=NHAP-1; i>=0; i--) { if ( freq[1].count > tot - freq[0].count ) break; // the top2 hapotypes cannot change anymore -//if ( !freq[i].count ) continue; // Find a similar haplotype with the highest frequency. Assuming errors go in 0->1 // direction only and considering one error only. @@ -618,8 +617,7 @@ static int correct_haplotype_errors(read_cns_t *rcns) } // Use only one consensus if the next best haplotype is populated by less than 10% of reads - rcns->ncns = (freq[1].count / (freq[0].count + freq[1].count) < 0.1) ? 1 : 2; -//if (freq[1].count) rcns->ncns = 2; + rcns->ncns = ((float)freq[1].count / (freq[0].count + freq[1].count) < 0.1) ? 1 : 2; // Remove unused candidate variants from the top two haplotypes int hap0 = freq[0].haplotype; From 4d18e8a8bd86e62d4dc8be7e92bd2d245054f105 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Tue, 24 May 2022 14:39:39 +0100 Subject: [PATCH 11/84] New --strictly-novel option to downplay alleles which violate Mendelian inheritance but are not novel --- plugins/trio-dnm2.c | 50 +++++++++++++++++++++------------ test/test.pl | 2 ++ test/trio-dnm/trio-dnm.11.1.out | 2 ++ test/trio-dnm/trio-dnm.11.2.out | 2 ++ test/trio-dnm/trio-dnm.11.vcf | 11 ++++++++ 5 files changed, 49 insertions(+), 18 deletions(-) create mode 100644 test/trio-dnm/trio-dnm.11.1.out create mode 100644 test/trio-dnm/trio-dnm.11.2.out create mode 100644 test/trio-dnm/trio-dnm.11.vcf diff --git a/plugins/trio-dnm2.c b/plugins/trio-dnm2.c index a23bc01ca..33ccf954c 100644 --- a/plugins/trio-dnm2.c +++ b/plugins/trio-dnm2.c @@ -1,19 +1,19 @@ /* The MIT License - Copyright (c) 2018-2021 Genome Research Ltd. + Copyright (c) 2018-2022 Genome Research Ltd. Author: Petr Danecek - + Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: - + The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. - + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE @@ -117,6 +117,7 @@ typedef struct int with_ppl, with_pad; // --with-pPL or --with-pAD int use_dng_priors; // --dng-priors int need_QS; + int strictly_novel; priors_t priors, priors_X, priors_XX; } args_t; @@ -130,7 +131,7 @@ const char *about(void) static const char *usage_text(void) { - return + return "\n" "About: Screen variants for possible de-novo mutations in trios\n" "Usage: bcftools +trio-dnm2 [OPTIONS]\n" @@ -168,6 +169,7 @@ static const char *usage_text(void) " --mrate NUM Mutation rate [1e-8]\n" " --pn FRAC[,NUM] Tolerance to parental noise or mosaicity, given as fraction of QS or number of reads [0.005,0]\n" " --pns FRAC[,NUM] Same as --pn but is not applied to alleles observed in both parents (fewer FPs, more FNs) [0.045,0]\n" + " -n, --strictly-novel When Mendelian inheritance is violiated, score highly only novel alleles (e.g. in LoH regions)\n" " --use-DNG The original DeNovoGear model, implies --dng-priors\n" " --use-NAIVE A naive calling model which uses only FMT/GT to determine DNMs\n" " --with-pAD Do not use FMT/QS but parental FMT/AD\n" @@ -365,7 +367,7 @@ static double init_mf_priors(args_t *args, int fi, int mi) gt_prior = p_poly / 57.; else if ( nref_mf==4 ) // 0 ALTs; 00,00 gt_prior = p_homref; - else if ( nref_mf==3 ) // this and all remaining have 1 unique ALT allele; 00,0x + else if ( nref_mf==3 ) // this and all remaining have 1 unique ALT allele; 00,0x gt_prior = p_nonref * (4.0/15.0) * (1.0/3.0); else if ( nref_mf==2 && ma==mb ) // hom alt; 00,xx gt_prior = p_nonref * (2.0/15.0) * (1.0/3.0); @@ -466,7 +468,7 @@ static void init_DNG_tprob_mprob(args_t *args, int fi, int mi, int ci, double *t } else { - if ( ca!=fa && ca!=fb && ca!=ma && ca!=mb && + if ( ca!=fa && ca!=fb && ca!=ma && ca!=mb && cb!=fa && cb!=fb && cb!=ma && cb!=mb ) *mprob = args->mrate * args->mrate; // two mutations else *mprob = args->mrate; @@ -502,7 +504,17 @@ static void init_tprob_mprob(args_t *args, int fi, int mi, int ci, double *tprob // tprob .. genotype transmission probability L(GC|GM,GF), 0 if not compatible with Mendelian inheritance // mprob .. probability of mutation - if ( ((ca==fa||ca==fb) && (cb==ma||cb==mb)) || ((ca==ma||ca==mb) && (cb==fa||cb==fb)) ) + int is_novel; + if ( args->strictly_novel ) // account for LoH sites, see chr1:10000057 in trio-dnm.11.vcf + { + is_novel = ( (ca!=fa && ca!=fb && ca!=ma && ca!=mb) || (cb!=fa && cb!=fb && cb!=ma && cb!=mb) ) ? 1 : 0; + } + else + { + is_novel = ( ((ca==fa||ca==fb) && (cb==ma||cb==mb)) || ((ca==ma||ca==mb) && (cb==fa||cb==fb)) ) ? 0 : 1; + } + + if ( !is_novel ) { if ( fa==fb && ma==mb ) *tprob = 1; else if ( fa==fb || ma==mb ) *tprob = 0.5; @@ -590,7 +602,7 @@ static void init_priors(args_t *args, priors_t *priors, init_priors_t type) if ( args->use_dng_priors ) init_DNG_tprob_mprob(args,fi,mi,ci,&tprob,&mprob,&allele); - else if ( type==autosomal ) + else if ( type==autosomal || args->strictly_novel ) init_tprob_mprob(args,fi,mi,ci,&tprob,&mprob,&allele); else if ( type==chrX ) init_tprob_mprob_chrX(args,mi,ci,&tprob,&mprob,&allele); @@ -849,7 +861,7 @@ static double process_trio_ACM(args_t *args, priors_t *priors, int nals, double else if ( fa==fb ) fpl += qs[iFATHER][i]; } - } + } int mi = 0; for (ma=0; madenovo[fi][mi][ci],fi,mi,ci,mpl,fpl,cpl,priors->pprob[fi][mi][ci], val,sum,(priors->denovo[fi][mi][ci] && max < val)?'*':'-'); #endif @@ -927,7 +939,7 @@ static double process_trio_DNG(args_t *args, priors_t *priors, int nals, double val = pl[iCHILD][ci] + pl[iFATHER][fi] + pl[iMOTHER][mi] + priors->pprob[fi][mi][ci]; sum = sum_log(val,sum); #if DEBUG - if(val!=-HUGE_VAL) + if(val!=-HUGE_VAL) fprintf(stderr,"m,f,c: %d%d+%d%d=%d%d dn=%d (%d,%d,%d) mpl,fpl,cpl: %+e %+e %+e \t prior:%+e \t pval=%+e sum=%+e %c\n", mb,ma,fb,fa,cb,ca,priors->denovo[fi][mi][ci],fi,mi,ci,pl[iMOTHER][mi],pl[iFATHER][fi],pl[iCHILD][ci],priors->pprob[fi][mi][ci], val,sum,(priors->denovo[fi][mi][ci] && max < val)?'*':'-'); #endif @@ -1029,7 +1041,7 @@ static void many_alts_trim(args_t *args, int *_nals, double *pl[3], int *_npl, d for (i=2; i1 && arr[idx[j]] < arr[idx[j-1]]; j--) tmp = idx[j], idx[j] = idx[j-1], idx[j-1] = tmp; - + for (i=0; i<3; i++) { for (j=0; j<4; j++) args->alt_tmp[j] = qs[i][args->alt_idx[j]]; @@ -1140,12 +1152,12 @@ static void set_trio_QS_noisy(args_t *args, trio_t *trio, double *pqs[3], int nq double tmp = qs[k]; if ( max_qs < tmp ) max_qs = tmp; } - for (k=0; kntrio; i++) { if ( args->filter && !args->trio[i].pass ) continue; - + int ignore_father = 0; // father is irrelevant for male proband on chrX and can have missing GT priors_t *priors; if ( !is_chrX ) priors = &args->priors; @@ -1541,6 +1553,7 @@ int run(int argc, char **argv) {"with-pad",no_argument,0,13}, {"chrX",required_argument,0,'X'}, {"min-score",required_argument,0,'m'}, + {"strictly-novel",no_argument,0,'n'}, {"include",required_argument,0,'i'}, {"exclude",required_argument,0,'e'}, {"output",required_argument,NULL,'o'}, @@ -1557,9 +1570,9 @@ int run(int argc, char **argv) }; int c; char *tmp; - while ((c = getopt_long(argc, argv, "p:P:o:O:s:i:e:r:R:t:T:m:au:X:",loptions,NULL)) >= 0) + while ((c = getopt_long(argc, argv, "p:P:o:O:s:i:e:r:R:t:T:m:au:X:n",loptions,NULL)) >= 0) { - switch (c) + switch (c) { case 1 : args->force_ad = 1; break; case 2 : free(args->dnm_score_tag); args->dnm_score_tag = strdup(optarg); break; @@ -1636,6 +1649,7 @@ int run(int argc, char **argv) case 'm': args->min_score = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: -M, --min-score %s\n", optarg); break; + case 'n': args->strictly_novel = 1; break; case 'h': case '?': default: error("%s", usage_text()); break; diff --git a/test/test.pl b/test/test.pl index 789579629..57f838e49 100755 --- a/test/test.pl +++ b/test/test.pl @@ -590,6 +590,8 @@ run_test(\&test_vcf_plugin,$opts,in=>'trio-dnm/trio-dnm.9',out=>'trio-dnm/trio-dnm.9.1.out',cmd=>'+trio-dnm2',args=>"-p 1X:proband,father,mother --use-NAIVE | $$opts{bin}/bcftools query -f'[\\t%DNM]\\n'"); run_test(\&test_vcf_plugin,$opts,in=>'trio-dnm/trio-dnm.9',out=>'trio-dnm/trio-dnm.9.2.out',cmd=>'+trio-dnm2',args=>"-p 2X:proband,father,mother --use-NAIVE | $$opts{bin}/bcftools query -f'[\\t%DNM]\\n'"); run_test(\&test_vcf_plugin,$opts,in=>'trio-dnm/trio-dnm.10',out=>'trio-dnm/trio-dnm.10.1.out',cmd=>'+trio-dnm2',args=>"-p proband,father,mother --with-pAD | $$opts{bin}/bcftools query -f'[\\t%DNM][\\t%VAF]\\n'"); +run_test(\&test_vcf_plugin,$opts,in=>'trio-dnm/trio-dnm.11',out=>'trio-dnm/trio-dnm.11.1.out',cmd=>'+trio-dnm2',args=>"-p proband,father,mother | $$opts{bin}/bcftools query -f'[\\t%DNM][\\t%VAF]\\n'"); +run_test(\&test_vcf_plugin,$opts,in=>'trio-dnm/trio-dnm.11',out=>'trio-dnm/trio-dnm.11.2.out',cmd=>'+trio-dnm2',args=>"-p 1X:proband,father,mother --strictly-novel | $$opts{bin}/bcftools query -f'[\\t%DNM][\\t%VAF]\\n'"); run_test(\&test_vcf_plugin,$opts,in=>'gvcfz',out=>'gvcfz.1.out',cmd=>'+gvcfz',args=>qq[-g 'PASS:GT!="alt"' -a | $$opts{bin}/bcftools query -f'%POS\\t%REF\\t%ALT\\t%END[\\t%GT][\\t%DP][\\t%GQ][\\t%RGQ]\\n']); run_test(\&test_vcf_plugin,$opts,in=>'gvcfz',out=>'gvcfz.2.out',cmd=>'+gvcfz',args=>qq[-g 'PASS:GQ>10; FLT:-' -a | $$opts{bin}/bcftools query -f'%POS\\t%REF\\t%ALT\\t%FILTER\\t%END[\\t%GT][\\t%DP][\\t%GQ][\\t%RGQ]\\n']); run_test(\&test_vcf_plugin,$opts,in=>'gvcfz.2',out=>'gvcfz.2.1.out',cmd=>'+gvcfz',args=>qq[-g 'PASS:GT!="alt"' -a | $$opts{bin}/bcftools query -f'%POS\\t%REF\\t%ALT\\t%FILTER\\t%END[\\t%GT][\\t%DP]\\n']); diff --git a/test/trio-dnm/trio-dnm.11.1.out b/test/trio-dnm/trio-dnm.11.1.out new file mode 100644 index 000000000..9a4d3078f --- /dev/null +++ b/test/trio-dnm/trio-dnm.11.1.out @@ -0,0 +1,2 @@ + -0.0953102 . . 100 100 0 + -20.5943 . . 79 56 0 diff --git a/test/trio-dnm/trio-dnm.11.2.out b/test/trio-dnm/trio-dnm.11.2.out new file mode 100644 index 000000000..04abbf9ee --- /dev/null +++ b/test/trio-dnm/trio-dnm.11.2.out @@ -0,0 +1,2 @@ + -inf . . 0 0 100 + -inf . . 79 56 0 diff --git a/test/trio-dnm/trio-dnm.11.vcf b/test/trio-dnm/trio-dnm.11.vcf new file mode 100644 index 000000000..bdaacabba --- /dev/null +++ b/test/trio-dnm/trio-dnm.11.vcf @@ -0,0 +1,11 @@ +##fileformat=VCFv4.2 +##reference=file:///lustre/scratch118/humgen/resources/ref/Homo_sapiens/GRCh38_15/Homo_sapiens.GRCh38_15.fa +##contig= +##contig= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT proband father mother +chr1 10000057 . C T . . . GT:PL:AD:QS 1/1:255,90,0:0,30:0,1116 1/1:255,78,0:0,26:0,921 0/0:0,114,255:38,0:1364,0 +chrX 10000804 . C G . . . GT:PL:AD:QS 0/1:255,0,85:5,19:174,671 0/1:202,0,157:7,9:255,323 0/0:0,30,227:10,0:370,0 From c4afbed9bf075e6a99f5c6eb034593b84b486a59 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Mon, 30 May 2022 15:08:17 +0100 Subject: [PATCH 12/84] Set --pn/--pns separately for SNVs and indels, make the indel default strict (0) --- plugins/trio-dnm2.c | 126 ++++++++++++++++++++++++++++++++------------ 1 file changed, 92 insertions(+), 34 deletions(-) diff --git a/plugins/trio-dnm2.c b/plugins/trio-dnm2.c index 33ccf954c..ee4e13014 100644 --- a/plugins/trio-dnm2.c +++ b/plugins/trio-dnm2.c @@ -82,6 +82,13 @@ typedef struct } priors_t; +typedef struct +{ + double abs, frac; + double abs1, frac1; // applied only if allele observed in a single parent, but not when observed in both +} +pnoise_t; + typedef struct { int argc, filter_logic, regions_is_file, targets_is_file, output_type, record_cmd_line, clevel; @@ -112,8 +119,7 @@ typedef struct *dnm_allele_tag; int dnm_score_type; // given by e.g. --dnm-tag DNM:log double mrate; // --mrate, mutation rate - double pn_abs,pn_frac; // --pn - double pns_abs,pns_frac; // --pns + pnoise_t pn_snv, pn_indel; // --pn and --pns for SNVs and indels int with_ppl, with_pad; // --with-pPL or --with-pAD int use_dng_priors; // --dng-priors int need_QS; @@ -167,8 +173,9 @@ static const char *usage_text(void) "Model options:\n" " --dng-priors Use the original DeNovoGear priors (including bugs in prior assignment, but with chrX bugs fixed)\n" " --mrate NUM Mutation rate [1e-8]\n" - " --pn FRAC[,NUM] Tolerance to parental noise or mosaicity, given as fraction of QS or number of reads [0.005,0]\n" - " --pns FRAC[,NUM] Same as --pn but is not applied to alleles observed in both parents (fewer FPs, more FNs) [0.045,0]\n" + " --pn FRAC[,NUM][:type] Tolerance to parental noise or mosaicity, given as fraction of QS or number of reads. The type is\n" + " 'snv', 'indel' or 'both' [--pn 0.005,0:snv --pn 0,0:indel]\n" + " --pns FRAC[,NUM][:type] Same as --pn but applied for alleles observed in a single parent [--pns 0.045,0:snv --pns 0,0:indel]\n" " -n, --strictly-novel When Mendelian inheritance is violiated, score highly only novel alleles (e.g. in LoH regions)\n" " --use-DNG The original DeNovoGear model, implies --dng-priors\n" " --use-NAIVE A naive calling model which uses only FMT/GT to determine DNMs\n" @@ -1088,11 +1095,11 @@ static void set_trio_QS(args_t *args, trio_t *trio, double *pqs[3], int nqs1) for (k=0; kpn_abs && !args->pns_abs && !args->pns_frac ) n_ad = 0; // AD is not required + if ( n_ad && !pnoise->abs && !pnoise->abs1 && !pnoise->frac1 ) n_ad = 0; // AD is not required if ( n_ad ) { // Noise tolerance will be applied only for alleles observed in a single parent (a possible mosaic @@ -1109,18 +1116,18 @@ static void set_trio_QS_noisy(args_t *args, trio_t *trio, double *pqs[3], int nq pqs[j] = args->qs3 + j*nqs1; double pn = 0, pns = 0; double sum_qs = 0, sum_ad = 0; - if ( (args->pn_frac || args->pns_frac) && j!=iCHILD ) + if ( (pnoise->frac || pnoise->frac1) && j!=iCHILD ) { for (k=0; kpn_frac; - pns = sum_qs * args->pns_frac; + pn = sum_qs * pnoise->frac; + pns = sum_qs * pnoise->frac1; if ( n_ad ) { // "absolute" threshold: find the average QS per read from AD and use that // if bigger than the relative threshold for (k=0; kpn_abs * sum_qs / sum_ad ) pn = args->pn_abs * sum_qs / sum_ad; - if ( pns < args->pns_abs * sum_qs / sum_ad ) pns = args->pns_abs * sum_qs / sum_ad; + if ( pn < pnoise->abs * sum_qs / sum_ad ) pn = pnoise->abs * sum_qs / sum_ad; + if ( pns < pnoise->abs1 * sum_qs / sum_ad ) pns = pnoise->abs1 * sum_qs / sum_ad; } } // Reduce QS for all alleles to account for noise @@ -1359,6 +1366,8 @@ static void process_record(args_t *args, bcf1_t *rec) hts_expand(double,3*nqs1,args->mqs3,args->qs3); } + pnoise_t *pnoise = (bcf_get_variant_types(rec) & VCF_INDEL) ? &args->pn_indel : &args->pn_snv; + int is_chrX = 0; if ( regidx_overlap(args->chrX_idx,bcf_seqname(args->hdr,rec),rec->pos,rec->pos+rec->rlen,NULL) ) is_chrX = 1; @@ -1378,7 +1387,7 @@ static void process_record(args_t *args, bcf1_t *rec) double *pqs[3]; if ( args->use_model==USE_ACM ) - set_trio_QS_noisy(args,&args->trio[i],pqs,nqs1,n_ad); + set_trio_QS_noisy(args,&args->trio[i],pqs,nqs1,n_ad,pnoise); else if ( rec->n_allele > 4 ) // DNG does not use QS, but QS is needed when trimming ALTs set_trio_QS(args,&args->trio[i],pqs,nqs1); @@ -1471,26 +1480,34 @@ static void set_option(args_t *args, char *optarg) else if ( !strcasecmp(opt,"pn") || !strcasecmp(opt,"pnoise") ) { if ( !val ) error("Error: expected value with -u %s, e.g. -u %s=0.05\n",opt,opt); - args->pn_frac = strtod(val,&tmp); + double pn_frac,pn_abs = 0; + pn_frac = strtod(val,&tmp); if ( *tmp && *tmp==',' ) { - args->pn_abs = strtod(tmp+1,&tmp); + pn_abs = strtod(tmp+1,&tmp); if ( *tmp ) error("Could not parse: -u %s\n", optarg); } - if ( args->pn_frac<0 || args->pn_frac>1 ) error("Error: expected value from the interval [0,1] for -u %s\n", optarg); - if ( args->pn_abs<0 ) error("Error: expected positive value for -u %s\n", optarg); + if ( pn_frac<0 || pn_frac>1 ) error("Error: expected value from the interval [0,1] for -u %s\n", optarg); + if ( pn_abs<0 ) error("Error: expected positive value for -u %s\n", optarg); + args->pn_snv.frac = pn_frac; + args->pn_snv.abs = pn_abs; + args->pn_indel = args->pn_snv; } else if ( !strcasecmp(opt,"pns") ) { if ( !val ) error("Error: expected value with -u %s, e.g. -u %s=0.05\n",opt,opt); - args->pns_frac = strtod(val,&tmp); + double pn_frac,pn_abs = 0; + pn_frac = strtod(val,&tmp); if ( *tmp && *tmp==',' ) { - args->pns_abs = strtod(tmp+1,&tmp); + pn_abs = strtod(tmp+1,&tmp); if ( *tmp ) error("Could not parse: -u %s\n", optarg); } - if ( args->pns_frac<0 || args->pn_frac>1 ) error("Error: expected value from the interval [0,1] for -u %s\n", optarg); - if ( args->pns_abs<0 ) error("Error: expected positive value for -u %s\n", optarg); + if ( pn_frac<0 || pn_frac>1 ) error("Error: expected value from the interval [0,1] for -u %s\n", optarg); + if ( pn_abs<0 ) error("Error: expected positive value for -u %s\n", optarg); + args->pn_snv.frac1 = pn_frac; + args->pn_snv.abs1 = pn_abs; + args->pn_indel = args->pn_snv; } else if ( !strcasecmp(opt,"DNG") ) { args->use_model = USE_DNG; args->use_dng_priors = 1; } else if ( !strcasecmp(opt,"dng-priors") ) args->use_dng_priors = 1; @@ -1524,10 +1541,10 @@ int run(int argc, char **argv) args->dnm_vaf_tag = strdup("VAF"); args->dnm_allele_tag = strdup("VA"); args->mrate = 1e-8; - args->pn_frac = 0.005; - args->pn_abs = 0; - args->pns_frac = 0.045; - args->pns_abs = 0; + args->pn_snv.frac = 0.005; + args->pn_snv.frac1 = 0.045; + args->pn_snv.abs = 0; + args->pn_snv.abs1 = 0; args->record_cmd_line = 1; args->regions_overlap = 1; args->targets_overlap = 0; @@ -1570,6 +1587,7 @@ int run(int argc, char **argv) }; int c; char *tmp; + double pn_abs, pn_frac; while ((c = getopt_long(argc, argv, "p:P:o:O:s:i:e:r:R:t:T:m:au:X:n",loptions,NULL)) >= 0) { switch (c) @@ -1581,24 +1599,64 @@ int run(int argc, char **argv) case 5 : args->use_dng_priors = 1; break; case 6 : args->mrate = strtod(optarg,&tmp); if ( *tmp ) error("Could not parse: --mrate %s\n", optarg); break; case 7 : - args->pn_frac = strtod(optarg,&tmp); + pn_frac = strtod(optarg,&tmp); + pn_abs = 0; if ( *tmp && *tmp==',' ) { - args->pn_abs = strtod(tmp+1,&tmp); - if ( *tmp ) error("Could not parse: --pn %s\n", optarg); + pn_abs = strtod(tmp+1,&tmp); + if ( *tmp ) + { + if ( *tmp!=':' ) error("Could not parse: --pn %s\n", optarg); + if ( !strcasecmp("snv",tmp+1) ) { args->pn_snv.frac = pn_frac; args->pn_snv.abs = pn_abs; } + else if ( !strcasecmp("indel",tmp+1) ) { args->pn_indel.frac = pn_frac; args->pn_indel.abs = pn_abs; } + else error("Could not parse: --pn %s\n", optarg); + } + else + { + args->pn_snv.frac = pn_frac; + args->pn_snv.abs = pn_abs; + args->pn_indel.frac = pn_frac; + args->pn_indel.abs = pn_abs; + } } - if ( args->pn_frac<0 || args->pn_frac>1 ) error("Error: expected value from the interval [0,1] for --pn %s\n", optarg); - if ( args->pn_abs<0 ) error("Error: expected positive value for --pn %s\n", optarg); + else if ( *tmp ) error("Could not parse: --pn %s\n", optarg); + else + { + args->pn_snv.frac = pn_frac; + args->pn_indel.frac = pn_frac; + } + if ( pn_frac<0 || pn_frac>1 ) error("Error: expected value from the interval [0,1] for --pn %s\n", optarg); + if ( pn_abs<0 ) error("Error: expected positive value for --pn %s\n", optarg); break; case 8 : - args->pns_frac = strtod(optarg,&tmp); + pn_frac = strtod(optarg,&tmp); + pn_abs = 0; if ( *tmp && *tmp==',' ) { - args->pns_abs = strtod(tmp+1,&tmp); - if ( *tmp ) error("Could not parse: --pns %s\n", optarg); + pn_abs = strtod(tmp+1,&tmp); + if ( *tmp ) + { + if ( *tmp!=':' ) error("Could not parse: --pns %s\n", optarg); + if ( !strcasecmp("snv",tmp+1) ) { args->pn_snv.frac1 = pn_frac; args->pn_snv.abs1 = pn_abs; } + else if ( !strcasecmp("indel",tmp+1) ) { args->pn_indel.frac1 = pn_frac; args->pn_indel.abs1 = pn_abs; } + else error("Could not parse: --pns %s\n", optarg); + } + else + { + args->pn_snv.frac1 = pn_frac; + args->pn_snv.abs1 = pn_abs; + args->pn_indel.frac1 = pn_frac; + args->pn_indel.abs1 = pn_abs; + } + } + else if ( *tmp ) error("Could not parse: --pns %s\n", optarg); + else + { + args->pn_snv.frac1 = pn_frac; + args->pn_indel.frac1 = pn_frac; } - if ( args->pns_frac<0 || args->pns_frac>1 ) error("Error: expected value from the interval [0,1] for --pns %s\n", optarg); - if ( args->pns_abs<0 ) error("Error: expected positive value for --pns %s\n", optarg); + if ( pn_frac<0 || pn_frac>1 ) error("Error: expected value from the interval [0,1] for --pns %s\n", optarg); + if ( pn_abs<0 ) error("Error: expected positive value for --pns %s\n", optarg); break; case 9 : args->use_model = USE_DNG; args->use_dng_priors = 1; break; case 10 : args->with_ppl = 1; break; From ddf37e1c887a7fe1d20b8250aafa44540cab835c Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Thu, 1 Sep 2022 17:26:53 +0200 Subject: [PATCH 13/84] Support sample reordering of annotation file. Resolves #1785 --- NEWS | 4 ++++ test/annotate28.1.out | 6 ++++++ test/annotate28.2.out | 6 ++++++ test/annotate28.3.out | 6 ++++++ test/annotate28.4.out | 6 ++++++ test/annotate28.vcf | 5 +++++ test/annots28.tab | 2 ++ test/test.pl | 4 ++++ vcfannotate.c | 2 +- 9 files changed, 40 insertions(+), 1 deletion(-) create mode 100644 test/annotate28.1.out create mode 100644 test/annotate28.2.out create mode 100644 test/annotate28.3.out create mode 100644 test/annotate28.4.out create mode 100644 test/annotate28.vcf create mode 100644 test/annots28.tab diff --git a/NEWS b/NEWS index 21fa1d519..3dd3f2c62 100644 --- a/NEWS +++ b/NEWS @@ -2,6 +2,10 @@ Changes affecting specific commands: +* bcftools annotate + + - Support sample reordering of annotation file ( #1785) + * bcftools +trio-dnm2 - New -n, --strictly-novel option to downplay alleles which violate Mendelian diff --git a/test/annotate28.1.out b/test/annotate28.1.out new file mode 100644 index 000000000..1f6fe8034 --- /dev/null +++ b/test/annotate28.1.out @@ -0,0 +1,6 @@ +##fileformat=VCFv4.2 +##FILTER= +##FORMAT= +##contig= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT smpl1 smpl2 +1 1 . G . . . . TEST 1 2 diff --git a/test/annotate28.2.out b/test/annotate28.2.out new file mode 100644 index 000000000..77cb2dbb3 --- /dev/null +++ b/test/annotate28.2.out @@ -0,0 +1,6 @@ +##fileformat=VCFv4.2 +##FILTER= +##FORMAT= +##contig= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT smpl1 smpl2 +1 1 . G . . . . TEST 2 1 diff --git a/test/annotate28.3.out b/test/annotate28.3.out new file mode 100644 index 000000000..97376e93b --- /dev/null +++ b/test/annotate28.3.out @@ -0,0 +1,6 @@ +##fileformat=VCFv4.2 +##FILTER= +##FORMAT= +##contig= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT smpl1 smpl2 +1 1 . G . . . . TEST 1 . diff --git a/test/annotate28.4.out b/test/annotate28.4.out new file mode 100644 index 000000000..1d8796e88 --- /dev/null +++ b/test/annotate28.4.out @@ -0,0 +1,6 @@ +##fileformat=VCFv4.2 +##FILTER= +##FORMAT= +##contig= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT smpl1 smpl2 +1 1 . G . . . . TEST . 1 diff --git a/test/annotate28.vcf b/test/annotate28.vcf new file mode 100644 index 000000000..a354d6d25 --- /dev/null +++ b/test/annotate28.vcf @@ -0,0 +1,5 @@ +##fileformat=VCFv4.2 +##FORMAT= +##contig= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT smpl1 smpl2 +1 1 . G . . . . . . . diff --git a/test/annots28.tab b/test/annots28.tab new file mode 100644 index 000000000..12a2164e5 --- /dev/null +++ b/test/annots28.tab @@ -0,0 +1,2 @@ +#CHROM POS REF ALT TEST +1 1 G . 1 2 diff --git a/test/test.pl b/test/test.pl index cc2757fda..4e50259e5 100755 --- a/test/test.pl +++ b/test/test.pl @@ -494,6 +494,10 @@ run_test(\&test_vcf_annotate,$opts,in=>'annotate.id',vcf=>'annots.id',out=>'annotate.id.1.out',args=>'-c ALT'); run_test(\&test_vcf_annotate,$opts,in=>'annotate.id',vcf=>'annots.id',out=>'annotate.id.2.out',args=>'-c +ALT'); run_test(\&test_vcf_annotate,$opts,in=>'annotate27',tab=>'annotate27',out=>'annotate.32.out',args=>'-c CHROM,POS,REF,ALT,EVIDENCE'); +run_test(\&test_vcf_annotate,$opts,in=>'annotate28',tab=>'annots28',out=>'annotate28.1.out',args=>'-c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2'); +run_test(\&test_vcf_annotate,$opts,in=>'annotate28',tab=>'annots28',out=>'annotate28.2.out',args=>'-c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1'); +run_test(\&test_vcf_annotate,$opts,in=>'annotate28',tab=>'annots28',out=>'annotate28.3.out',args=>'-c CHROM,POS,REF,ALT,FMT/TEST -s smpl1'); +run_test(\&test_vcf_annotate,$opts,in=>'annotate28',tab=>'annots28',out=>'annotate28.4.out',args=>'-c CHROM,POS,REF,ALT,FMT/TEST -s smpl2'); run_test(\&test_vcf_plugin,$opts,in=>'checkploidy',out=>'checkploidy.out',cmd=>'+check-ploidy --no-version'); run_test(\&test_vcf_plugin,$opts,in=>'checkploidy.2',out=>'checkploidy.2.out',cmd=>'+check-ploidy --no-version'); run_test(\&test_vcf_plugin,$opts,in=>'checkploidy.2',out=>'checkploidy.3.out',cmd=>'+check-ploidy --no-version',args=>'-- -m'); diff --git a/vcfannotate.c b/vcfannotate.c index d33fd9027..0cbf400bb 100644 --- a/vcfannotate.c +++ b/vcfannotate.c @@ -2022,7 +2022,7 @@ static int init_sample_map(args_t *args, bcf_hdr_t *src, bcf_hdr_t *dst) args->sample_map = (int*) malloc(sizeof(int)*args->nsample_map); for (i=0; insample_map; i++) args->sample_map[i] = -1; - int flags = !src ? SMPL_STRICT|SMPL_SINGLE : SMPL_STRICT|SMPL_SINGLE|SMPL_PAIR2; // is vcf vs tab annotation file + int flags = !src ? SMPL_STRICT|SMPL_SINGLE|SMPL_REORDER : SMPL_STRICT|SMPL_SINGLE|SMPL_PAIR2; // is tab vs vcf annotation file smpl_ilist_t *ilist = smpl_ilist_init(dst, args->sample_names, args->sample_is_file, flags); // gives mapping dst->src if ( !ilist || !ilist->n ) error("Could not parse the samples: %s\n", args->sample_names); args->nsmpl_annot = ilist->n; From 298583794e1f62de1420fc25e94fb677f7812356 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Mon, 5 Sep 2022 15:59:17 +0100 Subject: [PATCH 14/84] Remove debugging asserts (using a temporary debug printout instead) and check return values when there are no indels types (-1 is returned) --- bam2bcf_iaux.c | 2 +- read_consensus.c | 7 ++----- 2 files changed, 3 insertions(+), 6 deletions(-) diff --git a/bam2bcf_iaux.c b/bam2bcf_iaux.c index 1f2c35cba..fcee1091c 100644 --- a/bam2bcf_iaux.c +++ b/bam2bcf_iaux.c @@ -705,7 +705,7 @@ assert(!(ref == 0 || bca == 0)); // can this ever happen? when? // window boundaries. todo: We want this information cached so that for long reads we don't keep // redoing the whole analysis again and again int ntypes = iaux_init_types(iaux); - if ( !ntypes ) return -1; + if ( ntypes<=0 ) return -1; debug_print_types(iaux); diff --git a/read_consensus.c b/read_consensus.c index 326c6e9bd..1ba397a03 100644 --- a/read_consensus.c +++ b/read_consensus.c @@ -166,13 +166,11 @@ int rcns_reset(read_cns_t *rcns, hts_pos_t pos, hts_pos_t beg, hts_pos_t end) static inline void add_base(read_cns_t *rcns, int ref_pos, int nt16) { int i = ref_pos - rcns->beg; -assert(i>=0); rcns->base_freq[i].base[seq_nt16_int[nt16]]++; } static void add_ins(read_cns_t *rcns, int ref_pos, int seq_pos, uint8_t *raw_seq, int len) { int i = ref_pos - rcns->beg; -assert(i>=0); ins_freq_t *ifrq = &rcns->ins_freq[i]; char *str; if ( rcns->mstmp < len ) @@ -189,7 +187,7 @@ assert(i>=0); for (i=0; int16_seq[i]; i++) if ( ifrq->len[i]==len && !memcmp(ifrq->nt16_seq[i],str,len) ) break; - assert( i=NI ) fprintf(stderr,"xxx: many ins types at pos=%d\n",(int)rcns->pos); // how frequent is it to have too many insertion types? if ( i>=NI ) return; // too many choices; discard if ( !ifrq->nt16_seq[i] ) // new insertion @@ -203,7 +201,6 @@ assert(i>=0); static void add_del(read_cns_t *rcns, int ref_pos, int len) { int i = ref_pos - rcns->beg; -assert(i>=0); int j,n = rcns->end - rcns->beg + 1; if ( i + len + 1 < n ) n = i + len + 1; for (j=i+1; j=0); for (i=0; ilen[i]; i++) if ( dfrq->len[i]==len ) break; - assert( i=NI ) fprintf(stderr,"xxx: many del types at pos=%d\n",(int)rcns->pos); // how frequent is it to have too many insertion types? if ( i>=NI ) return; // too many choices; discard if ( !dfrq->len[i] ) dfrq->len[i] = len; // new deletion From f3b9ae63d8f73b2f156340e0cb58c2d52c88b32c Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Tue, 6 Sep 2022 15:22:17 +0100 Subject: [PATCH 15/84] Remove unused cns_seq_t.pos array. Fix two index errors The errors were: - pass correct position to cigar INS matching operator - set the correct offset in the consensus template --- bam2bcf_iaux.c | 15 ------------- cigar_state.h | 6 ++++- read_consensus.c | 58 ++++++++++++++++++++++++------------------------ read_consensus.h | 1 - 4 files changed, 34 insertions(+), 46 deletions(-) diff --git a/bam2bcf_iaux.c b/bam2bcf_iaux.c index fcee1091c..38b99b317 100644 --- a/bam2bcf_iaux.c +++ b/bam2bcf_iaux.c @@ -535,9 +535,6 @@ static int iaux_score_reads(indel_aux_t *iaux, int ismpl, int itype) uint8_t *ref_buf = (uint8_t*) realloc(iaux->ref_seq,sizeof(uint8_t)*ref_len); if ( !ref_buf ) return -1; iaux->ref_seq = ref_buf; - hts_pos_t *pos_buf = (hts_pos_t*) realloc(iaux->pos_seq,sizeof(hts_pos_t)*ref_len); - if ( !pos_buf ) return -1; - iaux->pos_seq = pos_buf; iaux->nref_seq = ref_len; } @@ -552,22 +549,10 @@ static int iaux_score_reads(indel_aux_t *iaux, int ismpl, int itype) memcpy(iaux->ref_seq + cns->ipos + 1 + iaux->types[itype], cns->seq + 1 + cns->ipos, (cns->nseq - cns->ipos - 1)*sizeof(*iaux->ref_seq)); } - // ...and corresponding ref positions - memcpy(iaux->pos_seq,cns->pos,(cns->ipos+1)*sizeof(*iaux->pos_seq)); - if ( iaux->types[itype] < 0 ) // deletion - memcpy(iaux->pos_seq + cns->ipos + 1, cns->pos + cns->ipos + 1 - iaux->types[itype], (cns->nseq - cns->ipos - 1 + iaux->types[itype])*sizeof(*iaux->pos_seq)); - else - { - for (i=0; itypes[itype]; i++) iaux->pos_seq[cns->ipos+1+i] = cns->pos[cns->ipos]; - memcpy(iaux->pos_seq + cns->ipos + 1 + iaux->types[itype], cns->pos + 1 + cns->ipos, (cns->nseq - cns->ipos - 1)*sizeof(*iaux->pos_seq)); - } - #if DEBUG_ALN fprintf(stderr,"template %d, type %d, sample %d: ",cns==iaux->cns_seq?0:1,itype,ismpl); for (i=0; iref_seq[i]]); fprintf(stderr,"\n"); - for (i=0; ipos_seq[i-1]+1==iaux->pos_seq[i])?' ':'x',(int)iaux->pos_seq[i]); - fprintf(stderr,"\n"); #endif // Align and score reads diff --git a/cigar_state.h b/cigar_state.h index c4763b255..adfb45d8d 100644 --- a/cigar_state.h +++ b/cigar_state.h @@ -125,6 +125,10 @@ inline int cstate_seek_fwd(cigar_state_t *cs, hts_pos_t *pos_ptr, int trim_left) * cstate_seek_op_fwd() - Move in the cigar forward to find query index that * matches the seek operator and the reference position. * + * In order to match a deletion, pass the position of the first deleted base. + * In order to match an insertion, pass the reference coordinate of the base + * after the inserted sequence. + * * Returns the index to the query sequence cs->seq * on success; -1 when there is no such matching position but the cigar * is still not entirely consumed (e.g. a deletion or a soft-clip); -2 @@ -152,7 +156,7 @@ inline int cstate_seek_op_fwd(cigar_state_t *cs, hts_pos_t pos, int seek_op, int } if ( op==BAM_CINS || op==BAM_CSOFT_CLIP ) { - if ( cs->ref_pos == pos + 1 && seek_op==op ) + if ( cs->ref_pos == pos && seek_op==op ) { if ( oplen ) *oplen = len; return cs->iseq; diff --git a/read_consensus.c b/read_consensus.c index 1ba397a03..1f94fce9e 100644 --- a/read_consensus.c +++ b/read_consensus.c @@ -47,6 +47,7 @@ typedef struct } del_freq_t; +#define BF_DEL 5 typedef struct { int base[6]; // frequencies of A,C,G,T,N,deletion @@ -106,10 +107,7 @@ void rcns_destroy(read_cns_t *rcns) for (j=0; jnt16_seq[j]; j++) free(ifrq->nt16_seq[j]); } for (i=0; i<2; i++) - { free(rcns->cns[i].seq); - free(rcns->cns[i].pos); - } free(rcns->ins_freq); free(rcns->del_freq); free(rcns->base_freq); @@ -204,7 +202,7 @@ static void add_del(read_cns_t *rcns, int ref_pos, int len) int j,n = rcns->end - rcns->beg + 1; if ( i + len + 1 < n ) n = i + len + 1; for (j=i+1; jbase_freq[j].base[5]++; + rcns->base_freq[j].base[BF_DEL]++; del_freq_t *dfrq = &rcns->del_freq[i]; for (i=0; ilen[i]; i++) @@ -328,6 +326,13 @@ static void debug_print_base_freqs(read_cns_t *rcns, const char *ref) fprintf(stderr,"\n"); } } +static const char *vtype2string(enum variant_type vtype) +{ + if ( vtype==snv ) return "snv"; + if ( vtype==ins ) return "ins"; + if ( vtype==del ) return "del"; + return "???"; +} static void debug_print_candidate_variants(read_cns_t *rcns) { int i; @@ -335,8 +340,8 @@ static void debug_print_candidate_variants(read_cns_t *rcns) for (i=0; incvar; i++) { candidate_var_t *var = &rcns->cvar[i]; - fprintf(stderr,"\tvar%d pos=%"PRIhts_pos" idx=%d vtype=%d which=%d depth=%d af=%f af_dev=%f\n", - i,var->pos+1,var->idx,var->vtype,var->which,var->depth,var->af,var->af_dev); + fprintf(stderr,"\tvar%d pos=%"PRIhts_pos" idx=%d vtype=%s which=%d depth=%d af=%f af_dev=%f\n", + i,var->pos+1,var->idx,vtype2string(var->vtype),var->which,var->depth,var->af,var->af_dev); } } static void debug_print_haplotype_frequency_spectrum(read_cns_t *rcns) @@ -359,7 +364,7 @@ static void debug_print_consensus(read_cns_t *rcns) { if ( !rcns->cns[i].nseq ) break; fprintf(stderr,"Consensus%d: ",i); - for (j=0; jcns[i].ipos; j++) + for (j=0; j<=rcns->cns[i].ipos; j++) fprintf(stderr,"%c","ACGTN"[(int)rcns->cns[i].seq[j]]); fprintf(stderr,"#"); for (; jcns[i].nseq; j++) @@ -482,10 +487,6 @@ static int select_candidate_variants(read_cns_t *rcns, const char *ref) char *seq = (char*) realloc(rcns->cns[i].seq,sizeof(char)*n); if ( !seq ) return -1; rcns->cns[i].seq = seq; - - hts_pos_t *pos = (hts_pos_t*) realloc(rcns->cns[i].pos,sizeof(hts_pos_t)*n); - if ( !pos ) return -1; - rcns->cns[i].pos = pos; } rcns->mcns = n; } @@ -527,7 +528,7 @@ static int create_haplotype_frequency_spectrum(read_cns_t *rcns) { int len; ins_freq_t *ifrq = &rcns->ins_freq[cvar->pos - rcns->beg]; - int iseq = cstate_seek_op_fwd(&cigar, cvar->pos, BAM_CINS, &len); + int iseq = cstate_seek_op_fwd(&cigar, cvar->pos+1, BAM_CINS, &len); if ( iseq==-2 ) break; if ( iseq==-1 ) continue; if ( len!=ifrq->len[cvar->which] ) continue; @@ -539,7 +540,7 @@ static int create_haplotype_frequency_spectrum(read_cns_t *rcns) { int len; del_freq_t *dfrq = &rcns->del_freq[cvar->pos - rcns->beg]; - int ret = cstate_seek_op_fwd(&cigar, cvar->pos, BAM_CDEL, &len); + int ret = cstate_seek_op_fwd(&cigar, cvar->pos+1, BAM_CDEL, &len); if ( ret==-2 ) break; if ( ret==-1 ) continue; if ( len!=dfrq->len[cvar->which] ) continue; @@ -661,7 +662,7 @@ static inline void apply_consensus_insertion(read_cns_t *rcns, cns_seq_t *cns, i base_freq_t *bfreq = rcns->base_freq; ins_freq_t *ifreq = rcns->ins_freq; int k, nreads = 0; - for (k=0; k<5; k++) nreads += bfreq[j].base[k]; + for (k=0; kpos[cns->nseq] = ref_pos; cns->seq[cns->nseq++] = seq_nt16_int[(int)seq[k]]; - } } +// For each position of the realignment window apply either the candidate variants +// from ith haplotype or decide on the base/ins/del by majority vote static void create_consensus(read_cns_t *rcns, const char *ref, int ith) { int n = rcns->end - rcns->beg + 1; @@ -685,11 +685,12 @@ static void create_consensus(read_cns_t *rcns, const char *ref, int ith) base_freq_t *bfreq = rcns->base_freq; ins_freq_t *ifreq = rcns->ins_freq; del_freq_t *dfreq = rcns->del_freq; + hts_pos_t prev_pos = 0; int j,k, ivar = 0; for (j=0; jbeg + j; - if ( rcns->pos == ref_pos ) cns->ipos = j; + if ( rcns->pos == ref_pos ) cns->ipos = cns->nseq; while ( ivar < rcns->ncvar && rcns->cvar[ivar].pos < ref_pos ) ivar++; @@ -699,13 +700,13 @@ static void create_consensus(read_cns_t *rcns, const char *ref, int ith) // a deletion if that is most frequent. However, for deleted bases make sure they are not part // of the deletion that is being tested at this positions int max_freq = 0, kmax = seq_nt16_int[seq_nt16_table[(int)ref[j]]]; - int nk = ( ref_pos < rcns->pos || ref_pos > rcns->pos + rcns->max_del ) ? 6 : 5; + int nk = ( ref_pos < rcns->pos || ref_pos > rcns->pos + rcns->max_del ) ? BF_DEL+1 : BF_DEL; for (k=0; kpos[cns->nseq] = ref_pos; + prev_pos = ref_pos; cns->seq[cns->nseq++] = kmax; } // Only apply consensus insertions that are not being tested by bam2bcf_iaux, i.e. not at the current pos @@ -723,9 +724,9 @@ static void create_consensus(read_cns_t *rcns, const char *ref, int ith) if ( rcns->cvar[ivar].vtype==snv && rcns->cvar[ivar].which==k ) continue; if ( max_freq < bfreq[j].base[k] ) max_freq = bfreq[j].base[k], kmax = k; } - if ( kmax!=5 && (!cns->nseq || cns->pos[cns->nseq-1] != ref_pos) ) + if ( kmax!=BF_DEL && (!cns->nseq || prev_pos != ref_pos) ) { - cns->pos[cns->nseq] = ref_pos; + prev_pos = ref_pos; cns->seq[cns->nseq++] = kmax; } apply_consensus_insertion(rcns, cns, j, ivar); @@ -733,7 +734,7 @@ static void create_consensus(read_cns_t *rcns, const char *ref, int ith) } if ( rcns->cvar[ivar].vtype == snv ) { - cns->pos[cns->nseq] = ref_pos; + prev_pos = ref_pos; cns->seq[cns->nseq++] = which; apply_consensus_insertion(rcns, cns, j, ivar); continue; @@ -741,7 +742,7 @@ static void create_consensus(read_cns_t *rcns, const char *ref, int ith) // There can be multiple variants at this position, for example snv+ins. SNVs come first // thanks to cvar_pos_cmp(), make sure the base has not been added already. - if ( !cns->nseq || cns->pos[cns->nseq-1] != ref_pos ) + if ( !cns->nseq || prev_pos != ref_pos ) { int max_freq = 0, kmax = seq_nt16_int[seq_nt16_table[(int)ref[j]]]; for (k=0; k<6; k++) @@ -749,9 +750,9 @@ static void create_consensus(read_cns_t *rcns, const char *ref, int ith) if ( rcns->cvar[ivar].vtype==snv && rcns->cvar[ivar].which==k ) continue; if ( max_freq < bfreq[j].base[k] ) max_freq = bfreq[j].base[k], kmax = k; } - if ( kmax!=5 ) + if ( kmax!=BF_DEL ) { - cns->pos[cns->nseq] = ref_pos; + prev_pos = ref_pos; cns->seq[cns->nseq++] = kmax; } } @@ -761,7 +762,7 @@ static void create_consensus(read_cns_t *rcns, const char *ref, int ith) char *seq = ifreq[j].nt16_seq[which]; for (k=0; kpos[cns->nseq] = ref_pos; + prev_pos = ref_pos; cns->seq[cns->nseq++] = seq_nt16_int[(int)seq[k]]; } } @@ -805,4 +806,3 @@ cns_seq_t *rcns_get_consensus(read_cns_t *rcns, const char *ref) return rcns->cns; } - diff --git a/read_consensus.h b/read_consensus.h index f90e518f0..9f5cb7979 100644 --- a/read_consensus.h +++ b/read_consensus.h @@ -37,7 +37,6 @@ typedef struct { char *seq; // nt5 sequence: "ACGTN"[(int)seq[i]] int nseq, ipos; // the sequence length and the `pos` index relative to seq - hts_pos_t *pos; // corresponding refseq coordinates, inserted bases appear as a block of equal positions } cns_seq_t; From 86330edaaa4e9d50bff16ca3f2b093516d055948 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Wed, 7 Sep 2022 11:31:10 +0100 Subject: [PATCH 16/84] Fix a bug in recognizing the need to end the error correction --- read_consensus.c | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/read_consensus.c b/read_consensus.c index 1f94fce9e..dfbc74ff2 100644 --- a/read_consensus.c +++ b/read_consensus.c @@ -347,7 +347,7 @@ static void debug_print_candidate_variants(read_cns_t *rcns) static void debug_print_haplotype_frequency_spectrum(read_cns_t *rcns) { int i,j; - fprintf(stderr,"Haplotype frequencies:\n"); + fprintf(stderr,"Haplotype frequencies (bits from left correspond to var0,1,..):\n"); for (i=0; ihap_freq[i] ) continue; @@ -357,9 +357,12 @@ static void debug_print_haplotype_frequency_spectrum(read_cns_t *rcns) fprintf(stderr,"\t%d\n", rcns->hap_freq[i]); } } -static void debug_print_consensus(read_cns_t *rcns) +static void debug_print_consensus(read_cns_t *rcns, const char *ref) { - int i,j; + int i,j,n = rcns->end - rcns->beg + 1; + fprintf(stderr,"ref: "); + for (i=0; icns[i].nseq ) break; @@ -370,16 +373,13 @@ static void debug_print_consensus(read_cns_t *rcns) for (; jcns[i].nseq; j++) fprintf(stderr,"%c","ACGTN"[(int)rcns->cns[i].seq[j]]); fprintf(stderr,"\n"); - for (j=0; jcns[i].nseq; j++) - fprintf(stderr," %d",(int)rcns->cns[i].pos[j]); - fprintf(stderr,"\n"); } } #else #define debug_print_base_freqs(rcns,ref) #define debug_print_candidate_variants(rcns) #define debug_print_haplotype_frequency_spectrum(rcns) -#define debug_print_consensus(rcns) +#define debug_print_consensus(rcns,ref) #endif static int cvar_pos_cmp(const void *aptr, const void *bptr) @@ -580,7 +580,8 @@ static int correct_haplotype_errors(read_cns_t *rcns) qsort(freq, NHAP, sizeof(ii_t), ii_cmp); // sort haplotypes in descending order for (i=NHAP-1; i>=0; i--) { - if ( freq[1].count > tot - freq[0].count ) break; // the top2 hapotypes cannot change anymore + if ( !freq[i].count ) continue; + if ( freq[1].count > tot - freq[0].count - freq[1].count ) break; // the top2 hapotypes cannot change anymore // Find a similar haplotype with the highest frequency. Assuming errors go in 0->1 // direction only and considering one error only. @@ -802,7 +803,7 @@ cns_seq_t *rcns_get_consensus(read_cns_t *rcns, const char *ref) // create consensus int i; for (i=0; incns; i++) create_consensus(rcns,ref,i); - debug_print_consensus(rcns); + debug_print_consensus(rcns,ref); return rcns->cns; } From bc3a52184efd250f01a18df31367ade4606c0d62 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Thu, 8 Sep 2022 13:40:10 +0100 Subject: [PATCH 17/84] Prevent segfault when no indels encountered; Add to 86330edaaa, end on time when correcting haplotypes --- Makefile | 2 +- bam2bcf_iaux.c | 2 ++ cigar_state.h | 3 --- read_consensus.c | 8 ++------ 4 files changed, 5 insertions(+), 10 deletions(-) diff --git a/Makefile b/Makefile index 9b52cf8b4..b38c8468a 100644 --- a/Makefile +++ b/Makefile @@ -280,7 +280,7 @@ mpileup.o: mpileup.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(hts bam2bcf.o: bam2bcf.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h) mw.h bam2bcf_indel.o: bam2bcf_indel.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_str2int_h) $(bam2bcf_h) $(htslib_ksort_h) str_finder.h bam2bcf_iaux.o: bam2bcf_iaux.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_str2int_h) $(bam2bcf_h) $(htslib_ksort_h) str_finder.h read_consensus.h cigar_state.h -read_consensus.o: read_consensus.c read_consensus.h $(htslib_hts_h) $(htslib_sam_h) +read_consensus.o: read_consensus.c read_consensus.h cigar_state.h $(htslib_hts_h) $(htslib_sam_h) bam_sample.o: bam_sample.c $(htslib_hts_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) $(khash_str2str_h) $(bam_sample_h) $(bcftools_h) version.o: version.h version.c hclust.o: hclust.c $(htslib_hts_h) $(htslib_kstring_h) $(bcftools_h) hclust.h diff --git a/bam2bcf_iaux.c b/bam2bcf_iaux.c index 38b99b317..5629a2d2a 100644 --- a/bam2bcf_iaux.c +++ b/bam2bcf_iaux.c @@ -388,6 +388,7 @@ static int iaux_set_consensus(indel_aux_t *iaux, int ismpl) return 0; } +#if 0 // Finds the smallest index in the seq_pos array holding value equal to pos, or if there is no // such value, the largest index with value smaller than pos. Starts at initial guess ioff. // This could use a binary search but the assumption is that the initial guess is indel-size close @@ -407,6 +408,7 @@ static int find_ref_offset(hts_pos_t pos, hts_pos_t *seq_pos, int nseq_pos, int while ( ioff > 0 && seq_pos[ioff-1] >= pos ) ioff--; return ioff; } +#endif static int iaux_align_read(indel_aux_t *iaux, bam1_t *bam, uint8_t *ref_seq, hts_pos_t *pos_seq, int nref_seq) { diff --git a/cigar_state.h b/cigar_state.h index adfb45d8d..5822d1cea 100644 --- a/cigar_state.h +++ b/cigar_state.h @@ -51,9 +51,6 @@ inline void cstate_init(cigar_state_t *cs, bam1_t *bam) cs->icig = 0; cs->iseq = 0; cs->ref_pos = bam->core.pos; - int op = cs->cigar[0] & BAM_CIGAR_MASK; - int len = cs->cigar[0] >> BAM_CIGAR_SHIFT; - if ( op==BAM_CINS || op==BAM_CSOFT_CLIP ) cs->ref_pos -= len; } /** diff --git a/read_consensus.c b/read_consensus.c index dfbc74ff2..2408aec73 100644 --- a/read_consensus.c +++ b/read_consensus.c @@ -100,6 +100,7 @@ struct _read_cns_t void rcns_destroy(read_cns_t *rcns) { + if ( !rcns ) return; int i,j; for (i=0; imfreq; i++) { @@ -118,7 +119,6 @@ void rcns_destroy(read_cns_t *rcns) static int init_arrays(read_cns_t *rcns) { int i,j,n = rcns->end - rcns->beg + 1; -//fprintf(stderr,"arrays: %d-%d n=%d\n",(int)rcns->beg+1,(int)rcns->end+1,n); if ( n > rcns->mfreq ) { ins_freq_t *ifrq = (ins_freq_t*) realloc(rcns->ins_freq,sizeof(*rcns->ins_freq)*n); @@ -236,8 +236,6 @@ int rcns_set_reads(read_cns_t *rcns, bam_pileup1_t *plp, int nplp) rcns->plp = plp; rcns->nplp = nplp; -//fprintf(stderr,"rcns_beg1,end1,pos1=%d %d %d\n\n",(int)rcns->beg+1,(int)rcns->end+1,(int)rcns->pos+1); - // fill consensus arrays int i,j,k, local_band_max = 0; // maximum absolute deviation from diagonal for (i=0; icore.n_cigar; ++k) { @@ -442,7 +439,6 @@ static void register_variant(read_cns_t *rcns, enum variant_type vtype, int cns_ static int select_candidate_variants(read_cns_t *rcns, const char *ref) { const float af_th = 0.1; -//const float af_th = 0.05;// just for debugging int i,j, n = rcns->end - rcns->beg + 1; int max_ins_len = 0; // maximum total length of all insertions applied to allocate big enough buffers base_freq_t *bfreq = rcns->base_freq; @@ -578,7 +574,7 @@ static int correct_haplotype_errors(read_cns_t *rcns) tot += rcns->hap_freq[i]; } qsort(freq, NHAP, sizeof(ii_t), ii_cmp); // sort haplotypes in descending order - for (i=NHAP-1; i>=0; i--) + for (i=NHAP-1; i>1; i--) { if ( !freq[i].count ) continue; if ( freq[1].count > tot - freq[0].count - freq[1].count ) break; // the top2 hapotypes cannot change anymore From fd9470ec84b4e7da378af5ca5847980d49ceb536 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Thu, 8 Sep 2022 17:15:08 +0200 Subject: [PATCH 18/84] Document explicitly output format of roh --- doc/bcftools.txt | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/doc/bcftools.txt b/doc/bcftools.txt index a2f60a219..eb6b6843a 100644 --- a/doc/bcftools.txt +++ b/doc/bcftools.txt @@ -3012,6 +3012,25 @@ Transition probabilities: Generate per-site output ('s') or per-region output ('r'). By default both types are printed and the output is uncompressed. Add 'z' for a compressed output. +---- + # Output fields: + RG = predicted homo/autozygous regions + - Sample + - Chromosome + - Start + - End + - Length (bp) + - Number of markers + - Quality .. average phred score in the region from the forward-backward algorithm + + ST = per-site output showing: + - Sample + - Chromosome + - Position + - State .. predicted state from the Viterbi algorithm, 0 for normal (HW, Hardy-Weinberg) or 1 for autozygous (AZ) + - Quality .. quality score from the forward-backward algorithm +---- + *-r, --regions* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]:: see *<>* From ea15bcb5c676001afcf0850687ced0a0bc315330 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Mon, 12 Sep 2022 15:42:10 +0200 Subject: [PATCH 19/84] Remove unused pos_seq array --- bam2bcf_iaux.c | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/bam2bcf_iaux.c b/bam2bcf_iaux.c index 5629a2d2a..70b904289 100644 --- a/bam2bcf_iaux.c +++ b/bam2bcf_iaux.c @@ -63,7 +63,6 @@ typedef struct cns_seq_t *cns_seq; // array of consensus sequences int *cns_pos; // array of relative pos indexes within cns_seq sequences uint8_t *ref_seq, *qry_seq; // reference and query sequence to align - hts_pos_t *pos_seq; // ref_seq consensus template positions in reference sequence (see also cns_seq_t.pos) int nref_seq, nqry_seq; // the allocated size of ref_seq and qry_seq uint8_t *qual; int nqual; @@ -105,7 +104,6 @@ void bcf_iaux_destroy(bcf_callaux_t *bca) free(iaux->inscns); free(iaux->ref_seq); free(iaux->qry_seq); - free(iaux->pos_seq); free(iaux->qual); free(iaux->read_scores); rcns_destroy(iaux->rcns); @@ -410,7 +408,7 @@ static int find_ref_offset(hts_pos_t pos, hts_pos_t *seq_pos, int nseq_pos, int } #endif -static int iaux_align_read(indel_aux_t *iaux, bam1_t *bam, uint8_t *ref_seq, hts_pos_t *pos_seq, int nref_seq) +static int iaux_align_read(indel_aux_t *iaux, bam1_t *bam, uint8_t *ref_seq, int nref_seq) { if ( bam->core.flag & BAM_FUNMAP ) return 1; // skip unmapped reads @@ -561,7 +559,7 @@ static int iaux_score_reads(indel_aux_t *iaux, int ismpl, int itype) for (i=0; inplp[ismpl]; i++) { const bam_pileup1_t *plp = iaux->plp[ismpl] + i; - int aln_score = iaux_align_read(iaux, plp->b, iaux->ref_seq, iaux->pos_seq, ref_len); + int aln_score = iaux_align_read(iaux, plp->b, iaux->ref_seq, ref_len); int *score = &iaux->read_scores[i*iaux->ntypes+itype]; if ( cns==iaux->cns_seq || *score > aln_score ) *score = aln_score; } From f4dee4bf7555b49fe4cc5be7f2f96fe526a49109 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Mon, 12 Sep 2022 15:58:09 +0200 Subject: [PATCH 20/84] Fix a rare bug where printing of SAMPLE field with `query` was incorrectly suppressed. This happened when the `-e` option contained a sample expression while the formatting query did not. Resolves #1783 --- NEWS | 6 ++++++ vcfquery.c | 5 +++-- 2 files changed, 9 insertions(+), 2 deletions(-) diff --git a/NEWS b/NEWS index 3dd3f2c62..d7ae94373 100644 --- a/NEWS +++ b/NEWS @@ -6,6 +6,12 @@ Changes affecting specific commands: - Support sample reordering of annotation file ( #1785) +* bcftools query + + - Fix a rare bug where the printing of SAMPLE field with `query` was incorrectly + suppressed when the `-e` option contained a sample expression while the formatting + query did not. See #1783 for details. + * bcftools +trio-dnm2 - New -n, --strictly-novel option to downplay alleles which violate Mendelian diff --git a/vcfquery.c b/vcfquery.c index 70b5f3061..889f36324 100644 --- a/vcfquery.c +++ b/vcfquery.c @@ -125,6 +125,7 @@ static void query_vcf(args_t *args) } int i,max_convert_unpack = convert_max_unpack(args->convert); + int max_filter_unpack = args->filter ? filter_max_unpack(args->filter) : 0; while ( bcf_sr_next_line(args->files) ) { if ( !bcf_sr_has_line(args->files,0) ) continue; @@ -143,7 +144,7 @@ static void query_vcf(args_t *args) if ( pass ) { if ( !args->smpl_pass ) continue; - if ( !(max_convert_unpack & BCF_UN_FMT) ) continue; + if ( !(max_convert_unpack & BCF_UN_FMT) && !(max_filter_unpack & BCF_UN_FMT) ) continue; pass = 0; for (i=0; in_sample; i++) @@ -292,7 +293,7 @@ int main_vcfquery(int argc, char *argv[]) case 'f': args->format_str = strdup(optarg); break; case 'H': args->print_header = 1; break; case 'v': args->vcf_list = optarg; break; - case 'c': + case 'c': error("The --collapse option is obsolete, pipe through `bcftools norm -c` instead.\n"); break; case 'a': From c46ca8a6b283e95e0c91b0bf66dc3ab809e988e7 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Tue, 13 Sep 2022 11:26:14 +0100 Subject: [PATCH 21/84] Consider all indel types one the site passed for indel evaluation --- bam2bcf_iaux.c | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/bam2bcf_iaux.c b/bam2bcf_iaux.c index 70b904289..541d3ced9 100644 --- a/bam2bcf_iaux.c +++ b/bam2bcf_iaux.c @@ -347,7 +347,13 @@ static int iaux_init_types(indel_aux_t *iaux) else { if ( j-i >= iaux->bca->min_support ) is_ok = 1; - if ( !iaux->bca->per_sample_flt && (double)(j-i) / n_tot < iaux->bca->min_frac ) is_ok = 0; + // What is the best way to handle the -pmF options: + // - consider only sites where a single indel type passes the -mF threshold, as opposed to all indel types cumulatively + // - once a site passes, include all indel types in the evaluation, as opposed to considering only the strong candidates + // In this implementation sites are selected by counting reads from all indel types cumulatively and all indel types + // are considered. + // Uncomment the following condition to consider only strong indel candidates once the site has been selected + // if ( !iaux->bca->per_sample_flt && (double)(j-i) / n_tot < iaux->bca->min_frac ) is_ok = 0; } if ( is_ok ) { From e9d22b1f5d24e0ceb2d613d9c390171d713d4252 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Tue, 13 Sep 2022 14:08:58 +0100 Subject: [PATCH 22/84] Add an experimental INFO/NM annotation --- bam2bcf.c | 4 ++++ bam2bcf.h | 4 +++- mpileup.c | 1 + 3 files changed, 8 insertions(+), 1 deletion(-) diff --git a/bam2bcf.c b/bam2bcf.c index cc7125123..6873274d4 100644 --- a/bam2bcf.c +++ b/bam2bcf.c @@ -209,6 +209,7 @@ void bcf_callaux_clean(bcf_callaux_t *bca, bcf_call_t *call) memset(bca->alt_scl, 0, 100*sizeof(int)); memset(bca->iref_scl, 0, 100*sizeof(int)); memset(bca->ialt_scl, 0, 100*sizeof(int)); + bca->nnm = bca->nm = 0; } /* @@ -368,6 +369,7 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t int imq = mapQ * nqual_over_60; int ibq = baseQ * nqual_over_60; int inm = get_aux_nm(p->b,p->qpos,is_diff?0:1); + if ( is_diff ) { bca->nnm++; bca->nm += inm; } if ( bam_is_rev(p->b) ) bca->rev_mqs[imq]++; @@ -990,6 +992,7 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, bcf_callaux_t *bca, int // calc_chisq_bias("XMQ", call->bcf_hdr->id[BCF_DT_CTG][call->tid].key, call->pos, bca->ref_mq, bca->alt_mq, bca->nqual); // calc_chisq_bias("XBQ", call->bcf_hdr->id[BCF_DT_CTG][call->tid].key, call->pos, bca->ref_bq, bca->alt_bq, bca->nqual); + call->nm = bca->nnm ? (float)bca->nm/bca->nnm : 0; if (bca->fmt_flag & B2B_INFO_ZSCORE) { // U z-normalised as +/- number of standard deviations from mean. if (call->ori_ref < 0) { // indel @@ -1140,6 +1143,7 @@ int bcf_call2bcf(bcf_call_t *bc, bcf1_t *rec, bcf_callret1_t *bcr, int fmt_flag, { if ( bc->vdb != HUGE_VAL ) bcf_update_info_float(hdr, rec, "VDB", &bc->vdb, 1); if ( bc->seg_bias != HUGE_VAL ) bcf_update_info_float(hdr, rec, "SGB", &bc->seg_bias, 1); + if ( bc->nm!=0 ) bcf_update_info_float(hdr, rec, "NM", &bc->nm, 1); if (bca->fmt_flag & B2B_INFO_ZSCORE) { if ( bc->mwu_pos != HUGE_VAL ) diff --git a/bam2bcf.h b/bam2bcf.h index 095f271ab..afaa77948 100644 --- a/bam2bcf.h +++ b/bam2bcf.h @@ -116,6 +116,8 @@ typedef struct __bcf_callaux_t { void *rghash; float indel_bias; // adjusts indel score threshold; lower => call more. int32_t *ref_nm, *alt_nm; // pointers to bcf_call_t.{ref_nm,alt_nm} + unsigned int nnm; + float nm; void *iaux; // auxiliary structure for --indels-2.0 calling char *chr; // current chromosome } bcf_callaux_t; @@ -155,7 +157,7 @@ typedef struct { int32_t *PL, *DP4, *ADR, *ADF, *SCR, *QS, *ref_nm, *alt_nm; uint8_t *fmt_arr; float vdb; // variant distance bias - float mwu_pos, mwu_mq, mwu_bq, mwu_mqs, mwu_sc, *mwu_nm; + float mwu_pos, mwu_mq, mwu_bq, mwu_mqs, mwu_sc, *mwu_nm, nm; #if CDF_MWU_TESTS float mwu_pos_cdf, mwu_mq_cdf, mwu_bq_cdf, mwu_mqs_cdf; #endif diff --git a/mpileup.c b/mpileup.c index 97452b989..a18635bb1 100644 --- a/mpileup.c +++ b/mpileup.c @@ -788,6 +788,7 @@ static int mpileup(mplp_conf_t *conf) bcf_hdr_append(conf->bcf_hdr,"##INFO="); bcf_hdr_append(conf->bcf_hdr,"##INFO="); bcf_hdr_append(conf->bcf_hdr,"##INFO="); + bcf_hdr_append(conf->bcf_hdr,"##INFO="); bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_FMT_NMBZ ) bcf_hdr_append(conf->bcf_hdr,"##FORMAT="); From 2f2d7640faaffe9ba8f57e46c7a2d723a72b56c5 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Wed, 14 Sep 2022 13:15:10 +0100 Subject: [PATCH 23/84] Attempt to reduce indel quality in problematic regions by counting badly matching reads as low quality reference reads. In the original code reads matching badly to any indel type or reference had indelQ set to 0 where thus effectively removed from calling. This leads to problems when there are many soft clipped reads and a few good matching indel reads (see noisy-softclips.bam in mpileup-tests). Only the few good quality indel reads would become visible to the caller and the indel is called with high quality. This commit changes the logic to make the badly matching reads low quality reference reads instead of removing them completely. The threshold was set to make the test case still be called as an indel, but with very low quality. --- bam2bcf.c | 9 +++++++-- bam2bcf_iaux.c | 35 ++++++++++++++++++++++++++++------- 2 files changed, 35 insertions(+), 9 deletions(-) diff --git a/bam2bcf.c b/bam2bcf.c index 6873274d4..4f8b7d8fe 100644 --- a/bam2bcf.c +++ b/bam2bcf.c @@ -256,7 +256,13 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t int ADF_ref_missed[4] = {0}; for (i = n = 0; i < _n; ++i) { const bam_pileup1_t *p = pl + i; - int q, b, mapQ, baseQ, is_diff, min_dist, seqQ; + int b; // the base or indel type + int q; // the base or indel quality used to calculate PL + int seqQ; // used to cap the indel quality given the sequence context + int mapQ; // to cap the quality for low MQ reads + int baseQ; // used only for supporting INFO annotations + int is_diff; // is this base or indel type different from the reference + int min_dist; // distance from the end, used for tail distance bias if ( bca->fmt_flag&(B2B_INFO_SCR|B2B_FMT_SCR) && PLP_HAS_SOFT_CLIP(&p->cd) ) r->SCR++; if (p->is_refskip || (p->b->core.flag&BAM_FUNMAP)) continue; if (p->is_del && !is_indel) continue; @@ -297,7 +303,6 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t if (_n > 20 && seqQ > 40) seqQ = 40; } baseQ = p->aux>>8&0xff; - is_diff = (b != 0); } else diff --git a/bam2bcf_iaux.c b/bam2bcf_iaux.c index 541d3ced9..2e0add15a 100644 --- a/bam2bcf_iaux.c +++ b/bam2bcf_iaux.c @@ -601,17 +601,38 @@ static int iaux_eval_scored_reads(indel_aux_t *iaux, int ismpl) // Reduce indelQ. High length-normalized alignment scores (i.e. bad alignments) // lower the quality more (e.g. gnuplot> plot [0:111] (1-x/111.)*255) - int adj_score = sc0 & 0xff; - int adj_indelQ = adj_score > 111 ? 0 : (int)((1. - adj_score/111.) * indelQ + .499); + int len_normQ = sc0 & 0xff; // length-normalized score of the best match (ref or alt) + int adj_indelQ; // final indelQ used in calling + if ( len_normQ > 111 ) + { + // In the original code reads matching badly to any indel type or reference had indelQ set to 0 + // here and thus would be effectively removed from calling. This leads to problems when there are + // many soft clipped reads and a few good matching indel reads (see noisy-softclips.bam in + // mpileup-tests). Only the few good quality indel reads would become visible to the caller and + // the indel would be called with high quality. Here we change the logic to make the badly matching + // reads low quality reference reads. The threshold was set to make the test case still be called + // as an indel, but with very low quality. + // + // Original code: + // adj_indelQ = 0; + // + adj_indelQ = 12; + j0 = iaux->iref_type; + } + else + adj_indelQ = (int)((1. - len_normQ/111.) * indelQ + .499); #if DEBUG_ALN - fprintf(stderr,"indelQ: %d (raw_indelQ=%d adj_score=%d; ref=%d alt=%d) j0=%d\t%s\n",adj_indelQ,indelQ,adj_score,ref_score,alt_score,j0,bam_get_qname(plp->b)); + // Prints the selected indel type (itype); adjusted indelQ which will be used if bigger than seqQ; + // raw indelQ; length-normalized indelQ and sequence context quality; ref and best alt indel type + // and their raw and length-normalized scores + fprintf(stderr,"itype=%d adj_indelQ=%d\trawQ=%d\tlen_normQ=%d\tseqQ=%d\tref:%d=%d/%d alt:%d=%d/%d)\t%s\n", + j0,adj_indelQ,indelQ,len_normQ,seqQ,iaux->iref_type,ref_score>>8,ref_score&0xff,alt_j,alt_score>>8,alt_score&0xff,bam_get_qname(plp->b)); #endif - if ( adj_indelQ > seqQ ) adj_indelQ = seqQ; // seqQ already capped at 255 + if ( adj_indelQ > seqQ ) adj_indelQ = seqQ; // seqQ already capped at 255 plp->aux = j0<<16 | seqQ<<8 | adj_indelQ; // use 22 bits in total iaux->sum_qual[j0] += adj_indelQ; - } return 0; } @@ -671,8 +692,8 @@ static int iaux_eval_best_indels(indel_aux_t *iaux) /* notes: - n .. number of samples - - the routine sets bam_pileup1_t.aux of each read as follows: - - 6: unused + - the routine sets bam_pileup1_t.aux (27 bits) of each read as follows: + - 5: unused - 6: the call; index to bcf_callaux_t.indel_types .. (aux>>16)&0x3f - 8: estimated sequence quality .. (aux>>8)&0xff - 8: indel quality .. aux&0xff From fdaf9c93ccb6da009c42d01bdc3590f29421fc7a Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Fri, 16 Sep 2022 15:02:01 +0100 Subject: [PATCH 24/84] Split the new NM annotation (e9d22b1f5d) into ref/alt counts, originally only alts were counted --- bam2bcf.c | 104 +++++++++++++++++++++++++++++++----------------------- bam2bcf.h | 6 ++-- mpileup.c | 4 +-- 3 files changed, 64 insertions(+), 50 deletions(-) diff --git a/bam2bcf.c b/bam2bcf.c index 4f8b7d8fe..0ff955e05 100644 --- a/bam2bcf.c +++ b/bam2bcf.c @@ -209,7 +209,9 @@ void bcf_callaux_clean(bcf_callaux_t *bca, bcf_call_t *call) memset(bca->alt_scl, 0, 100*sizeof(int)); memset(bca->iref_scl, 0, 100*sizeof(int)); memset(bca->ialt_scl, 0, 100*sizeof(int)); - bca->nnm = bca->nm = 0; + int i; + for (i=0; i<2; i++) bca->nnm[i] = 0; + for (i=0; i<2; i++) bca->nm[i] = 0; } /* @@ -265,30 +267,28 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t int min_dist; // distance from the end, used for tail distance bias if ( bca->fmt_flag&(B2B_INFO_SCR|B2B_FMT_SCR) && PLP_HAS_SOFT_CLIP(&p->cd) ) r->SCR++; if (p->is_refskip || (p->b->core.flag&BAM_FUNMAP)) continue; - if (p->is_del && !is_indel) continue; + + // The meaning of the indel related variables: + // is_indel .. is this position currently tested for an indel + // p->is_del .. is the current base a deletion in this read (unrelated to the tested indel) + // p->indel .. is there an indel starting after this position (i.e. does this read have the tested indel) + if (p->is_del && !is_indel) continue; // not testing an indel and the read has a spanning deletion + + int inm; + ++ori_depth; - if (is_indel) + if (is_indel) // testing an indel position { - b = p->aux>>16&0x3f; + b = p->aux>>16&0x3f; // indel type seqQ = q = (p->aux & 0xff); // mp2 + builtin indel-bias - if (q < bca->min_baseQ) - { - if (!p->indel && b < 4) - { - if (bam_is_rev(p->b)) - ADR_ref_missed[b]++; - else - ADF_ref_missed[b]++; - } - continue; - } + if ( !bca->indels_v20 ) { /* This heuristics was introduced by e4e161068 and claims to fix #1446. However, we obtain correct result on the provided test case even when this code is commented out, so this may not be needed anymore. Leaving it in only for backward compatibility for now. - See mpileup-tests homdel-issue-1446 and CHM1_CHM13_2.45x-1-1701408 that work only when + See mpileup-tests homdel-issue-1446 and CHM1_CHM13_2.45x-1-1701408 which work only when this code is disabled. */ if (p->indel == 0 && (q < _n/2 || _n > 20)) { @@ -302,8 +302,27 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t } if (_n > 20 && seqQ > 40) seqQ = 40; } + + is_diff = b ? 1 : 0; + inm = get_aux_nm(p->b,p->qpos,is_diff?0:1); + if ( inm>=0 ) + { + bca->nnm[is_diff]++; + bca->nm[is_diff] += inm; + } + + if (q < bca->min_baseQ) + { + if (!p->indel && b < 4) // not an indel read + { + if (bam_is_rev(p->b)) + ADR_ref_missed[b]++; + else + ADF_ref_missed[b]++; + } + continue; + } baseQ = p->aux>>8&0xff; - is_diff = (b != 0); } else { @@ -325,6 +344,12 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t baseQ = q; seqQ = 99; is_diff = (ref4 < 4 && b == ref4)? 0 : 1; + inm = get_aux_nm(p->b,p->qpos,is_diff?0:1); + if ( inm>=0 ) + { + bca->nnm[is_diff]++; + bca->nm[is_diff] += inm; + } } mapQ = p->b->core.qual < 255? p->b->core.qual : DEF_MAPQ; // special case for mapQ==255 if ( !mapQ ) r->mq0++; @@ -373,8 +398,6 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t } int imq = mapQ * nqual_over_60; int ibq = baseQ * nqual_over_60; - int inm = get_aux_nm(p->b,p->qpos,is_diff?0:1); - if ( is_diff ) { bca->nnm++; bca->nm += inm; } if ( bam_is_rev(p->b) ) bca->rev_mqs[imq]++; @@ -997,31 +1020,22 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, bcf_callaux_t *bca, int // calc_chisq_bias("XMQ", call->bcf_hdr->id[BCF_DT_CTG][call->tid].key, call->pos, bca->ref_mq, bca->alt_mq, bca->nqual); // calc_chisq_bias("XBQ", call->bcf_hdr->id[BCF_DT_CTG][call->tid].key, call->pos, bca->ref_bq, bca->alt_bq, bca->nqual); - call->nm = bca->nnm ? (float)bca->nm/bca->nnm : 0; if (bca->fmt_flag & B2B_INFO_ZSCORE) { // U z-normalised as +/- number of standard deviations from mean. if (call->ori_ref < 0) { // indel if (bca->fmt_flag & B2B_INFO_RPB) - call->mwu_pos = calc_mwu_biasZ(bca->iref_pos, bca->ialt_pos, - bca->npos, 0, 1); - call->mwu_mq = calc_mwu_biasZ(bca->iref_mq, bca->ialt_mq, - bca->nqual,1,1); + call->mwu_pos = calc_mwu_biasZ(bca->iref_pos, bca->ialt_pos, bca->npos, 0, 1); + call->mwu_mq = calc_mwu_biasZ(bca->iref_mq, bca->ialt_mq, bca->nqual,1,1); if ( bca->fmt_flag & B2B_INFO_SCB ) - call->mwu_sc = calc_mwu_biasZ(bca->iref_scl, bca->ialt_scl, - 100, 0,1); + call->mwu_sc = calc_mwu_biasZ(bca->iref_scl, bca->ialt_scl, 100, 0,1); } else { if (bca->fmt_flag & B2B_INFO_RPB) - call->mwu_pos = calc_mwu_biasZ(bca->ref_pos, bca->alt_pos, - bca->npos, 0, 1); - call->mwu_mq = calc_mwu_biasZ(bca->ref_mq, bca->alt_mq, - bca->nqual,1,1); - call->mwu_bq = calc_mwu_biasZ(bca->ref_bq, bca->alt_bq, - bca->nqual,0,1); - call->mwu_mqs = calc_mwu_biasZ(bca->fwd_mqs, bca->rev_mqs, - bca->nqual,0,1); + call->mwu_pos = calc_mwu_biasZ(bca->ref_pos, bca->alt_pos, bca->npos, 0, 1); + call->mwu_mq = calc_mwu_biasZ(bca->ref_mq, bca->alt_mq, bca->nqual,1,1); + call->mwu_bq = calc_mwu_biasZ(bca->ref_bq, bca->alt_bq, bca->nqual,0,1); + call->mwu_mqs = calc_mwu_biasZ(bca->fwd_mqs, bca->rev_mqs, bca->nqual,0,1); if ( bca->fmt_flag & B2B_INFO_SCB ) - call->mwu_sc = calc_mwu_biasZ(bca->ref_scl, bca->alt_scl, - 100, 0,1); + call->mwu_sc = calc_mwu_biasZ(bca->ref_scl, bca->alt_scl, 100, 0,1); } call->mwu_nm[0] = calc_mwu_biasZ(bca->ref_nm, bca->alt_nm, B2B_N_NM,0,1); if ( bca->fmt_flag & B2B_FMT_NMBZ ) @@ -1035,14 +1049,10 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, bcf_callaux_t *bca, int } else { // Old method; U as probability between 0 and 1 if ( bca->fmt_flag & B2B_INFO_RPB ) - call->mwu_pos = calc_mwu_biasZ(bca->ref_pos, bca->alt_pos, - bca->npos, 0, 0); - call->mwu_mq = calc_mwu_biasZ(bca->ref_mq, bca->alt_mq, - bca->nqual, 1, 0); - call->mwu_bq = calc_mwu_biasZ(bca->ref_bq, bca->alt_bq, - bca->nqual, 0, 0); - call->mwu_mqs = calc_mwu_biasZ(bca->fwd_mqs, bca->rev_mqs, - bca->nqual, 0, 0); + call->mwu_pos = calc_mwu_biasZ(bca->ref_pos, bca->alt_pos, bca->npos, 0, 0); + call->mwu_mq = calc_mwu_biasZ(bca->ref_mq, bca->alt_mq, bca->nqual, 1, 0); + call->mwu_bq = calc_mwu_biasZ(bca->ref_bq, bca->alt_bq, bca->nqual, 0, 0); + call->mwu_mqs = calc_mwu_biasZ(bca->fwd_mqs, bca->rev_mqs, bca->nqual, 0, 0); } #if CDF_MWU_TESTS @@ -1148,7 +1158,11 @@ int bcf_call2bcf(bcf_call_t *bc, bcf1_t *rec, bcf_callret1_t *bcr, int fmt_flag, { if ( bc->vdb != HUGE_VAL ) bcf_update_info_float(hdr, rec, "VDB", &bc->vdb, 1); if ( bc->seg_bias != HUGE_VAL ) bcf_update_info_float(hdr, rec, "SGB", &bc->seg_bias, 1); - if ( bc->nm!=0 ) bcf_update_info_float(hdr, rec, "NM", &bc->nm, 1); + if ( bca->nnm[0] || bca->nnm[1] ) + { + for (i=0; i<2; i++) bc->nm[i] = bca->nnm[i] ? bca->nm[i]/bca->nnm[i] : 0; + bcf_update_info_float(hdr, rec, "NM", bc->nm, 2); + } if (bca->fmt_flag & B2B_INFO_ZSCORE) { if ( bc->mwu_pos != HUGE_VAL ) diff --git a/bam2bcf.h b/bam2bcf.h index afaa77948..f295f2a91 100644 --- a/bam2bcf.h +++ b/bam2bcf.h @@ -116,8 +116,8 @@ typedef struct __bcf_callaux_t { void *rghash; float indel_bias; // adjusts indel score threshold; lower => call more. int32_t *ref_nm, *alt_nm; // pointers to bcf_call_t.{ref_nm,alt_nm} - unsigned int nnm; - float nm; + unsigned int nnm[2]; // number of nm observations + float nm[2]; // cumulative count of mismatches in ref and alt reads void *iaux; // auxiliary structure for --indels-2.0 calling char *chr; // current chromosome } bcf_callaux_t; @@ -157,7 +157,7 @@ typedef struct { int32_t *PL, *DP4, *ADR, *ADF, *SCR, *QS, *ref_nm, *alt_nm; uint8_t *fmt_arr; float vdb; // variant distance bias - float mwu_pos, mwu_mq, mwu_bq, mwu_mqs, mwu_sc, *mwu_nm, nm; + float mwu_pos, mwu_mq, mwu_bq, mwu_mqs, mwu_sc, *mwu_nm, nm[2]; #if CDF_MWU_TESTS float mwu_pos_cdf, mwu_mq_cdf, mwu_bq_cdf, mwu_mqs_cdf; #endif diff --git a/mpileup.c b/mpileup.c index a18635bb1..2d29bb7f6 100644 --- a/mpileup.c +++ b/mpileup.c @@ -788,8 +788,8 @@ static int mpileup(mplp_conf_t *conf) bcf_hdr_append(conf->bcf_hdr,"##INFO="); bcf_hdr_append(conf->bcf_hdr,"##INFO="); bcf_hdr_append(conf->bcf_hdr,"##INFO="); - bcf_hdr_append(conf->bcf_hdr,"##INFO="); - bcf_hdr_append(conf->bcf_hdr,"##INFO="); + bcf_hdr_append(conf->bcf_hdr,"##INFO="); + bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_FMT_NMBZ ) bcf_hdr_append(conf->bcf_hdr,"##FORMAT="); if ( conf->fmt_flag&B2B_INFO_SCB ) From 1eba45c22597e432940ec92ed372f466888ba5a3 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Sun, 18 Sep 2022 16:34:31 +0200 Subject: [PATCH 25/84] Add INFO/FIXREF annotation, add a new -m swap mode Resolves #1743 --- plugins/fixref.c | 176 ++++++++++++++++++++++++++++++++-------------- test/fixref.2.out | 13 ++-- test/fixref.3.out | 17 ++--- test/fixref.4.out | 13 ++-- test/fixref.5.out | 13 ++-- test/fixref.6.out | 13 ++-- test/fixref.7.out | 13 ++++ test/test.pl | 3 +- 8 files changed, 175 insertions(+), 86 deletions(-) create mode 100644 test/fixref.7.out diff --git a/plugins/fixref.c b/plugins/fixref.c index 94c2419f8..abb3367ea 100644 --- a/plugins/fixref.c +++ b/plugins/fixref.c @@ -88,12 +88,21 @@ #include #include "bcftools.h" -#define MODE_STATS 1 -#define MODE_TOP2FWD 2 -#define MODE_FLIP2FWD 3 -#define MODE_USE_ID 4 -#define MODE_REF_ALT 5 -#define MODE_FLIP_ALL 6 +#define MODE_STATS 1 +#define MODE_TOP2FWD 2 +#define MODE_FLIP2FWD 3 +#define MODE_USE_ID 4 +#define MODE_REF_ALT 5 +#define MODE_FLIP_ALL 6 +#define MODE_SWAP_REF_ALT 7 + +#define FIX_ERR (1<<0) +#define FIX_SKIP (1<<1) +#define FIX_NONE (1<<2) +#define FIX_FLIP (1<<3) +#define FIX_SWAP (1<<4) +#define FIX_GT (1<<5) +const char *info_annots[] = {"err","skip","none","flip","swap","GT"}; typedef struct { @@ -109,13 +118,16 @@ typedef struct { char *dbsnp_fname; int mode, discard; - bcf_hdr_t *hdr; + bcf_hdr_t *hdr_in, *hdr_out; faidx_t *fai; int rid, skip_rid; i2m_t *i2m; int32_t *gts, ngts, pos; - uint32_t nsite,nok,nflip,nunresolved,nswap,nflip_swap,nonSNP,nonACGT,nonbiallelic; + uint32_t nsite,nok,nflip,nunresolved,nswap,nflip_swap,nonSNP,nonACGT,nonbiallelic,nerr; uint32_t count[4][4], npos_err, unsorted; + uint32_t dirty; + kstring_t str; + char *info_tag; } args_t; @@ -132,12 +144,20 @@ const char *usage(void) "\n" "About: This tool helps to determine and fix strand orientation.\n" " Currently the following modes are recognised:\n" - " flip .. flip REF/ALT columns and GTs for non-ambiguous SNPs and ignore the rest\n" - " flip-all .. flip REF/ALT columns and GTs for all SNPs, including ambiguous (A/T, C/G) sites\n" - " id .. swap REF/ALT columns and GTs using the ID column to determine the REF allele\n" - " ref-alt .. swap REF/ALT columns to match the reference but not modify the genotypes\n" + " flip .. swap or flip REF/ALT columns and GTs for non-ambiguous SNPs and ignore the rest\n" + " flip-all .. swap or flip REF/ALT columns and GTs for all SNPs, including ambiguous (A/T, C/G) sites\n" + " id .. swap or flip REF/ALT columns and GTs using the ID column to determine the REF allele\n" + " ref-alt .. swap or flip REF/ALT columns to match the reference, do not modify the genotypes\n" " stats .. collect and print stats\n" + " swap .. swap REF/ALT columns to match the reference, do not modify the genotypes\n" " top .. convert from Illumina TOP strand to fwd\n" + " Each record is annotated with the INFO/FIXREF tag which records what change was made:\n" + " err .. the alleles are invalid and could not be repaired\n" + " skip .. the record was not considered at all (e.g. multiallelic or indel)\n" + " none .. the alleles were valid and no change was required\n" + " flip .. the REF and ALT alleles were flipped (e.g. A,C -> T,G)\n" + " swap .. the REF and ALT columns were swapped (e.g. A,C -> C,A)\n" + " GT .. FORMAT/GT was modified to reflect REF,ALT swap (e.g. 1/1 -> 0/0)\n" "\n" " WARNING: Do not use the program blindly, make an effort to\n" " understand what strand convention your data uses! Make sure\n" @@ -152,12 +172,13 @@ const char *usage(void) " run \"bcftools plugin\" for a list of common options\n" "\n" "Plugin options:\n" - " -d, --discard Discard sites which could not be resolved\n" - " -f, --fasta-ref Reference sequence\n" - " -i, --use-id Swap REF/ALT using the ID column to determine the REF allele, implies -m id.\n" - " Download the dbSNP file from\n" - " https://www.ncbi.nlm.nih.gov/variation/docs/human_variation_vcf\n" - " -m, --mode Collect stats (\"stats\") or convert (\"flip\", \"id\", \"ref-alt\", \"top\") [stats]\n" + " -d, --discard Discard sites which could not be resolved\n" + " -f, --fasta-ref FILE.fa Reference sequence\n" + " -i, --use-id FILE.vcf Swap REF/ALT using the ID column to determine the REF allele, implies -m id.\n" + " Download the dbSNP file from\n" + " https://www.ncbi.nlm.nih.gov/variation/docs/human_variation_vcf\n" + " -m, --mode STRING Collect statistics (\"stats\") or convert (see the list of modes above) [stats]\n" + " -t, --tag-name STRING The name of the INFO annotation to record what change was made [FIXREF]\n" "\n" "Examples:\n" " # run stats\n" @@ -178,19 +199,22 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out) { memset(&args,0,sizeof(args_t)); args.skip_rid = -1; - args.hdr = in; + args.hdr_in = in; + args.hdr_out = out; args.mode = MODE_STATS; + args.info_tag = "FIXREF"; char *ref_fname = NULL; static struct option loptions[] = { {"mode",required_argument,NULL,'m'}, + {"tag-name",required_argument,NULL,'t'}, {"discard",no_argument,NULL,'d'}, {"fasta-ref",required_argument,NULL,'f'}, {"use-id",required_argument,NULL,'i'}, {NULL,0,NULL,0} }; int c; - while ((c = getopt_long(argc, argv, "?hf:m:di:",loptions,NULL)) >= 0) + while ((c = getopt_long(argc, argv, "?hf:m:di:t:",loptions,NULL)) >= 0) { switch (c) { @@ -200,12 +224,14 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out) else if ( !strcasecmp(optarg,"flip-all") ) args.mode = MODE_FLIP_ALL; else if ( !strcasecmp(optarg,"id") ) args.mode = MODE_USE_ID; else if ( !strcasecmp(optarg,"ref-alt") ) args.mode = MODE_REF_ALT; + else if ( !strcasecmp(optarg,"swap") ) args.mode = MODE_SWAP_REF_ALT; else if ( !strcasecmp(optarg,"stats") ) args.mode = MODE_STATS; else error("The source strand convention not recognised: %s\n", optarg); break; case 'i': args.dbsnp_fname = optarg; args.mode = MODE_USE_ID; break; case 'd': args.discard = 1; break; case 'f': ref_fname = optarg; break; + case 't': args.info_tag = optarg; break; case 'h': case '?': default: error("%s", usage()); break; @@ -215,22 +241,24 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out) args.fai = fai_load(ref_fname); if ( !args.fai ) error("Failed to load the fai index: %s\n", ref_fname); + if ( bcf_hdr_printf(args.hdr_out,"##INFO=",args.info_tag) ) return -1; + if ( args.mode==MODE_STATS ) return 1; return 0; } -static bcf1_t *set_ref_alt(args_t *args, bcf1_t *rec, const char ref, const char alt, int swap) +static bcf1_t *set_ref_alt(args_t *args, bcf1_t *rec, const char ref, const char alt, int swap_gt) { rec->d.allele[0][0] = ref; rec->d.allele[1][0] = alt; rec->d.shared_dirty |= BCF1_DIRTY_ALS; - if ( !swap ) return rec; // only fix the alleles, leaving GTs unchanged + if ( !swap_gt ) return rec; // only fix the alleles, leaving GTs unchanged - int ngts = bcf_get_genotypes(args->hdr, rec, &args->gts, &args->ngts); + int ngts = bcf_get_genotypes(args->hdr_in, rec, &args->gts, &args->ngts); if ( ngts<=0 ) return rec; // no samples, no genotypes - int i, j, nsmpl = bcf_hdr_nsamples(args->hdr); + int i, j, nsmpl = bcf_hdr_nsamples(args->hdr_in); ngts /= nsmpl; for (i=0; ihdr,rec,args->gts,args->ngts); + bcf_update_genotypes(args->hdr_out,rec,args->gts,args->ngts); return rec; } @@ -264,16 +292,16 @@ static int fetch_ref(args_t *args, bcf1_t *rec) { // Get the reference allele int len; - char *ref = faidx_fetch_seq(args->fai, (char*)bcf_seqname(args->hdr,rec), rec->pos, rec->pos, &len); + char *ref = faidx_fetch_seq(args->fai, (char*)bcf_seqname(args->hdr_in,rec), rec->pos, rec->pos, &len); if ( !ref ) { - if ( faidx_has_seq(args->fai, bcf_seqname(args->hdr,rec))==0 ) + if ( faidx_has_seq(args->fai, bcf_seqname(args->hdr_in,rec))==0 ) { - fprintf(stderr,"Ignoring sequence \"%s\"\n", bcf_seqname(args->hdr,rec)); + fprintf(stderr,"Ignoring sequence \"%s\"\n", bcf_seqname(args->hdr_in,rec)); args->skip_rid = rec->rid; return -2; } - error("faidx_fetch_seq failed at %s:%"PRId64"\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1); + error("faidx_fetch_seq failed at %s:%"PRId64"\n", bcf_seqname(args->hdr_in,rec),(int64_t) rec->pos+1); } int ir = nt2int(*ref); free(ref); @@ -337,23 +365,25 @@ static bcf1_t *dbsnp_check(args_t *args, bcf1_t *rec, int ir, int ia, int ib) ref = kh_val(args->i2m, k).ref; if ( ref!=ir ) - error("Reference base mismatch at %s:%"PRId64" .. %c vs %c\n",bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1,int2nt(ref),int2nt(ir)); + error("Reference base mismatch at %s:%"PRId64" .. %c vs %c\n",bcf_seqname(args->hdr_in,rec),(int64_t) rec->pos+1,int2nt(ref),int2nt(ir)); - if ( ia==ref ) return rec; - if ( ib==ref ) { args->nswap++; return set_ref_alt(args,rec,int2nt(ib),int2nt(ia),1); } + if ( ia==ref ) { args->dirty = FIX_NONE; return rec; } + if ( ib==ref ) { args->dirty = FIX_SWAP; args->nswap++; return set_ref_alt(args,rec,int2nt(ib),int2nt(ia),1); } no_info: args->nunresolved++; return args->discard ? NULL : rec; } -bcf1_t *process(bcf1_t *rec) +static bcf1_t *process_record(bcf1_t *rec) { if ( rec->rid == args.skip_rid ) return NULL; bcf1_t *ret = args.mode==MODE_STATS ? NULL : rec; args.nsite++; + args.dirty = FIX_SKIP; + // Skip non-SNPs if ( bcf_get_variant_types(rec)!=VCF_SNP ) { @@ -409,7 +439,7 @@ bcf1_t *process(bcf1_t *rec) { args.pos = 0; args.rid = rec->rid; - dbsnp_init(&args,bcf_seqname(args.hdr,rec)); + dbsnp_init(&args,bcf_seqname(args.hdr_in,rec)); } ret = dbsnp_check(&args, rec, ir,ia,ib); if ( !args.unsorted && args.pos > rec->pos ) @@ -417,21 +447,31 @@ bcf1_t *process(bcf1_t *rec) fprintf(stderr, "Warning: corrected position(s) results in unsorted VCF, for example %s:%"PRId64" comes after %s:%d\n" " The command `bcftools sort` can be used to fix the order.\n", - bcf_seqname(args.hdr,rec),(int64_t) rec->pos+1,bcf_seqname(args.hdr,rec),args.pos); + bcf_seqname(args.hdr_in,rec),(int64_t) rec->pos+1,bcf_seqname(args.hdr_in,rec),args.pos); args.unsorted = 1; } args.pos = rec->pos; return ret; } - else if ( args.mode==MODE_REF_ALT ) // only change the REF/ALT column, leave the genotypes as is + if ( args.mode==MODE_REF_ALT ) // only change the REF/ALT column, leave the genotypes as is { - if ( ir==ia ) return ret; - if ( ir==ib ) { args.nswap++; return set_ref_alt(&args,rec,int2nt(ib),int2nt(ia),0); } - if ( ir==revint(ia) ) { args.nflip++; return set_ref_alt(&args,rec,int2nt(revint(ia)),int2nt(revint(ib)),0); } - if ( ir==revint(ib) ) { args.nflip_swap++; return set_ref_alt(&args,rec,int2nt(revint(ib)),int2nt(revint(ia)),0); } - error("FIXME: this should not happen %s:%"PRId64"\n", bcf_seqname(args.hdr,rec),(int64_t) rec->pos+1); + if ( ir==ia ) { args.dirty = FIX_NONE; return ret; } + if ( ir==ib ) { args.dirty = FIX_SWAP; args.nswap++; return set_ref_alt(&args,rec,int2nt(ib),int2nt(ia),0); } + if ( ir==revint(ia) ) { args.dirty = FIX_FLIP; args.nflip++; return set_ref_alt(&args,rec,int2nt(revint(ia)),int2nt(revint(ib)),0); } + if ( ir==revint(ib) ) { args.dirty = FIX_FLIP|FIX_SWAP; args.nflip_swap++; return set_ref_alt(&args,rec,int2nt(revint(ib)),int2nt(revint(ia)),0); } + args.dirty = FIX_ERR; + args.nerr++; + return ret; } - else if ( args.mode==MODE_FLIP2FWD || args.mode==MODE_FLIP_ALL ) + if ( args.mode==MODE_SWAP_REF_ALT ) // only swap the REF/ALT column but never flip, leave the genotypes as is + { + if ( ir==ia ) { args.dirty = FIX_NONE; return ret; } + if ( ir==ib ) { args.dirty = FIX_SWAP; args.nswap++; return set_ref_alt(&args,rec,int2nt(ib),int2nt(ia),0); } + args.dirty = FIX_ERR; + args.nerr++; + return ret; + } + if ( args.mode==MODE_FLIP2FWD || args.mode==MODE_FLIP_ALL ) { int pair = 1 << ia | 1 << ib; if ( args.mode==MODE_FLIP2FWD && (pair==0x9 || pair==0x6) ) // skip ambiguous pairs: A/T or C/G @@ -439,13 +479,15 @@ bcf1_t *process(bcf1_t *rec) args.nunresolved++; return args.discard ? NULL : ret; } - if ( ir==ia ) return ret; - if ( ir==ib ) { args.nswap++; return set_ref_alt(&args,rec,int2nt(ib),int2nt(ia),1); } - if ( ir==revint(ia) ) { args.nflip++; return set_ref_alt(&args,rec,int2nt(revint(ia)),int2nt(revint(ib)),0); } - if ( ir==revint(ib) ) { args.nflip_swap++; return set_ref_alt(&args,rec,int2nt(revint(ib)),int2nt(revint(ia)),1); } - error("FIXME: this should not happen %s:%"PRId64"\n", bcf_seqname(args.hdr,rec),(int64_t) rec->pos+1); + if ( ir==ia ) { args.dirty = FIX_NONE; return ret; } + if ( ir==ib ) { args.dirty = FIX_SWAP|FIX_GT; args.nswap++; return set_ref_alt(&args,rec,int2nt(ib),int2nt(ia),1); } + if ( ir==revint(ia) ) { args.dirty = FIX_FLIP; args.nflip++; return set_ref_alt(&args,rec,int2nt(revint(ia)),int2nt(revint(ib)),0); } + if ( ir==revint(ib) ) { args.dirty = FIX_FLIP|FIX_SWAP|FIX_GT; args.nflip_swap++; return set_ref_alt(&args,rec,int2nt(revint(ib)),int2nt(revint(ia)),1); } + args.dirty = FIX_ERR; + args.nerr++; + return ret; } - else if ( args.mode==MODE_TOP2FWD ) + if ( args.mode==MODE_TOP2FWD ) { int pair = 1 << ia | 1 << ib; if ( pair != 0x9 && pair != 0x6 ) // unambiguous pair: A/C or A/G @@ -455,25 +497,28 @@ bcf1_t *process(bcf1_t *rec) int ia_rev = revint(ia); if ( ir==ia_rev ) // vcfref is A, faref is T, flip { + args.dirty = FIX_FLIP; args.nflip++; return set_ref_alt(&args,rec,int2nt(ia_rev),int2nt(revint(ib)),0); } if ( ir==ib ) // vcfalt is faref, swap { + args.dirty = FIX_SWAP|FIX_GT; args.nswap++; return set_ref_alt(&args,rec,int2nt(ib),int2nt(ia),1); } - assert( ib==revint(ir) ); + if ( ib!=revint(ir) ) { args.dirty = FIX_ERR; args.nerr++; return ret; } + args.dirty = FIX_FLIP|FIX_SWAP|FIX_GT; args.nflip_swap++; return set_ref_alt(&args,rec,int2nt(revint(ib)),int2nt(revint(ia)),1); } else // ambiguous pair, sequence walking must be performed { int len, win = rec->pos > 100 ? 100 : rec->pos, beg = rec->pos - win, end = rec->pos + win; - char *ref = faidx_fetch_seq(args.fai, (char*)bcf_seqname(args.hdr,rec), beg,end, &len); - if ( !ref ) error("faidx_fetch_seq failed at %s:%"PRId64"\n", bcf_seqname(args.hdr,rec),(int64_t) rec->pos+1); - if ( end - beg + 1 != len ) error("FIXME: check win=%d,len=%d at %s:%"PRId64" (%d %d)\n", win,len, bcf_seqname(args.hdr,rec),(int64_t) rec->pos+1, end,beg); + char *ref = faidx_fetch_seq(args.fai, (char*)bcf_seqname(args.hdr_in,rec), beg,end, &len); + if ( !ref ) error("faidx_fetch_seq failed at %s:%"PRId64"\n", bcf_seqname(args.hdr_in,rec),(int64_t) rec->pos+1); + if ( end - beg + 1 != len ) error("FIXME: check win=%d,len=%d at %s:%"PRId64" (%d %d)\n", win,len, bcf_seqname(args.hdr_in,rec),(int64_t) rec->pos+1, end,beg); int i, mid = rec->pos - beg, strand = 0; for (i=1; i<=win; i++) @@ -490,9 +535,10 @@ bcf1_t *process(bcf1_t *rec) if ( strand==1 ) { - if ( ir==ia ) return ret; + if ( ir==ia ) { args.dirty = FIX_NONE; return ret; } if ( ir==ib ) { + args.dirty = FIX_SWAP|FIX_GT; args.nswap++; return set_ref_alt(&args,rec,int2nt(ib),int2nt(ia),1); } @@ -503,11 +549,13 @@ bcf1_t *process(bcf1_t *rec) int ib_rev = revint(ib); if ( ir==ia_rev ) { + args.dirty = FIX_FLIP; args.nflip++; return set_ref_alt(&args,rec,int2nt(ia_rev),int2nt(ib_rev),0); } if ( ir==ib_rev ) { + args.dirty = FIX_FLIP|FIX_SWAP|FIX_GT; args.nflip_swap++; return set_ref_alt(&args,rec,int2nt(ib_rev),int2nt(ia_rev),1); } @@ -520,6 +568,26 @@ bcf1_t *process(bcf1_t *rec) return ret; } +bcf1_t *process(bcf1_t *rec) +{ + args.dirty = 0; + bcf1_t *ret = process_record(rec); + if ( ret && args.dirty ) + { + args.str.l = 0; + int i; + for (i=0; i<6; i++) + { + if ( !(args.dirty & (1< ##contig= +##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT XY00001 -1 1 rs1 C T . . . GT 0/1 -1 2 rs2 T A . . . GT 0/1 -1 3 rs3 A T . . . GT 0/1 -1 4 rs4 A T . . . GT 0/1 -1 5 rs5 C T . . . GT 0/1 -1 6 rs6 C T . . . GT 0/1 +1 1 rs1 C T . . FIXREF=none GT 0/1 +1 2 rs2 T A . . FIXREF=swap GT 0/1 +1 3 rs3 A T . . FIXREF=none GT 0/1 +1 4 rs4 A T . . FIXREF=swap GT 0/1 +1 5 rs5 C T . . FIXREF=none GT 0/1 +1 6 rs6 C T . . FIXREF=swap GT 0/1 diff --git a/test/fixref.3.out b/test/fixref.3.out index 63b61574a..1cfcb2bac 100644 --- a/test/fixref.3.out +++ b/test/fixref.3.out @@ -9,12 +9,13 @@ ##contig= ##contig= ##contig= +##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE -1 11 rs1535632 A T . . . GT 1/1 -2 11 rs363334 C G . . . GT 0/0 -3 11 rs7101540 A T . . . GT 0/0 -4 11 rs7113791 A T . . . GT 1/1 -5 11 rs778833 C G . . . GT 1/1 -6 11 rs4933195 A T . . . GT 0/0 -7 11 rs903997 C G . . . GT 0/0 -8 11 rs1942968 C G . . . GT 1/1 +1 11 rs1535632 A T . . FIXREF=flip,swap,GT GT 1/1 +2 11 rs363334 C G . . FIXREF=none GT 0/0 +3 11 rs7101540 A T . . FIXREF=none GT 0/0 +4 11 rs7113791 A T . . FIXREF=flip,swap,GT GT 1/1 +5 11 rs778833 C G . . FIXREF=flip,swap,GT GT 1/1 +6 11 rs4933195 A T . . FIXREF=none GT 0/0 +7 11 rs903997 C G . . FIXREF=none GT 0/0 +8 11 rs1942968 C G . . FIXREF=flip,swap,GT GT 1/1 diff --git a/test/fixref.4.out b/test/fixref.4.out index 90b42de4d..a676d4336 100644 --- a/test/fixref.4.out +++ b/test/fixref.4.out @@ -3,10 +3,11 @@ ##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta ##FORMAT= ##contig= +##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT XY00001 -1 1 rs1 C T . . . GT 0/1 -1 2 rs2 T A . . . GT 1/0 -1 3 rs3 A T . . . GT 0/1 -1 4 rs4 A T . . . GT 1/0 -1 5 rs5 C T . . . GT 0/1 -1 6 rs6 C T . . . GT 1/0 +1 1 rs1 C T . . FIXREF=none GT 0/1 +1 2 rs2 T A . . FIXREF=swap GT 1/0 +1 3 rs3 A T . . FIXREF=none GT 0/1 +1 4 rs4 A T . . FIXREF=swap GT 1/0 +1 5 rs5 C T . . FIXREF=none GT 0/1 +1 6 rs6 C T . . FIXREF=swap GT 1/0 diff --git a/test/fixref.5.out b/test/fixref.5.out index ba96c52a1..70ac99a65 100644 --- a/test/fixref.5.out +++ b/test/fixref.5.out @@ -3,10 +3,11 @@ ##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta ##FORMAT= ##contig= +##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT XY00001 -1 1 rs1 C T . . . GT 0/1 -1 2 rs2 A T . . . GT 1/0 -1 3 rs3 A T . . . GT 0/1 -1 4 rs4 T A . . . GT 1/0 -1 5 rs5 C T . . . GT 0/1 -1 6 rs6 C T . . . GT 0/1 +1 1 rs1 C T . . FIXREF=none GT 0/1 +1 2 rs2 A T . . FIXREF=skip GT 1/0 +1 3 rs3 A T . . FIXREF=skip GT 0/1 +1 4 rs4 T A . . FIXREF=skip GT 1/0 +1 5 rs5 C T . . FIXREF=none GT 0/1 +1 6 rs6 C T . . FIXREF=swap,GT GT 0/1 diff --git a/test/fixref.6.out b/test/fixref.6.out index 6c1aaac40..a70f14ba9 100644 --- a/test/fixref.6.out +++ b/test/fixref.6.out @@ -3,10 +3,11 @@ ##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta ##FORMAT= ##contig= +##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT XY00001 -1 1 rs1 C T . . . GT 0/1 -1 2 rs2 T A . . . GT 0/1 -1 3 rs3 A T . . . GT 0/1 -1 4 rs4 A T . . . GT 0/1 -1 5 rs5 C T . . . GT 0/1 -1 6 rs6 C T . . . GT 0/1 +1 1 rs1 C T . . FIXREF=none GT 0/1 +1 2 rs2 T A . . FIXREF=swap,GT GT 0/1 +1 3 rs3 A T . . FIXREF=none GT 0/1 +1 4 rs4 A T . . FIXREF=swap,GT GT 0/1 +1 5 rs5 C T . . FIXREF=none GT 0/1 +1 6 rs6 C T . . FIXREF=swap,GT GT 0/1 diff --git a/test/fixref.7.out b/test/fixref.7.out new file mode 100644 index 000000000..a676d4336 --- /dev/null +++ b/test/fixref.7.out @@ -0,0 +1,13 @@ +##fileformat=VCFv4.2 +##FILTER= +##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta +##FORMAT= +##contig= +##INFO= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT XY00001 +1 1 rs1 C T . . FIXREF=none GT 0/1 +1 2 rs2 T A . . FIXREF=swap GT 1/0 +1 3 rs3 A T . . FIXREF=none GT 0/1 +1 4 rs4 A T . . FIXREF=swap GT 1/0 +1 5 rs5 C T . . FIXREF=none GT 0/1 +1 6 rs6 C T . . FIXREF=swap GT 1/0 diff --git a/test/test.pl b/test/test.pl index 4e50259e5..68381e7a7 100755 --- a/test/test.pl +++ b/test/test.pl @@ -565,7 +565,8 @@ run_test(\&test_vcf_plugin,$opts,in=>'fixref.3',out=>'fixref.3.out',cmd=>'+fixref',args=>'-- -f {PATH}/fixref.3.fa -m top'); run_test(\&test_vcf_plugin,$opts,in=>'fixref.2a',out=>'fixref.4.out',index=>['fixref.2b'],cmd=>'+fixref',args=>'-- -f {PATH}/norm.fa -m ref-alt'); run_test(\&test_vcf_plugin,$opts,in=>'fixref.2a',out=>'fixref.5.out',index=>['fixref.2b'],cmd=>'+fixref',args=>'-- -f {PATH}/norm.fa -m flip'); -run_test(\&test_vcf_plugin,$opts,in=>'fixref.2a',out=>'fixref.2.out',cmd=>'+fixref',args=>'-- -f {PATH}/norm.fa -m flip-all'); +run_test(\&test_vcf_plugin,$opts,in=>'fixref.2a',out=>'fixref.6.out',cmd=>'+fixref',args=>'-- -f {PATH}/norm.fa -m flip-all'); +run_test(\&test_vcf_plugin,$opts,in=>'fixref.2a',out=>'fixref.7.out',cmd=>'+fixref',args=>'-- -f {PATH}/norm.fa -m swap'); run_test(\&test_vcf_plugin,$opts,in=>'aa',out=>'aa.out',cmd=>'+fill-from-fasta',args=>'-- -f {PATH}/aa.fa -c AA -h {PATH}/aa.hdr -i \'TYPE="snp"\''); run_test(\&test_vcf_plugin,$opts,in=>'aa',out=>'aa.2.out',cmd=>'+fill-from-fasta',args=>'-- -f {PATH}/aa.fa -c REF -N'); run_test(\&test_vcf_plugin,$opts,in=>'ref',out=>'ref.out',cmd=>'+fill-from-fasta',args=>'-- -f {PATH}/norm.fa -c REF'); From 99f3988f685b73955359ce0a2fe818e613a493d9 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Tue, 20 Sep 2022 10:29:56 +0200 Subject: [PATCH 26/84] Fix a memory corruption bug with too many alleles passed to `-C alleles` via `-T` Resolves #1790 --- NEWS | 5 +++++ mcall.c | 33 +++++++++++---------------------- 2 files changed, 16 insertions(+), 22 deletions(-) diff --git a/NEWS b/NEWS index d7ae94373..f50143cc0 100644 --- a/NEWS +++ b/NEWS @@ -6,6 +6,11 @@ Changes affecting specific commands: - Support sample reordering of annotation file ( #1785) +* bcftools call + + - Fix a bug where too many alleles passed to `-C alleles` via `-T` caused memory + corruption (#1790) + * bcftools query - Fix a rare bug where the printing of SAMPLE field with `query` was incorrectly diff --git a/mcall.c b/mcall.c index 57618961b..804ff0131 100644 --- a/mcall.c +++ b/mcall.c @@ -1,6 +1,6 @@ /* mcall.c -- multiallelic and rare variant calling. - Copyright (C) 2012-2021 Genome Research Ltd. + Copyright (C) 2012-2022 Genome Research Ltd. Author: Petr Danecek @@ -314,7 +314,7 @@ static void init_sample_groups(call_t *call) while ( *ptr && isspace(*ptr) ) ptr++; if ( !*ptr ) error("Could not parse the line in %s, expected a sample name followed by tab and a population name: %s\n",call->sample_groups,lines[i]); *tmp = 0; - int ismpl = bcf_hdr_id2int(call->hdr, BCF_DT_SAMPLE, lines[i]); + int ismpl = bcf_hdr_id2int(call->hdr, BCF_DT_SAMPLE, lines[i]); if ( ismpl<0 ) continue; if ( smpl2grp[ismpl] ) error("Error: the sample \"%s\" is listed twice in %s\n", lines[i],call->sample_groups); if ( !khash_str2int_has_key(grp2idx,ptr+1) ) @@ -336,7 +336,7 @@ static void init_sample_groups(call_t *call) { if ( !smpl2grp[i] ) error("Error: The sample \"%s\" is not listed in %s\n",call->hdr->samples[i],call->sample_groups); int igrp = smpl2grp[i] - 1; - if ( !call->smpl_grp[igrp].nsmpl ) + if ( !call->smpl_grp[igrp].nsmpl ) call->smpl_grp[igrp].smpl = (uint32_t*)calloc(grp2n[igrp],sizeof(uint32_t)); call->smpl_grp[igrp].smpl[call->smpl_grp[igrp].nsmpl] = i; call->smpl_grp[igrp].nsmpl++; @@ -745,7 +745,7 @@ static void mcall_set_ref_genotypes(call_t *call, int nals_ori) static void mcall_call_genotypes(call_t *call, int nals_ori, smpl_grp_t *grp) { int ia, ib, i; - int ngts_ori = nals_ori*(nals_ori+1)/2; + int ngts_ori = nals_ori*(nals_ori+1)/2; int ngts_new = call->nals_new*(call->nals_new+1)/2; int nsmpl = grp->nsmpl; @@ -1271,8 +1271,9 @@ void mcall_trim_and_update_numberR(call_t *call, bcf1_t *rec, int nals_ori, int static int mcall_constrain_alleles(call_t *call, bcf1_t *rec, int *unseen) { assert( call->tgt_als->n ); - if ( call->tgt_als->n>5 ) error("Maximum accepted number of alleles is 5, got %d\n", call->tgt_als->n); hts_expand(char*,call->tgt_als->n+1,call->nals,call->als); + hts_expand(int,call->tgt_als->n+1,call->nals_map,call->als_map); + hts_expand(int,(call->tgt_als->n+1)*(call->tgt_als->n+2)/2,call->npl_map,call->pl_map); int has_new = 0; @@ -1290,18 +1291,6 @@ static int mcall_constrain_alleles(call_t *call, bcf1_t *rec, int *unseen) { call->als[nals] = call->tgt_als->allele[i]; j = vcmp_find_allele(call->vcmp, rec->d.allele+1, rec->n_allele - 1, call->tgt_als->allele[i]); - - // if ( j+1==*unseen ) - // { - // fprintf(stderr,"Fixme? Cannot constrain to %d-th allele (%s); j=%d,unseen=%d. VCF=",i,call->tgt_als->allele[i],j,*unseen); - // int k; - // for (k=0; kn_allele; k++) fprintf(stderr,"%s%s",k==0?"":",",rec->d.allele[k]); - // fprintf(stderr,"\tTAB="); - // for (k=0; ktgt_als->n; k++) fprintf(stderr,"%s%s",k==0?"":",",call->tgt_als->allele[k]); - // fprintf(stderr,"\n"); - // return -1; - // } - if ( j>=0 ) { // existing allele @@ -1537,9 +1526,9 @@ int mcall(call_t *call, bcf1_t *rec) bcf_update_info_int32(call->hdr, rec, "QS", NULL, 0); // remove QS tag if ( nals_ori > 8*sizeof(call->als_new) ) - { + { fprintf(stderr,"Too many alleles at %s:%"PRId64", skipping.\n", bcf_seqname(call->hdr,rec),(int64_t) rec->pos+1); - return 0; + return 0; } // For each group find the best combination of alleles @@ -1596,9 +1585,9 @@ int mcall(call_t *call, bcf1_t *rec) for (i=0; inals_new; i++) call->ac[i] = 0; if ( call->flag & CALL_CONSTR_TRIO && call->nals_new>4 ) - { + { fprintf(stderr,"Too many alleles at %s:%"PRId64", skipping.\n", bcf_seqname(call->hdr,rec),(int64_t) rec->pos+1); - return 0; + return 0; } if ( call->output_tags & (CALL_FMT_GQ|CALL_FMT_GP) ) { @@ -1670,7 +1659,7 @@ int mcall(call_t *call, bcf1_t *rec) anno16_t a; float tmpf[4]; int is_tested = test16(call->anno16, &a) >= 0 && a.is_tested ? 1 : 0; - if ( is_tested ) + if ( is_tested ) { for (i=0; i<4; i++) tmpf[i] = a.p[i]; bcf_update_info_float(call->hdr, rec, "PV4", tmpf, 4); From 518c819571d44abe77aa18684ce314c25270a657 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Wed, 21 Sep 2022 17:24:00 +0200 Subject: [PATCH 27/84] Sanitize VEP field names to enforce VCF conventions as in htslib/bcf_hrec_check. Fixes #1795 --- plugins/split-vep.c | 33 +++++++++++++++++++++++---------- 1 file changed, 23 insertions(+), 10 deletions(-) diff --git a/plugins/split-vep.c b/plugins/split-vep.c index 08955970a..b8dc9d9f4 100644 --- a/plugins/split-vep.c +++ b/plugins/split-vep.c @@ -407,29 +407,42 @@ static const uint8_t valid_tag[256] = 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }; -static void sanitize_field_name(char *fmt) +static char *sanitize_field_name(const char *str) { - while ( *fmt ) + if ( !strcmp(str,"1000G") ) return strdup(str); + char *tmp; + if ( str[0]=='.' || (str[0]>='0' && str[0]<='9') ) + { + // the field starts with an invalid character, prefix with underscore + int len = 1 + strlen(str); + tmp = (char*)malloc(len+1); + tmp[0] = '_'; + memcpy(tmp+1,str,len); + } + else tmp = strdup(str); + char *out = tmp; + while ( *tmp ) { - if ( !valid_tag[(uint8_t)*fmt] ) *fmt = '_'; - fmt++; + if ( !valid_tag[(uint8_t)*tmp] ) *tmp = '_'; + tmp++; } + return out; } char *strdup_annot_prefix(args_t *args, const char *str) { char *out; if ( !args->annot_prefix ) { - out = strdup(str); - sanitize_field_name(out); + out = sanitize_field_name(str); return out; } int str_len = strlen(str); int prefix_len = strlen(args->annot_prefix); - out = calloc(str_len+prefix_len+1,1); - memcpy(out,args->annot_prefix,prefix_len); - memcpy(out+prefix_len,str,str_len); - sanitize_field_name(out); + char *tmp = calloc(str_len+prefix_len+1,1); + memcpy(tmp,args->annot_prefix,prefix_len); + memcpy(tmp+prefix_len,str,str_len); + out = sanitize_field_name(tmp); + free(tmp); return out; } static void init_data(args_t *args) From bc635c014c162fe29ea1d7b424cce58595f6449c Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Thu, 22 Sep 2022 15:42:08 +0100 Subject: [PATCH 28/84] Experimental filtering annotation MIN_PL_SUM, roughly corresponds to phred-scaled product of sample genotype likelihoods --- bam2bcf.c | 4 ++++ bam2bcf.h | 3 ++- mpileup.c | 1 + 3 files changed, 7 insertions(+), 1 deletion(-) diff --git a/bam2bcf.c b/bam2bcf.c index 0ff955e05..b4e0c4a86 100644 --- a/bam2bcf.c +++ b/bam2bcf.c @@ -359,6 +359,8 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t if (q > 63) q = 63; if (q < 4) q = 4; // MQ=0 reads count as BQ=4 bca->bases[n++] = q<<5 | (int)bam_is_rev(p->b)<<4 | b; + //if (is_indel) fprintf(stderr,"xx:base,q,strand\t%d\t%d\t%d\n",b,q,bam_is_rev(p->b)?0:1); + // collect annotations if (b < 4) { @@ -997,6 +999,7 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, bcf_callaux_t *bca, int } // if (ref_base < 0) fprintf(stderr, "%d,%d,%f,%d\n", call->n_alleles, x, sum_min, call->unseen); + // fprintf(stderr,"sum_min=%f\n",sum_min); call->shift = (int)(sum_min + .499); } // combine annotations @@ -1153,6 +1156,7 @@ int bcf_call2bcf(bcf_call_t *bc, bcf1_t *rec, bcf_callret1_t *bcr, int fmt_flag, for (i=0; i<16; i++) tmpf[i] = bc->anno[i]; bcf_update_info_float(hdr, rec, "I16", tmpf, 16); bcf_update_info_float(hdr, rec, "QS", bc->qsum, nals); + bcf_update_info_int32(hdr, rec, "MIN_PL_SUM", &bc->shift, 1); if ( has_alt ) { diff --git a/bam2bcf.h b/bam2bcf.h index f295f2a91..67bda58b3 100644 --- a/bam2bcf.h +++ b/bam2bcf.h @@ -150,7 +150,8 @@ typedef struct { bcf_hdr_t *bcf_hdr; int a[5]; // alleles: ref, alt, alt2, alt3 float qsum[B2B_MAX_ALLELES]; // INFO/QS tag - int n, n_alleles, shift, ori_ref, unseen; + int n, n_alleles, ori_ref, unseen; + int32_t shift; // shift is the sum of min_PL before normalization to 0 across all samples int n_supp; // number of supporting non-reference reads double anno[16]; unsigned int depth, ori_depth, mq0; diff --git a/mpileup.c b/mpileup.c index 2d29bb7f6..3fe0a16e5 100644 --- a/mpileup.c +++ b/mpileup.c @@ -788,6 +788,7 @@ static int mpileup(mplp_conf_t *conf) bcf_hdr_append(conf->bcf_hdr,"##INFO="); bcf_hdr_append(conf->bcf_hdr,"##INFO="); bcf_hdr_append(conf->bcf_hdr,"##INFO="); + bcf_hdr_append(conf->bcf_hdr,"##INFO="); bcf_hdr_append(conf->bcf_hdr,"##INFO="); bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_FMT_NMBZ ) From be80c5a9950cecfab8559365c5acd1826955f6da Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Fri, 30 Sep 2022 16:32:35 +0200 Subject: [PATCH 29/84] New -H option to print header with -f. Resolves #1798 --- plugins/split-vep.c | 15 ++++++++++++++- test/split-vep.12.2.out | 8 ++++++++ test/test.pl | 1 + 3 files changed, 23 insertions(+), 1 deletion(-) create mode 100644 test/split-vep.12.2.out diff --git a/plugins/split-vep.c b/plugins/split-vep.c index b8dc9d9f4..7aa96b765 100644 --- a/plugins/split-vep.c +++ b/plugins/split-vep.c @@ -117,6 +117,7 @@ typedef struct int ncolumn2type; int raw_vep_request; // raw VEP tag requested and will need subsetting int allow_undef_tags; + int print_header; } args_t; @@ -197,6 +198,7 @@ static const char *usage_text(void) " -d, --duplicate Output per transcript/allele consequences on a new line rather rather than\n" " as comma-separated fields on a single line\n" " -f, --format STR Create non-VCF output; similar to `bcftools query -f` but drops lines w/o consequence\n" + " -H, --print-header Print header\n" " -l, --list Parse the VCF header and list the annotation fields\n" " -p, --annot-prefix STR Before doing anything else, prepend STR to all CSQ fields to avoid tag name conflicts\n" " -s, --select TR:CSQ Select transcripts to extract by type and/or consequence severity. (See also -S and -x.)\n" @@ -1120,7 +1122,7 @@ int run(int argc, char **argv) }; int c; char *tmp; - while ((c = getopt_long(argc, argv, "o:O:i:e:r:R:t:T:lS:s:c:p:a:f:dA:xu",loptions,NULL)) >= 0) + while ((c = getopt_long(argc, argv, "o:O:i:e:r:R:t:T:lS:s:c:p:a:f:dA:xuH",loptions,NULL)) >= 0) { switch (c) { @@ -1131,6 +1133,7 @@ int run(int argc, char **argv) else if ( !strcasecmp(optarg,"space") ) args->all_fields_delim = " "; else args->all_fields_delim = optarg; break; + case 'H': args->print_header = 1; break; case 'x': args->drop_sites = 1; break; case 'd': args->duplicate = 1; break; case 'f': args->format_str = strdup(optarg); break; @@ -1184,6 +1187,7 @@ int run(int argc, char **argv) } } if ( args->drop_sites && args->format_str ) error("Error: the -x behavior is the default (and only supported) with -f\n"); + if ( args->print_header && !args->format_str ) error("Error: the -H header printing is supported only with -f\n"); if ( args->all_fields_delim && !args->format_str ) error("Error: the -A option must be used with -f\n"); if ( args->severity && (!strcmp("?",args->severity) || !strcmp("-",args->severity)) ) error("%s", default_severity()); if ( args->column_types && !strcmp("-",args->column_types) ) error("%s", default_column_types()); @@ -1210,7 +1214,16 @@ int run(int argc, char **argv) } if ( args->format_str ) + { args->fh_bgzf = bgzf_open(args->output_fname, args->output_type&FT_GZ ? "wg" : "wu"); + if ( args->print_header ) + { + args->kstr.l = 0; + convert_header(args->convert,&args->kstr); + if ( args->kstr.l && bgzf_write(args->fh_bgzf, args->kstr.s, args->kstr.l)!=args->kstr.l ) + error("Failed to write to %s\n", args->output_fname); + } + } else { char wmode[8]; diff --git a/test/split-vep.12.2.out b/test/split-vep.12.2.out new file mode 100644 index 000000000..60a8c1996 --- /dev/null +++ b/test/split-vep.12.2.out @@ -0,0 +1,8 @@ +# [1]POS [2]Allele [3]Consequence [4]IMPACT [5]SYMBOL [6]Gene [7]Feature_type [8]Feature [9]BIOTYPE [10]EXON [11]INTRON [12]HGVSc [13]HGVSp [14]cDNA_position [15]CDS_position [16]Protein_position [17]Amino_acids [18]Codons [19]Existing_variation [20]ALLELE_NUM [21]DISTANCE [22]STRAND [23]FLAGS [24]VARIANT_CLASS [25]SYMBOL_SOURCE [26]HGNC_ID [27]CANONICAL [28]TSL [29]APPRIS [30]CCDS [31]ENSP [32]SWISSPROT [33]TREMBL [34]UNIPARC [35]SOURCE [36]GENE_PHENO [37]SIFT [38]PolyPhen [39]DOMAINS [40]miRNA [41]HGVS_OFFSET [42]AF [43]AFR_AF [44]AMR_AF [45]EAS_AF [46]EUR_AF [47]SAS_AF [48]AA_AF [49]EA_AF [50]gnomAD_AF [51]gnomAD_AFR_AF [52]gnomAD_AMR_AF [53]gnomAD_ASJ_AF [54]gnomAD_EAS_AF [55]gnomAD_FIN_AF [56]gnomAD_NFE_AF [57]gnomAD_OTH_AF [58]gnomAD_SAS_AF [59]MAX_AF [60]MAX_AF_POPS [61]CLIN_SIG [62]SOMATIC [63]PHENO [64]PUBMED [65]MOTIF_NAME [66]MOTIF_POS [67]HIGH_INF_POS [68]MOTIF_SCORE_CHANGE [69]LoF [70]LoF_filter [71]LoF_flags [72]LoF_info [73]CADD_PHRED [74]CADD_RAW [75]gnomAD2.1 [76]gnomAD2.1_AF_raw [77]gnomAD2.1_AF_popmax [78]gnomAD2.1_AF_afr [79]gnomAD2.1_AF_amr [80]gnomAD2.1_AF_asj [81]gnomAD2.1_AF_eas [82]gnomAD2.1_AF_fin [83]gnomAD2.1_AF_nfe [84]gnomAD2.1_AF_oth [85]gnomAD2.1_AF_sas +14464 T non_coding_transcript_exon_variant MODIFIER WASH7P ENSG00000227232 Transcript ENST00000423562 unprocessed_pseudogene 10/10 . ENST00000423562.1:n.1568T>A . 1568 . . . . rs546169444 1 . -1 . SNV HGNC 38034 . . . . . . . . . . . . . . . 0.0958 0.0144 0.1138 0.005 0.1859 0.1943 . . . . . . . . . . . 0.1943 SAS . . . . . . . . . . . . . . . . . . . . . . . . . +14464 T non_coding_transcript_exon_variant MODIFIER WASH7P ENSG00000227232 Transcript ENST00000438504 unprocessed_pseudogene 12/12 . ENST00000438504.2:n.1682T>A . 1682 . . . . rs546169444 1 . -1 . SNV HGNC 38034 YES . . . . . . . . . . . . . . 0.0958 0.0144 0.1138 0.005 0.1859 0.1943 . . . . . . . . . . . 0.1943 SAS . . . . . . . . . . . . . . . . . . . . . . . . . +14464 T downstream_gene_variant MODIFIER DDX11L1 ENSG00000223972 Transcript ENST00000456328 processed_transcript . . . . . . . . . rs546169444 1 55 1 . SNV HGNC 37102 YES . . . . . . . . . . . . . . 0.0958 0.0144 0.1138 0.005 0.1859 0.1943 . . . . . . . . . . . 0.1943 SAS . . . . . . . . . . . . . . . . . . . . . . . . . +14464 T non_coding_transcript_exon_variant MODIFIER WASH7P ENSG00000227232 Transcript ENST00000488147 unprocessed_pseudogene 11/11 . ENST00000488147.1:n.1291T>A . 1291 . . . . rs546169444 1 . -1 . SNV HGNC 38034 . . . . . . . . . . . . . . . 0.0958 0.0144 0.1138 0.005 0.1859 0.1943 . . . . . . . . . . . 0.1943 SAS . . . . . . . . . . . . . . . . . . . . . . . . . +14464 T non_coding_transcript_exon_variant MODIFIER WASH7P ENSG00000227232 Transcript ENST00000538476 unprocessed_pseudogene 13/13 . ENST00000538476.1:n.1530T>A . 1530 . . . . rs546169444 1 . -1 . SNV HGNC 38034 . . . . . . . . . . . . . . . 0.0958 0.0144 0.1138 0.005 0.1859 0.1943 . . . . . . . . . . . 0.1943 SAS . . . . . . . . . . . . . . . . . . . . . . . . . +14464 T non_coding_transcript_exon_variant MODIFIER WASH7P ENSG00000227232 Transcript ENST00000541675 unprocessed_pseudogene 9/9 . ENST00000541675.1:n.1315T>A . 1315 . . . . rs546169444 1 . -1 . SNV HGNC 38034 . . . . . . . . . . . . . . . 0.0958 0.0144 0.1138 0.005 0.1859 0.1943 . . . . . . . . . . . 0.1943 SAS . . . . . . . . . . . . . . . . . . . . . . . . . +14464 T regulatory_region_variant MODIFIER . . RegulatoryFeature ENSR00000000002 open_chromatin_region . . . . . . . . . rs546169444 1 . . . SNV . . . . . . . . . . . . . . . . . 0.0958 0.0144 0.1138 0.005 0.1859 0.1943 . . . . . . . . . . . 0.1943 SAS . . . . . . . . . . . . . . . . . . . . . . . . . diff --git a/test/test.pl b/test/test.pl index 68381e7a7..9709b0432 100755 --- a/test/test.pl +++ b/test/test.pl @@ -620,6 +620,7 @@ run_test(\&test_vcf_plugin,$opts,in=>'split-vep',out=>'split-vep.10.out',cmd=>'+split-vep',args=>qq[-t 1:14464 -f '%POS\\t%CANONICAL\\t%Consequence\\n' -d]); run_test(\&test_vcf_plugin,$opts,in=>'split-vep',out=>'split-vep.11.out',cmd=>'+split-vep',args=>qq[-t 1:14464 -f '%POS\\t%CSQ\\n' -A tab]); run_test(\&test_vcf_plugin,$opts,in=>'split-vep',out=>'split-vep.12.out',cmd=>'+split-vep',args=>qq[-t 1:14464 -f '%POS\\t%CSQ\\n' -A tab -d]); +run_test(\&test_vcf_plugin,$opts,in=>'split-vep',out=>'split-vep.12.2.out',cmd=>'+split-vep',args=>qq[-t 1:14464 -f '%POS\\t%CSQ\\n' -A tab -d -H]); run_test(\&test_vcf_plugin,$opts,in=>'split-vep.4',out=>'split-vep.13.out',cmd=>'+split-vep',args=>qq[-f '%POS\\t%BCSQ\\n' -a BCSQ -A tab -d]); run_test(\&test_vcf_plugin,$opts,in=>'split-vep',out=>'split-vep.14.out',cmd=>'+split-vep',args=>qq[-c gnomAD_NFE_AF:real,ALLELE_NUM:int | $$opts{bin}/bcftools query -f'%POS\\t%gnomAD_NFE_AF\\t%ALLELE_NUM\\n']); run_test(\&test_vcf_plugin,$opts,in=>'split-vep',out=>'split-vep.14.out',cmd=>'+split-vep',args=>qq[-c gnomAD_NFE_AF,ALLELE_NUM | $$opts{bin}/bcftools query -f'%POS\\t%gnomAD_NFE_AF\\t%ALLELE_NUM\\n']); From e11d999bf9881f780b2cb49c8ed6486787a6bc64 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Sat, 8 Oct 2022 11:12:03 +0100 Subject: [PATCH 30/84] Check failed memory alloc in `sort`. Resolves #1801 --- vcfsort.c | 22 ++++++++++++---------- 1 file changed, 12 insertions(+), 10 deletions(-) diff --git a/vcfsort.c b/vcfsort.c index a8052d03d..1de2b2867 100644 --- a/vcfsort.c +++ b/vcfsort.c @@ -1,19 +1,19 @@ /* vcfsort.c -- sort subcommand - Copyright (C) 2017-2021 Genome Research Ltd. + Copyright (C) 2017-2022 Genome Research Ltd. Author: Petr Danecek - + Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: - + The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. - + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE @@ -77,7 +77,7 @@ void clean_files(args_t *args) unlink(blk->fname); free(blk->fname); } - if ( blk->rec ) + if ( blk->rec ) bcf_destroy(blk->rec); } rmdir(args->tmp_dir); @@ -107,7 +107,7 @@ int cmp_bcf_pos(const void *aptr, const void *bptr) int i; for (i=0; in_allele; i++) - { + { if ( i >= b->n_allele ) return 1; int ret = strcasecmp(a->d.allele[i],b->d.allele[i]); if ( ret ) return ret; @@ -124,6 +124,7 @@ void buf_flush(args_t *args) args->nblk++; args->blk = (blk_t*) realloc(args->blk, sizeof(blk_t)*args->nblk); + if ( !args->blk ) error("Error: could not allocate %zu bytes of memory, try reducing --max-mem\n",sizeof(blk_t)*args->nblk); blk_t *blk = args->blk + args->nblk - 1; kstring_t str = {0,0,0}; @@ -135,7 +136,7 @@ void buf_flush(args_t *args) htsFile *fh = hts_open(blk->fname, "wbu"); if ( fh == NULL ) clean_files_and_throw(args, "Cannot write %s: %s\n", blk->fname, strerror(errno)); if ( bcf_hdr_write(fh, args->hdr)!=0 ) clean_files_and_throw(args, "[%s] Error: cannot write to %s\n", __func__,blk->fname); - + int i; for (i=0; inbuf; i++) { @@ -226,7 +227,7 @@ void buf_push(args_t *args, bcf1_t *rec) bcf_destroy(rec); } -void sort_blocks(args_t *args) +void sort_blocks(args_t *args) { htsFile *in = hts_open(args->fname, "r"); if ( !in ) clean_files_and_throw(args, "Could not read %s\n", args->fname); @@ -278,7 +279,7 @@ void blk_read(args_t *args, khp_blk_t *bhp, bcf_hdr_t *hdr, blk_t *blk) khp_insert(blk, bhp, &blk); } -void merge_blocks(args_t *args) +void merge_blocks(args_t *args) { fprintf(stderr,"Merging %d temporary files\n", (int)args->nblk); khp_blk_t *bhp = khp_init(blk); @@ -336,7 +337,7 @@ static void usage(args_t *args) exit(1); } -size_t parse_mem_string(const char *str) +size_t parse_mem_string(const char *str) { char *tmp; double mem = strtod(str, &tmp); @@ -352,6 +353,7 @@ static void init(args_t *args) { args->max_mem *= 0.9; args->mem_block = malloc(args->max_mem); + if ( !args->mem_block ) error("Error: could not allocate %zu bytes of memory, try reducing --max-mem\n",args->max_mem); args->mem = 0; args->tmp_dir = init_tmp_prefix(args->tmp_dir); From 87bf15961b0dcb89ff623d2aef1eedf9063157bd Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Tue, 11 Oct 2022 14:51:43 +0100 Subject: [PATCH 31/84] Add new `--new-gt X` option. Resolves #1800 --- NEWS | 4 +++ plugins/setGT.c | 68 ++++++++++++++++++++++++++++++++++++---------- test/setGT.5.1.out | 8 ++++++ test/setGT.5.vcf | 7 +++++ test/test.pl | 1 + 5 files changed, 74 insertions(+), 14 deletions(-) create mode 100644 test/setGT.5.1.out create mode 100644 test/setGT.5.vcf diff --git a/NEWS b/NEWS index f50143cc0..fdb2238c5 100644 --- a/NEWS +++ b/NEWS @@ -17,6 +17,10 @@ Changes affecting specific commands: suppressed when the `-e` option contained a sample expression while the formatting query did not. See #1783 for details. +* bcftools +setGT + + - Add new `--new-gt X` option (#1800) + * bcftools +trio-dnm2 - New -n, --strictly-novel option to downplay alleles which violate Mendelian diff --git a/plugins/setGT.c b/plugins/setGT.c index d55d7287d..a3b3f3032 100644 --- a/plugins/setGT.c +++ b/plugins/setGT.c @@ -48,7 +48,7 @@ static int cmp_gt(double a, double b) { return a>b ? 1 : 0; } typedef struct { bcf_hdr_t *in_hdr, *out_hdr; - int32_t *gts, mgts, *iarr, miarr; + int32_t *gts, mgts, *iarr, miarr, *xarr, mxarr; int *arr, marr; uint64_t nchanged; int tgt_mask, new_mask, new_gt; @@ -79,6 +79,7 @@ args_t *args = NULL; #define GT_BINOM (1<<8) #define GT_MINOR (1<<9) #define GT_CUSTOM (1<<10) +#define GT_X_VAF (1<<11) #define MINOR_ALLELE -1 #define MAJOR_ALLELE -2 @@ -102,8 +103,9 @@ const char *usage(void) " . .. missing (\".\" or \"./.\", keeps ploidy)\n" " 0 .. reference allele (e.g. 0/0 or 0, keeps ploidy)\n" " c:GT .. custom genotype (e.g. 0/0, 0, 0/1, m/M, overrides ploidy)\n" - " m .. minor (the second most common) allele (e.g. 1/1 or 1, keeps ploidy)\n" - " M .. major allele (e.g. 1/1 or 1, keeps ploidy)\n" + " m .. minor (the second most common) allele as determined from INFO/AC or FMT/GT (e.g. 1/1 or 1, keeps ploidy)\n" + " M .. major allele as determined from INFO/AC or FMT/GT (e.g. 1/1 or 1, keeps ploidy)\n" + " X .. allele with bigger read depth as determined from FMT/AD\n" " p .. phase genotype (0/1 becomes 0|1)\n" " u .. unphase genotype and sort by allele (1|0 becomes 0/1)\n" "Usage: bcftools +setGT [General Options] -- [Plugin Options]\n" @@ -218,6 +220,7 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out) if ( strchr(optarg,'0') ) args->new_mask |= GT_REF; if ( strchr(optarg,'m') ) args->new_mask |= GT_MINOR; if ( strchr(optarg,'M') ) args->new_mask |= GT_MAJOR; + if ( strchr(optarg,'X') ) args->new_mask |= GT_X_VAF; if ( strchr(optarg,'p') ) args->new_mask |= GT_PHASED; if ( strchr(optarg,'u') ) args->new_mask |= GT_UNPHASED; if ( !strncmp(optarg,"c:",2) ) { args->new_mask |= GT_CUSTOM; args->custom.gt_str = optarg; } @@ -287,10 +290,13 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out) int id = bcf_hdr_id2int(args->in_hdr,BCF_DT_ID,"GT"); if ( !bcf_hdr_idinfo_exists(args->in_hdr,BCF_HL_FMT,id) ) bcf_hdr_printf(args->out_hdr, "##FORMAT="); + if ( (args->new_mask & GT_X_VAF) && !bcf_hdr_idinfo_exists(args->in_hdr,BCF_HL_FMT,bcf_hdr_id2int(args->in_hdr,BCF_DT_ID,"AD")) ) + error("Error: the FORMAT/AD annotation does exist, cannot run with --new-gt X\n"); return 0; } +// sets GT phase for a single sample, ngts is the ploidy static inline int phase_gt(int32_t *ptr, int ngts) { int j, changed = 0; @@ -304,6 +310,7 @@ static inline int phase_gt(int32_t *ptr, int ngts) return changed; } +// unphase GT for a single sample, ngts is the ploidy static inline int unphase_gt(int32_t *ptr, int ngts) { int j, changed = 0; @@ -330,17 +337,21 @@ static inline int unphase_gt(int32_t *ptr, int ngts) } return changed; } -static inline int set_gt(int32_t *ptr, int ngts, int gt) + +// sets GT for a single sample, ngts is the ploidy, allele +static inline int set_gt(int32_t *ptr, int ngts, int allele) { int j, changed = 0; for (j=0; jtgt_mask & GT_BINOM ) - { - nbinom = bcf_get_format_int32(args->in_hdr, rec, args->binom_tag, &args->iarr, &args->miarr); - if ( nbinom<0 ) nbinom = 0; - nbinom /= rec->n_sample; - } - // Calculating allele frequency for each allele and determining major allele // only do this if use_major is true if ( args->new_mask & GT_MAJOR ) @@ -455,6 +458,36 @@ bcf1_t *process(bcf1_t *rec) args->new_gt = args->new_mask & GT_PHASED ? bcf_gt_phased(imax2) : bcf_gt_unphased(imax2); if ( args->new_mask & GT_CUSTOM ) args->custom.m_allele = imax2; } + if ( args->new_mask & GT_X_VAF ) + { + if ( bcf_get_format_int32(args->in_hdr,rec,"AD",&args->xarr,&args->mxarr)==rec->n_allele*rec->n_sample ) + { + int n = rec->n_allele*rec->n_sample; + int32_t *src = args->xarr, *dst = args->xarr; + for (i=0; in_allele; j++) + { + if ( src[j]==bcf_int32_vector_end ) break; + if ( src[j]==bcf_int32_missing ) continue; + if ( j==0 || src[jmax] < src[j] ) jmax = j; + } + *dst = jmax==-1 ? bcf_gt_missing : bcf_gt_unphased(jmax); + src += rec->n_allele; + dst++; + } + } + else return rec; + } + + int nbinom = 0; + if ( args->tgt_mask & GT_BINOM ) + { + nbinom = bcf_get_format_int32(args->in_hdr, rec, args->binom_tag, &args->iarr, &args->miarr); + if ( nbinom<0 ) nbinom = 0; + nbinom /= rec->n_sample; + } // replace gts if ( nbinom && ngts>=2 ) // only diploid genotypes are considered: higher ploidy ignored further, haploid here @@ -485,6 +518,8 @@ bcf1_t *process(bcf1_t *rec) changed += phase_gt(ptr, ngts); else if ( args->new_mask & GT_CUSTOM ) changed += set_gt_custom(args, ptr, ngts, rec->n_allele); + else if ( args->new_mask & GT_X_VAF ) + changed += set_gt(ptr, ngts, args->xarr[i]); else changed += set_gt(ptr, ngts, args->new_gt); } @@ -520,6 +555,8 @@ bcf1_t *process(bcf1_t *rec) changed += phase_gt(args->gts + i*ngts, ngts); else if ( args->new_mask & GT_CUSTOM ) changed += set_gt_custom(args, args->gts + i*ngts, ngts, rec->n_allele); + else if ( args->new_mask & GT_X_VAF ) + changed += set_gt(args->gts + i*ngts, ngts, args->xarr[i]); else changed += set_gt(args->gts + i*ngts, ngts, args->new_gt); } @@ -550,6 +587,8 @@ bcf1_t *process(bcf1_t *rec) changed += phase_gt(ptr, ngts); else if ( args->new_mask & GT_CUSTOM ) changed += set_gt_custom(args, args->gts + i*ngts, ngts, rec->n_allele); + else if ( args->new_mask & GT_X_VAF ) + changed += set_gt(ptr, ngts, args->xarr[i]); else changed += set_gt(ptr, ngts, args->new_gt); } @@ -572,6 +611,7 @@ void destroy(void) if ( args->filter ) filter_destroy(args->filter); free(args->arr); free(args->iarr); + free(args->xarr); free(args->gts); free(args); } diff --git a/test/setGT.5.1.out b/test/setGT.5.1.out new file mode 100644 index 000000000..d75684a1e --- /dev/null +++ b/test/setGT.5.1.out @@ -0,0 +1,8 @@ +##fileformat=VCFv4.2 +##FILTER= +##contig= +##reference=file:ref.fa +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B +1 1890 . A G . . . GT:AD 0/0:10,0 1/1:0,10 diff --git a/test/setGT.5.vcf b/test/setGT.5.vcf new file mode 100644 index 000000000..42ff705b2 --- /dev/null +++ b/test/setGT.5.vcf @@ -0,0 +1,7 @@ +##fileformat=VCFv4.2 +##contig= +##reference=file:ref.fa +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B +1 1890 . A G . . . GT:AD ./.:10,0 ./.:0,10 diff --git a/test/test.pl b/test/test.pl index 68381e7a7..a9271b2da 100755 --- a/test/test.pl +++ b/test/test.pl @@ -514,6 +514,7 @@ run_test(\&test_vcf_plugin,$opts,in=>'setGT.3',out=>'setGT.3.6.out',cmd=>'+setGT --no-version',args=>'-- -t a -n c:0/1/1'); run_test(\&test_vcf_plugin,$opts,in=>'setGT.4',out=>'setGT.4.1.out',cmd=>'+setGT --no-version',args=>q[-- -t q -n . -e 'FMT/DP>90']); run_test(\&test_vcf_plugin,$opts,in=>'setGT.4',out=>'setGT.4.2.out',cmd=>'+setGT --no-version',args=>q[-- -t q -n . -e 'FMT/DP>100']); +run_test(\&test_vcf_plugin,$opts,in=>'setGT.5',out=>'setGT.5.1.out',cmd=>'+setGT --no-version',args=>q[-- -t a -n X]); run_test(\&test_vcf_plugin,$opts,in=>'plugin1',out=>'fill-AN-AC.out',cmd=>'+fill-AN-AC --no-version'); run_test(\&test_vcf_plugin,$opts,in=>'dosage',out=>'dosage.1.out',cmd=>'+dosage',args=>'-- -t PL'); run_test(\&test_vcf_plugin,$opts,in=>'dosage',out=>'dosage.2.out',cmd=>'+dosage',args=>'-- -t GL'); From d984ce9bc10507a88ad8f26b59a5f1775bfb1666 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Tue, 11 Oct 2022 17:01:47 +0100 Subject: [PATCH 32/84] New `norm --multi-overlaps` option. Resolves #1802 and #1764 --- NEWS | 5 +++++ doc/bcftools.txt | 4 ++++ test/norm.5.1.out | 9 +++++++++ test/norm.5.2.out | 9 +++++++++ test/norm.5.vcf | 6 ++++++ test/test.pl | 2 ++ vcfnorm.c | 19 +++++++++++++++---- 7 files changed, 50 insertions(+), 4 deletions(-) create mode 100644 test/norm.5.1.out create mode 100644 test/norm.5.2.out create mode 100644 test/norm.5.vcf diff --git a/NEWS b/NEWS index fdb2238c5..bbcfbdcc4 100644 --- a/NEWS +++ b/NEWS @@ -11,6 +11,11 @@ Changes affecting specific commands: - Fix a bug where too many alleles passed to `-C alleles` via `-T` caused memory corruption (#1790) +* bcftools norm + + - New --multi-overlaps option allows to set overlapping alleles either to the + ref allele (the current default) or to a missing allele (#1764 and #1802) + * bcftools query - Fix a rare bug where the printing of SAMPLE field with `query` was incorrectly diff --git a/doc/bcftools.txt b/doc/bcftools.txt index eb6b6843a..457bde783 100644 --- a/doc/bcftools.txt +++ b/doc/bcftools.txt @@ -2366,6 +2366,10 @@ the *<>* option is supplied. 'both'; if SNPs and indels should be merged into a single record, specify 'any'. +*--multi-overlaps* '0'|'.':: + use the reference ('0') or missing ('.') allele for overlapping alleles after + splitting multiallelic sites + *--no-version*:: see *<>* diff --git a/test/norm.5.1.out b/test/norm.5.1.out new file mode 100644 index 000000000..180509fe2 --- /dev/null +++ b/test/norm.5.1.out @@ -0,0 +1,9 @@ +##fileformat=VCFv4.2 +##FILTER= +##reference=ref.fasta +##contig= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B +1 511 . CAGCA CAG . . . GT 1|0 0|1 +1 511 . CAGCA CAA . . . GT 0|0 1|0 +1 511 . CAGCA CCA . . . GT 0|0 0|0 diff --git a/test/norm.5.2.out b/test/norm.5.2.out new file mode 100644 index 000000000..fd57823a1 --- /dev/null +++ b/test/norm.5.2.out @@ -0,0 +1,9 @@ +##fileformat=VCFv4.2 +##FILTER= +##reference=ref.fasta +##contig= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B +1 511 . CAGCA CAG . . . GT 1|0 .|1 +1 511 . CAGCA CAA . . . GT .|. 1|. +1 511 . CAGCA CCA . . . GT .|. .|. diff --git a/test/norm.5.vcf b/test/norm.5.vcf new file mode 100644 index 000000000..4832f9c78 --- /dev/null +++ b/test/norm.5.vcf @@ -0,0 +1,6 @@ +##fileformat=VCFv4.2 +##reference=ref.fasta +##contig= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B +1 511 . CAGCA CAG,CAA,CCA . . . GT 1|0 2|1 diff --git a/test/test.pl b/test/test.pl index ad9fb1e1d..f15eda3d7 100755 --- a/test/test.pl +++ b/test/test.pl @@ -264,6 +264,8 @@ run_test(\&test_vcf_norm,$opts,in=>'atomize.split.3',out=>'atomize.split.3.1.out',args=>'--atomize --atom-overlaps .'); run_test(\&test_vcf_norm,$opts,in=>'norm.4',out=>'norm.4.1.out',args=>'-m +both'); run_test(\&test_vcf_norm,$opts,in=>'norm.4',out=>'norm.4.2.out',args=>'-m +any'); +run_test(\&test_vcf_norm,$opts,in=>'norm.5',out=>'norm.5.1.out',args=>'-m - --multi-overlaps 0'); +run_test(\&test_vcf_norm,$opts,in=>'norm.5',out=>'norm.5.2.out',args=>'-m - --multi-overlaps .'); run_test(\&test_vcf_view,$opts,in=>'view',out=>'view.1.out',args=>'-aUc1 -C1 -s NA00002 -v snps',reg=>''); run_test(\&test_vcf_view,$opts,in=>'view',out=>'view.2.out',args=>'-f PASS -Xks NA00003',reg=>'-r20,Y'); run_test(\&test_vcf_view,$opts,in=>'view',out=>'view.3.out',args=>'-xs NA00003',reg=>''); diff --git a/vcfnorm.c b/vcfnorm.c index 38c5de4e5..73ef2071d 100644 --- a/vcfnorm.c +++ b/vcfnorm.c @@ -1,6 +1,6 @@ /* vcfnorm.c -- Left-align and normalize indels. - Copyright (C) 2013-2021 Genome Research Ltd. + Copyright (C) 2013-2022 Genome Research Ltd. Author: Petr Danecek @@ -102,7 +102,7 @@ typedef struct int record_cmd_line, force, force_warned, keep_sum_ad; abuf_t *abuf; abuf_opt_t atomize; - int use_star_allele; + int use_star_allele, ma_use_ref_allele; char *old_rec_tag; htsFile *out; } @@ -711,11 +711,14 @@ static void split_format_genotype(args_t *args, bcf1_t *src, bcf_fmt_t *fmt, int for (j=0; jma_use_ref_allele) && bcf_gt_allele(gt[j])==0 ) continue; // ref && `--multi-overlaps 0`: leave as is if ( bcf_gt_allele(gt[j])==ialt+1 ) gt[j] = bcf_gt_unphased(1) | bcf_gt_is_phased(gt[j]); // set to first ALT - else + else if ( args->ma_use_ref_allele ) gt[j] = bcf_gt_unphased(0) | bcf_gt_is_phased(gt[j]); // set to REF + else + gt[j] = bcf_gt_missing | bcf_gt_is_phased(gt[j]); // set to missing } gt += ngts; } @@ -2087,6 +2090,7 @@ static void usage(void) fprintf(stderr, " --force Try to proceed even if malformed tags are encountered. Experimental, use at your own risk\n"); fprintf(stderr, " --keep-sum TAG,.. Keep vector sum constant when splitting multiallelics (see github issue #360)\n"); fprintf(stderr, " -m, --multiallelics -|+TYPE Split multiallelics (-) or join biallelics (+), type: snps|indels|both|any [both]\n"); + fprintf(stderr, " --multi-overlaps 0|. Fill in the reference (0) or missing (.) allele when splitting multiallelics [0]\n"); fprintf(stderr, " --no-version Do not append version and command line to the header\n"); fprintf(stderr, " -N, --do-not-normalize Do not normalize indels (with -m or -c s)\n"); fprintf(stderr, " --old-rec-tag STR Annotate modified records with INFO/STR indicating the original variant\n"); @@ -2126,6 +2130,7 @@ int main_vcfnorm(int argc, char *argv[]) args->buf_win = 1000; args->mrows_collapse = COLLAPSE_BOTH; args->do_indels = 1; + args->ma_use_ref_allele = 1; args->clevel = -1; int region_is_file = 0; int targets_is_file = 0; @@ -2144,6 +2149,7 @@ int main_vcfnorm(int argc, char *argv[]) {"fasta-ref",required_argument,NULL,'f'}, {"do-not-normalize",no_argument,NULL,'N'}, {"multiallelics",required_argument,NULL,'m'}, + {"multi-overlaps",required_argument,NULL,13}, {"regions",required_argument,NULL,'r'}, {"regions-file",required_argument,NULL,'R'}, {"regions-overlap",required_argument,NULL,1}, @@ -2177,6 +2183,11 @@ int main_vcfnorm(int argc, char *argv[]) else error("Invalid argument to --atom-overlaps. Perhaps you wanted: \"--atom-overlaps '*'\"?\n"); break; case 12 : args->old_rec_tag = optarg; break; + case 13 : + if ( optarg[0]=='0' ) args->ma_use_ref_allele = 1; + else if ( optarg[0]=='.' ) args->ma_use_ref_allele = 0; + else error("Invalid argument to --multi-overlaps\n"); + break; case 'N': args->do_indels = 0; break; case 'd': if ( !strcmp("snps",optarg) ) args->rmdup = BCF_SR_PAIR_SNPS; From 9f0dad98aa63eaf8a5b7d1d597cabc24d4fe979f Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Wed, 12 Oct 2022 08:25:53 +0100 Subject: [PATCH 33/84] Fix a silly bug in 87bf15961b0 --- plugins/setGT.c | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/plugins/setGT.c b/plugins/setGT.c index a3b3f3032..ddcbb388d 100644 --- a/plugins/setGT.c +++ b/plugins/setGT.c @@ -462,9 +462,8 @@ bcf1_t *process(bcf1_t *rec) { if ( bcf_get_format_int32(args->in_hdr,rec,"AD",&args->xarr,&args->mxarr)==rec->n_allele*rec->n_sample ) { - int n = rec->n_allele*rec->n_sample; int32_t *src = args->xarr, *dst = args->xarr; - for (i=0; in_sample; i++) { int jmax = -1; for (j=0; jn_allele; j++) From 254325205f88c07d9491548159ec2cb5fa9f8d14 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Thu, 13 Oct 2022 16:59:15 +0200 Subject: [PATCH 34/84] Prevent out of range indices and consequent segfault. Fixes #1805 --- bam2bcf.c | 7 +- test/mpileup/annot-NMBZ.1.1.out | 10 +- test/mpileup/annot-NMBZ.2.1.out | 2 +- test/mpileup/annot-NMBZ.3.1.out | 4 +- test/mpileup/indel-AD.1.out | 200 ++++++++++++++++---------------- test/mpileup/indel-AD.2.out | 2 +- test/mpileup/indel-AD.3.out | 2 +- test/mpileup/indel-AD.4.out | 2 +- test/mpileup/mpileup-SCR.out | 2 +- test/mpileup/mpileup.1.out | 2 +- test/mpileup/mpileup.10.out | 2 +- test/mpileup/mpileup.11.out | 22 ++-- test/mpileup/mpileup.2.out | 50 ++++---- test/mpileup/mpileup.4.out | 50 ++++---- test/mpileup/mpileup.5.out | 50 ++++---- test/mpileup/mpileup.6.out | 50 ++++---- 16 files changed, 229 insertions(+), 228 deletions(-) diff --git a/bam2bcf.c b/bam2bcf.c index d373e99cb..05ca5a91a 100644 --- a/bam2bcf.c +++ b/bam2bcf.c @@ -346,12 +346,13 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t if ( bca->fmt_flag & (B2B_INFO_RPB|B2B_INFO_VDB|B2B_INFO_SCB) ) { int pos = get_position(p, &len, &sc_len, &sc_dist); - epos = (double)pos/(len+1) * bca->npos; - + epos = (double)pos/(len+1) * (bca->npos - 1); if (sc_len) { - sc_len = 15.0*sc_len / sc_dist; + sc_len = 15.0*sc_len / (sc_dist+1); if (sc_len > 99) sc_len = 99; } + assert( epos>=0 && eposnpos ); + assert( sc_len>=0 && sc_lennpos ); } int imq = mapQ * nqual_over_60; int ibq = baseQ * nqual_over_60; diff --git a/test/mpileup/annot-NMBZ.1.1.out b/test/mpileup/annot-NMBZ.1.1.out index 0168f0a00..0ce549095 100644 --- a/test/mpileup/annot-NMBZ.1.1.out +++ b/test/mpileup/annot-NMBZ.1.1.out @@ -20,16 +20,16 @@ ##INFO= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample -chr19 69 . G C,<*> 0 . DP=46;I16=18,21,2,3,1377,50689,217,10339,2340,140400,266,14324,759,16653,92,1754;QS=0.868222,0.131778,0;VDB=0.213368;SGB=-0.590765;RPBZ=0.0739965;MQBZ=-4.95028;MQSBZ=-0.485415;BQBZ=-0.0931785;NMBZ=6.54221;SCBZ=6.54221;FS=0;MQ0F=0 PL 60,0,255,177,255,255 +chr19 69 . G C,<*> 0 . DP=46;I16=18,21,2,3,1377,50689,217,10339,2340,140400,266,14324,759,16653,92,1754;QS=0.868222,0.131778,0;VDB=0.216674;SGB=-0.590765;RPBZ=0.0924924;MQBZ=-4.95028;MQSBZ=-0.485415;BQBZ=-0.0931785;NMBZ=6.54221;SCBZ=6.54221;FS=0;MQ0F=0 PL 60,0,255,177,255,255 chr19 70 . G <*> 0 . DP=47;I16=19,25,0,0,1638,63732,0,0,2606,154724,0,0,829,18007,0,0;QS=1,0;MQ0F=0 PL 0,132,255 chr19 71 . T <*> 0 . DP=47;I16=19,25,0,0,1488,54040,0,0,2606,154724,0,0,827,17989,0,0;QS=1,0;MQ0F=0 PL 0,132,255 -chr19 72 . G A,<*> 0 . DP=48;I16=18,22,2,3,1377,49347,203,9477,2400,144000,266,14324,733,16223,92,1796;QS=0.874841,0.125159,0;VDB=0.197286;SGB=-0.590765;RPBZ=0.361277;MQBZ=-5.01073;MQSBZ=-0.448951;BQBZ=0.145086;NMBZ=6.61856;SCBZ=6.61856;FS=0;MQ0F=0 PL 48,0,255,169,255,255 +chr19 72 . G A,<*> 0 . DP=48;I16=18,22,2,3,1377,49347,203,9477,2400,144000,266,14324,733,16223,92,1796;QS=0.874841,0.125159,0;VDB=0.206846;SGB=-0.590765;RPBZ=0.415523;MQBZ=-5.01073;MQSBZ=-0.448951;BQBZ=0.145086;NMBZ=6.61856;SCBZ=6.61856;FS=0;MQ0F=0 PL 48,0,255,169,255,255 chr19 73 . G <*> 0 . DP=48;I16=20,25,0,0,1608,61094,0,0,2666,158324,0,0,823,18049,0,0;QS=1,0;MQ0F=0 PL 0,135,255 chr19 74 . T <*> 0 . DP=48;I16=20,25,0,0,1478,53810,0,0,2666,158324,0,0,820,18080,0,0;QS=1,0;MQ0F=0 PL 0,135,255 chr19 75 . G <*> 0 . DP=48;I16=20,25,0,0,1617,61719,0,0,2666,158324,0,0,813,17961,0,0;QS=1,0;MQ0F=0 PL 0,135,255 -chr19 76 . A C,<*> 0 . DP=47;I16=18,21,2,3,1383,50589,220,10546,2340,140400,266,14324,715,15927,92,1964;QS=0.867085,0.132915,0;VDB=0.181959;SGB=-0.590765;RPBZ=0.573514;MQBZ=-4.95028;MQSBZ=-0.485415;BQBZ=0.556487;NMBZ=6.54221;SCBZ=5.78316;FS=0;MQ0F=0 PL 63,0,255,180,255,255 +chr19 76 . A C,<*> 0 . DP=47;I16=18,21,2,3,1383,50589,220,10546,2340,140400,266,14324,715,15927,92,1964;QS=0.867085,0.132915,0;VDB=0.187998;SGB=-0.590765;RPBZ=0.573514;MQBZ=-4.95028;MQSBZ=-0.485415;BQBZ=0.556487;NMBZ=6.54221;SCBZ=5.78316;FS=0;MQ0F=0 PL 63,0,255,180,255,255 chr19 77 . G <*> 0 . DP=47;I16=20,24,0,0,1639,63567,0,0,2606,154724,0,0,799,17769,0,0;QS=1,0;MQ0F=0 PL 0,132,255 -chr19 78 . G C,<*> 0 . DP=46;I16=17,21,2,3,1392,52920,202,9494,2280,136800,266,14324,702,15700,88,1896;QS=0.87768,0.12232,0;VDB=0.187998;SGB=-0.590765;RPBZ=0.682374;MQBZ=-4.88906;MQSBZ=-0.44293;BQBZ=-0.380581;NMBZ=6.46493;SCBZ=5.71324;FS=0;MQ0F=0 PL 51,0,255,166,255,255 +chr19 78 . G C,<*> 0 . DP=46;I16=17,21,2,3,1392,52920,202,9494,2280,136800,266,14324,702,15700,88,1896;QS=0.87768,0.12232,0;VDB=0.181959;SGB=-0.590765;RPBZ=0.739183;MQBZ=-4.88906;MQSBZ=-0.44293;BQBZ=-0.380581;NMBZ=6.46493;SCBZ=5.71324;FS=0;MQ0F=0 PL 51,0,255,166,255,255 chr19 79 . G <*> 0 . DP=45;I16=18,24,0,0,1560,60778,0,0,2486,147524,0,0,780,17370,0,0;QS=1,0;MQ0F=0 PL 0,126,255 chr19 80 . G <*> 0 . DP=43;I16=17,23,0,0,1448,55202,0,0,2366,140324,0,0,771,17137,0,0;QS=1,0;MQ0F=0 PL 0,120,255 chr19 81 . C <*> 0 . DP=43;I16=17,23,0,0,1493,58329,0,0,2366,140324,0,0,762,16946,0,0;QS=1,0;MQ0F=0 PL 0,120,255 @@ -42,7 +42,7 @@ chr19 87 . C <*> 0 . DP=39;I16=15,22,0,0,1325,50283,0,0,2186,129524,0,0,724,1610 chr19 88 . C <*> 0 . DP=38;I16=14,23,0,0,1377,52341,0,0,2186,129524,0,0,735,16311,0,0;QS=1,0;MQ0F=0 PL 0,111,255 chr19 89 . G <*> 0 . DP=37;I16=13,23,0,0,1343,51159,0,0,2126,125924,0,0,720,15832,0,0;QS=1,0;MQ0F=0 PL 0,108,255 chr19 90 . C <*> 0 . DP=37;I16=13,23,0,0,1311,49173,0,0,2126,125924,0,0,704,15346,0,0;QS=1,0;MQ0F=0 PL 0,108,255 -chr19 91 . A G,<*> 0 . DP=37;I16=13,18,0,5,1128,42894,164,5518,1860,111600,266,14324,579,12347,107,2459;QS=0.873065,0.126935,0;VDB=0.00744022;SGB=-0.590765;RPBZ=1.55676;MQBZ=-4.43656;MQSBZ=-1.33955;BQBZ=-1.63294;NMBZ=5.89499;SCBZ=5.1969;FS=0;MQ0F=0 PL 27,0,255,121,255,255 +chr19 91 . A G,<*> 0 . DP=37;I16=13,18,0,5,1128,42894,164,5518,1860,111600,266,14324,579,12347,107,2459;QS=0.873065,0.126935,0;VDB=0.0081677;SGB=-0.590765;RPBZ=1.60224;MQBZ=-4.43656;MQSBZ=-1.33955;BQBZ=-1.63294;NMBZ=5.89499;SCBZ=5.1969;FS=0;MQ0F=0 PL 27,0,255,121,255,255 chr19 92 . T <*> 0 . DP=36;I16=13,23,0,0,1262,45858,0,0,2126,125924,0,0,668,14314,0,0;QS=1,0;MQ0F=0 PL 0,108,255 chr19 93 . C <*> 0 . DP=36;I16=13,23,0,0,1250,44748,0,0,2126,125924,0,0,649,13819,0,0;QS=1,0;MQ0F=0 PL 0,108,255 chr19 94 . G <*> 0 . DP=35;I16=12,23,0,0,1262,46192,0,0,2066,122324,0,0,631,13369,0,0;QS=1,0;MQ0F=0 PL 0,105,255 diff --git a/test/mpileup/annot-NMBZ.2.1.out b/test/mpileup/annot-NMBZ.2.1.out index 6f626ae5e..0398cf827 100644 --- a/test/mpileup/annot-NMBZ.2.1.out +++ b/test/mpileup/annot-NMBZ.2.1.out @@ -20,4 +20,4 @@ ##INFO= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample -chr6 75 . G A,<*> 0 . DP=283;I16=131,25,98,28,5557,200289,4591,168791,9360,561600,7560,453600,2484,51052,2121,45743;QS=0.547596,0.452404,0;VDB=1.58389e-09;SGB=-0.693147;RPBZ=-0.269598;MQBZ=0;MQSBZ=0;BQBZ=1.5258;NMBZ=-2.02395;SCBZ=-1.56217;FS=0;MQ0F=0 PL 255,0,255,255,255,255 +chr6 75 . G A,<*> 0 . DP=283;I16=131,25,98,28,5557,200289,4591,168791,9360,561600,7560,453600,2484,51052,2121,45743;QS=0.547596,0.452404,0;VDB=3.5699e-10;SGB=-0.693147;RPBZ=-0.269598;MQBZ=0;MQSBZ=0;BQBZ=1.5258;NMBZ=-2.02395;SCBZ=-1.56217;FS=0;MQ0F=0 PL 255,0,255,255,255,255 diff --git a/test/mpileup/annot-NMBZ.3.1.out b/test/mpileup/annot-NMBZ.3.1.out index 26b95fb87..73ab8a829 100644 --- a/test/mpileup/annot-NMBZ.3.1.out +++ b/test/mpileup/annot-NMBZ.3.1.out @@ -20,5 +20,5 @@ ##INFO= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample sample2 -chr16 75 . C T,<*> 0 . DP=246;I16=114,125,1,0,8929,339403,8,64,14340,860400,40,1600,3901,80155,11,121;QS=1.99845,0.00154859,0;SGB=-0.516033;RPBZ=-1.13322;MQBZ=-15.4596;MQSBZ=1.04257;BQBZ=-1.74564;NMBZ=7.74597;SCBZ=10.8628;FS=0;MQ0F=0 PL 0,255,255,255,255,255 0,255,255,255,255,255 -chr16 75 . CTTTTTTTT CTTTTTTTTT,CTTTTTTTTTT 0 . INDEL;IDV=38;IMF=0.368932;DP=246;I16=78,96,23,16,6960,278400,1580,64400,10440,626400,2340,140400,3155,66991,675,13499;QS=1.40527,0.576876,0.0178571;VDB=0.543627;SGB=-13.9289;RPBZ=-1.68678;MQBZ=0.434057;MQSBZ=1.04257;BQBZ=-1.74564;NMBZ=-0.823886;SCBZ=-0.615101;FS=0;MQ0F=0 PL 255,0,128,255,206,255 0,255,201,255,204,214 +chr16 75 . C T,<*> 0 . DP=246;I16=114,125,1,0,8929,339403,8,64,14340,860400,40,1600,3901,80155,11,121;QS=1.99845,0.00154859,0;SGB=-0.516033;RPBZ=-1.14044;MQBZ=-15.4596;MQSBZ=1.04257;BQBZ=-1.74564;NMBZ=7.74597;SCBZ=10.8628;FS=0;MQ0F=0 PL 0,255,255,255,255,255 0,255,255,255,255,255 +chr16 75 . CTTTTTTTT CTTTTTTTTT,CTTTTTTTTTT 0 . INDEL;IDV=38;IMF=0.368932;DP=246;I16=78,96,23,16,6960,278400,1580,64400,10440,626400,2340,140400,3155,66991,675,13499;QS=1.40527,0.576876,0.0178571;VDB=0.506381;SGB=-13.9289;RPBZ=-1.68678;MQBZ=0.434057;MQSBZ=1.04257;BQBZ=-1.74564;NMBZ=-0.823886;SCBZ=-0.615101;FS=0;MQ0F=0 PL 255,0,128,255,206,255 0,255,201,255,204,214 diff --git a/test/mpileup/indel-AD.1.out b/test/mpileup/indel-AD.1.out index d852bd8f9..30bd16536 100644 --- a/test/mpileup/indel-AD.1.out +++ b/test/mpileup/indel-AD.1.out @@ -58,18 +58,18 @@ 000000F 426 . G T,<*> 0 . DP=15;I16=9,5,0,1,519,20109,12,144,840,50400,60,3600,288,6570,4,16;QS=0.977401,0.0225989,0;SGB=-0.379885;RPBZ=-1.28103;MQBZ=0;MQSBZ=0;BQBZ=-1.70698;NMBZ=-0.582288;SCBZ=-0.879593;FS=0;MQ0F=0 PL:AD 0,31,255,42,255,255:14,1,0 000000F 427 . C <*> 0 . DP=15;I16=9,6,0,0,550,21100,0,0,900,54000,0,0,300,6828,0,0;QS=1,0;MQ0F=0 PL:AD 0,45,255:15,0 000000F 428 . T <*> 0 . DP=15;I16=9,6,0,0,521,19363,0,0,900,54000,0,0,306,6984,0,0;QS=1,0;MQ0F=0 PL:AD 0,45,255:15,0 -000000F 429 . C A,<*> 0 . DP=17;I16=10,6,0,1,533,19507,12,144,960,57600,60,3600,287,6527,25,625;QS=0.977982,0.0220183,0;SGB=-0.379885;RPBZ=1.33501;MQBZ=0;MQSBZ=0;BQBZ=-1.55274;NMBZ=-0.307698;SCBZ=-0.886638;FS=0;MQ0F=0 PL:AD 0,37,255,48,255,255:16,1,0 +000000F 429 . C A,<*> 0 . DP=17;I16=10,6,0,1,533,19507,12,144,960,57600,60,3600,287,6527,25,625;QS=0.977982,0.0220183,0;SGB=-0.379885;RPBZ=1.33584;MQBZ=0;MQSBZ=0;BQBZ=-1.55274;NMBZ=-0.307698;SCBZ=-0.887279;FS=0;MQ0F=0 PL:AD 0,37,255,48,255,255:16,1,0 000000F 430 . A <*> 0 . DP=18;I16=10,8,0,0,583,20803,0,0,1080,64800,0,0,320,7334,0,0;QS=1,0;MQ0F=0 PL:AD 0,54,255:18,0 000000F 431 . A <*> 0 . DP=19;I16=10,8,0,0,616,23012,0,0,1080,64800,0,0,328,7482,0,0;QS=1,0;MQ0F=0 PL:AD 0,54,255:18,0 000000F 432 . T <*> 0 . DP=19;I16=11,8,0,0,682,26264,0,0,1140,68400,0,0,337,7647,0,0;QS=1,0;MQ0F=0 PL:AD 0,57,255:19,0 000000F 433 . T <*> 0 . DP=19;I16=11,8,0,0,696,26452,0,0,1140,68400,0,0,346,7830,0,0;QS=1,0;MQ0F=0 PL:AD 0,57,255:19,0 000000F 434 . T <*> 0 . DP=19;I16=11,8,0,0,678,25728,0,0,1140,68400,0,0,354,7980,0,0;QS=1,0;MQ0F=0 PL:AD 0,57,255:19,0 000000F 435 . T <*> 0 . DP=20;I16=11,9,0,0,717,26931,0,0,1200,72000,0,0,362,8146,0,0;QS=1,0;MQ0F=0 PL:AD 0,60,255:20,0 -000000F 436 . A C,<*> 0 . DP=21;I16=11,9,0,1,728,28034,12,144,1200,72000,60,3600,346,7704,25,625;QS=0.983784,0.0162162,0;SGB=-0.379885;RPBZ=0.993127;MQBZ=0;MQSBZ=0;BQBZ=-1.66309;NMBZ=0.165792;SCBZ=-0.82685;FS=0;MQ0F=0 PL:AD 0,49,255,60,255,255:20,1,0 +000000F 436 . A C,<*> 0 . DP=21;I16=11,9,0,1,728,28034,12,144,1200,72000,60,3600,346,7704,25,625;QS=0.983784,0.0162162,0;SGB=-0.379885;RPBZ=0.909477;MQBZ=0;MQSBZ=0;BQBZ=-1.66309;NMBZ=0.165792;SCBZ=-0.82685;FS=0;MQ0F=0 PL:AD 0,49,255,60,255,255:20,1,0 000000F 437 . T <*> 0 . DP=21;I16=11,10,0,0,770,29698,0,0,1260,75600,0,0,381,8531,0,0;QS=1,0;MQ0F=0 PL:AD 0,63,255:21,0 000000F 438 . T <*> 0 . DP=22;I16=11,10,0,0,726,26976,0,0,1260,75600,0,0,391,8753,0,0;QS=1,0;MQ0F=0 PL:AD 0,63,255:21,0 000000F 439 . T <*> 0 . DP=25;I16=14,10,0,0,804,30038,0,0,1440,86400,0,0,444,9912,0,0;QS=1,0;MQ0F=0 PL:AD 0,72,255:24,0 -000000F 440 . T A,<*> 0 . DP=27;I16=15,11,1,0,896,33856,12,144,1560,93600,60,3600,455,10163,25,625;QS=0.986784,0.0132159,0;SGB=-0.379885;RPBZ=1.28585;MQBZ=0;MQSBZ=0;BQBZ=-1.41134;NMBZ=0.643909;SCBZ=0.485449;FS=0;MQ0F=0 PL:AD 0,66,255,78,255,255:26,1,0 +000000F 440 . T A,<*> 0 . DP=27;I16=15,11,1,0,896,33856,12,144,1560,93600,60,3600,455,10163,25,625;QS=0.986784,0.0132159,0;SGB=-0.379885;RPBZ=1.28585;MQBZ=0;MQSBZ=0;BQBZ=-1.41134;NMBZ=0.643909;SCBZ=0.48519;FS=0;MQ0F=0 PL:AD 0,66,255,78,255,255:26,1,0 000000F 441 . G <*> 0 . DP=29;I16=17,11,0,0,1033,39137,0,0,1680,100800,0,0,495,11163,0,0;QS=1,0;MQ0F=0 PL:AD 0,84,255:28,0 000000F 442 . T <*> 0 . DP=29;I16=18,11,0,0,1067,41223,0,0,1740,104400,0,0,531,11951,0,0;QS=1,0;MQ0F=0 PL:AD 0,87,255:29,0 000000F 443 . A <*> 0 . DP=31;I16=20,11,0,0,1078,40562,0,0,1860,111600,0,0,544,12226,0,0;QS=1,0;MQ0F=0 PL:AD 0,93,255:31,0 @@ -80,45 +80,45 @@ 000000F 448 . T <*> 0 . DP=35;I16=23,12,0,0,1220,45736,0,0,2100,126000,0,0,667,15037,0,0;QS=1,0;MQ0F=0 PL:AD 0,105,255:35,0 000000F 449 . T <*> 0 . DP=35;I16=23,12,0,0,1249,47703,0,0,2100,126000,0,0,679,15245,0,0;QS=1,0;MQ0F=0 PL:AD 0,105,255:35,0 000000F 450 . G <*> 0 . DP=38;I16=25,13,0,0,1449,56453,0,0,2280,136800,0,0,715,16059,0,0;QS=1,0;MQ0F=0 PL:AD 0,114,255:38,0 -000000F 451 . T A,<*> 0 . DP=43;I16=24,16,0,1,1485,57079,12,144,2400,144000,60,3600,708,15882,0,0;QS=0.991984,0.00801603,0;SGB=-0.379885;RPBZ=-1.56599;MQBZ=0;MQSBZ=0;BQBZ=-1.91213;NMBZ=-0.383201;SCBZ=-0.839076;FS=0;MQ0F=0 PL:AD 0,107,255,120,255,255:40,1,0 -000000F 452 . G T,<*> 0 . DP=45;I16=24,18,0,1,1541,58723,12,144,2520,151200,60,3600,707,15841,23,529;QS=0.992273,0.00772698,0;SGB=-0.379885;RPBZ=0.645585;MQBZ=0;MQSBZ=0;BQBZ=-1.75577;NMBZ=0.933309;SCBZ=0.62983;FS=0;MQ0F=0 PL:AD 0,113,255,126,255,255:42,1,0 +000000F 451 . T A,<*> 0 . DP=43;I16=24,16,0,1,1485,57079,12,144,2400,144000,60,3600,708,15882,0,0;QS=0.991984,0.00801603,0;SGB=-0.379885;RPBZ=-1.56545;MQBZ=0;MQSBZ=0;BQBZ=-1.91213;NMBZ=-0.383201;SCBZ=-0.839032;FS=0;MQ0F=0 PL:AD 0,107,255,120,255,255:40,1,0 +000000F 452 . G T,<*> 0 . DP=45;I16=24,18,0,1,1541,58723,12,144,2520,151200,60,3600,707,15841,23,529;QS=0.992273,0.00772698,0;SGB=-0.379885;RPBZ=0.645561;MQBZ=0;MQSBZ=0;BQBZ=-1.75577;NMBZ=0.933309;SCBZ=0.629801;FS=0;MQ0F=0 PL:AD 0,113,255,126,255,255:42,1,0 000000F 453 . C <*> 0 . DP=45;I16=24,19,0,0,1623,65335,0,0,2580,154800,0,0,753,16853,0,0;QS=1,0;MQ0F=0 PL:AD 0,129,255:43,0 -000000F 454 . A C,<*> 0 . DP=47;I16=24,20,1,0,1699,68295,12,144,2640,158400,60,3600,774,17286,25,625;QS=0.992987,0.00701344,0;SGB=-0.379885;RPBZ=1.46457;MQBZ=0;MQSBZ=0;BQBZ=-1.87433;NMBZ=0.5422;SCBZ=0.719352;FS=0;MQ0F=0 PL:AD 0,119,255,132,255,255:44,1,0 +000000F 454 . A C,<*> 0 . DP=47;I16=24,20,1,0,1699,68295,12,144,2640,158400,60,3600,774,17286,25,625;QS=0.992987,0.00701344,0;SGB=-0.379885;RPBZ=1.46482;MQBZ=0;MQSBZ=0;BQBZ=-1.87433;NMBZ=0.5422;SCBZ=0.550575;FS=0;MQ0F=0 PL:AD 0,119,255,132,255,255:44,1,0 000000F 455 . G <*> 0 . DP=48;I16=26,20,0,0,1807,74553,0,0,2760,165600,0,0,823,18385,0,0;QS=1,0;MQ0F=0 PL:AD 0,138,255:46,0 000000F 456 . T <*> 0 . DP=49;I16=26,21,0,0,1757,69583,0,0,2820,169200,0,0,845,18853,0,0;QS=1,0;MQ0F=0 PL:AD 0,141,255:47,0 000000F 457 . T <*> 0 . DP=49;I16=26,21,0,0,1836,73528,0,0,2820,169200,0,0,866,19264,0,0;QS=1,0;MQ0F=0 PL:AD 0,141,255:47,0 000000F 458 . A <*> 0 . DP=50;I16=26,22,0,0,1817,72337,0,0,2880,172800,0,0,887,19717,0,0;QS=1,0;MQ0F=0 PL:AD 0,144,255:48,0 000000F 459 . G <*> 0 . DP=50;I16=26,22,0,0,1791,70171,0,0,2880,172800,0,0,909,20213,0,0;QS=1,0;MQ0F=0 PL:AD 0,144,255:48,0 000000F 460 . A <*> 0 . DP=49;I16=26,22,0,0,1675,63873,0,0,2880,172800,0,0,923,20689,0,0;QS=1,0;MQ0F=0 PL:AD 0,144,255:48,0 -000000F 461 . A T,C,<*> 0 . DP=52;I16=25,22,1,1,1650,63298,24,288,2820,169200,120,7200,927,21061,17,145;QS=0.985663,0.00716846,0.00716846,0;VDB=0.06;SGB=-0.453602;RPBZ=-1.92182;MQBZ=0;MQSBZ=0;BQBZ=-2.2578;NMBZ=0.127077;SCBZ=0.055405;FS=0;MQ0F=0 PL:AD 0,128,255,128,255,255,141,255,255,255:47,1,1,0 -000000F 462 . A T,<*> 0 . DP=52;I16=26,22,0,1,1705,65163,12,144,2880,172800,60,3600,955,21615,10,100;QS=0.993011,0.00698893,0;SGB=-0.379885;RPBZ=-1.09711;MQBZ=0;MQSBZ=0;BQBZ=-1.74927;NMBZ=0.0355665;SCBZ=-0.853136;FS=0;MQ0F=0 PL:AD 0,130,255,144,255,255:48,1,0 +000000F 461 . A T,C,<*> 0 . DP=52;I16=25,22,1,1,1650,63298,24,288,2820,169200,120,7200,927,21061,17,145;QS=0.985663,0.00716846,0.00716846,0;VDB=0.06;SGB=-0.453602;RPBZ=-1.92231;MQBZ=0;MQSBZ=0;BQBZ=-2.2578;NMBZ=0.127077;SCBZ=-0.055422;FS=0;MQ0F=0 PL:AD 0,128,255,128,255,255,141,255,255,255:47,1,1,0 +000000F 462 . A T,<*> 0 . DP=52;I16=26,22,0,1,1705,65163,12,144,2880,172800,60,3600,955,21615,10,100;QS=0.993011,0.00698893,0;SGB=-0.379885;RPBZ=-1.09702;MQBZ=0;MQSBZ=0;BQBZ=-1.74927;NMBZ=0.0355665;SCBZ=-0.853241;FS=0;MQ0F=0 PL:AD 0,130,255,144,255,255:48,1,0 000000F 463 . A <*> 0 . DP=52;I16=26,24,0,0,1836,71956,0,0,3000,180000,0,0,996,22366,0,0;QS=1,0;MQ0F=0 PL:AD 0,151,255:50,0 -000000F 464 . T G,<*> 0 . DP=52;I16=26,23,0,1,1873,73813,12,144,2940,176400,60,3600,993,22355,25,625;QS=0.993634,0.00636605,0;SGB=-0.379885;RPBZ=0.24274;MQBZ=0;MQSBZ=0;BQBZ=-1.93908;NMBZ=-0.453085;SCBZ=-0.840233;FS=0;MQ0F=0 PL:AD 0,133,255,148,255,255:49,1,0 +000000F 464 . T G,<*> 0 . DP=52;I16=26,23,0,1,1873,73813,12,144,2940,176400,60,3600,993,22355,25,625;QS=0.993634,0.00636605,0;SGB=-0.379885;RPBZ=0.173386;MQBZ=0;MQSBZ=0;BQBZ=-1.93908;NMBZ=-0.453085;SCBZ=-0.840331;FS=0;MQ0F=0 PL:AD 0,133,255,148,255,255:49,1,0 000000F 465 . A <*> 0 . DP=52;I16=26,24,0,0,1950,78232,0,0,3000,180000,0,0,1039,23587,0,0;QS=1,0;MQ0F=0 PL:AD 0,151,255:50,0 -000000F 466 . A C,<*> 0 . DP=52;I16=25,24,1,0,1858,74740,12,144,2940,176400,60,3600,1033,23509,25,625;QS=0.993583,0.00641711,0;SGB=-0.379885;RPBZ=-1.07535;MQBZ=0;MQSBZ=0;BQBZ=-1.79438;NMBZ=1.18468;SCBZ=1.87154;FS=0;MQ0F=0 PL:AD 0,133,255,148,255,255:49,1,0 +000000F 466 . A C,<*> 0 . DP=52;I16=25,24,1,0,1858,74740,12,144,2940,176400,60,3600,1033,23509,25,625;QS=0.993583,0.00641711,0;SGB=-0.379885;RPBZ=-1.24865;MQBZ=0;MQSBZ=0;BQBZ=-1.79438;NMBZ=1.18468;SCBZ=1.87165;FS=0;MQ0F=0 PL:AD 0,133,255,148,255,255:49,1,0 000000F 467 . T <*> 0 . DP=53;I16=26,25,0,0,1890,74962,0,0,3060,183600,0,0,1076,24668,0,0;QS=1,0;MQ0F=0 PL:AD 0,154,255:51,0 000000F 468 . A <*> 0 . DP=54;I16=27,25,0,0,1967,78281,0,0,3120,187200,0,0,1095,25239,0,0;QS=1,0;MQ0F=0 PL:AD 0,157,255:52,0 000000F 469 . T <*> 0 . DP=54;I16=27,25,0,0,2046,83348,0,0,3120,187200,0,0,1113,25747,0,0;QS=1,0;MQ0F=0 PL:AD 0,157,255:52,0 000000F 470 . G <*> 0 . DP=55;I16=28,25,0,0,2047,81939,0,0,3180,190800,0,0,1131,26291,0,0;QS=1,0;MQ0F=0 PL:AD 0,160,255:53,0 000000F 471 . A <*> 0 . DP=56;I16=28,26,0,0,2028,80100,0,0,3240,194400,0,0,1150,26872,0,0;QS=1,0;MQ0F=0 PL:AD 0,163,255:54,0 000000F 472 . T <*> 0 . DP=59;I16=29,28,0,0,2122,83726,0,0,3420,205200,0,0,1191,27925,0,0;QS=1,0;MQ0F=0 PL:AD 0,172,255:57,0 -000000F 473 . C A,G,<*> 0 . DP=63;I16=19,15,12,13,1263,49285,963,39221,2040,122400,1500,90000,705,16449,548,12960;QS=0.567385,0.427224,0.00539084,0;VDB=2.3202e-06;SGB=-0.692914;RPBZ=1.06722;MQBZ=0;MQSBZ=0;BQBZ=1.40915;NMBZ=1.4735;SCBZ=0.597801;FS=0;MQ0F=0 PL:AD 255,0,255,255,255,255,255,255,255,255:34,24,1,0 +000000F 473 . C A,G,<*> 0 . DP=63;I16=19,15,12,13,1263,49285,963,39221,2040,122400,1500,90000,705,16449,548,12960;QS=0.567385,0.427224,0.00539084,0;VDB=1.64281e-06;SGB=-0.692914;RPBZ=1.05908;MQBZ=0;MQSBZ=0;BQBZ=1.40915;NMBZ=1.4735;SCBZ=0.597801;FS=0;MQ0F=0 PL:AD 255,0,255,255,255,255,255,255,255,255:34,24,1,0 000000F 474 . A <*> 0 . DP=64;I16=33,28,0,0,2172,84276,0,0,3660,219600,0,0,1296,30488,0,0;QS=1,0;MQ0F=0 PL:AD 0,184,255:61,0 000000F 475 . A <*> 0 . DP=64;I16=34,28,0,0,2092,79478,0,0,3720,223200,0,0,1322,31258,0,0;QS=1,0;MQ0F=0 PL:AD 0,187,255:62,0 -000000F 476 . A G,<*> 0 . DP=65;I16=34,28,0,1,2176,83678,12,144,3720,223200,60,3600,1319,31299,25,625;QS=0.994516,0.00548446,0;SGB=-0.379885;RPBZ=1.01845;MQBZ=0;MQSBZ=0;BQBZ=-1.59705;NMBZ=0.856031;SCBZ=0.684189;FS=0;MQ0F=0 PL:AD 0,172,255,187,255,255:62,1,0 -000000F 477 . T G,<*> 0 . DP=65;I16=34,28,0,1,2352,93436,12,144,3720,223200,60,3600,1338,31806,25,625;QS=0.994924,0.00507614,0;SGB=-0.379885;RPBZ=-0.57793;MQBZ=0;MQSBZ=0;BQBZ=-1.84472;NMBZ=-0.0276069;SCBZ=-0.892409;FS=0;MQ0F=0 PL:AD 0,172,255,187,255,255:62,1,0 +000000F 476 . A G,<*> 0 . DP=65;I16=34,28,0,1,2176,83678,12,144,3720,223200,60,3600,1319,31299,25,625;QS=0.994516,0.00548446,0;SGB=-0.379885;RPBZ=1.04564;MQBZ=0;MQSBZ=0;BQBZ=-1.59705;NMBZ=0.856031;SCBZ=0.713967;FS=0;MQ0F=0 PL:AD 0,172,255,187,255,255:62,1,0 +000000F 477 . T G,<*> 0 . DP=65;I16=34,28,0,1,2352,93436,12,144,3720,223200,60,3600,1338,31806,25,625;QS=0.994924,0.00507614,0;SGB=-0.379885;RPBZ=-0.687896;MQBZ=0;MQSBZ=0;BQBZ=-1.84472;NMBZ=-0.0276069;SCBZ=-0.892396;FS=0;MQ0F=0 PL:AD 0,172,255,187,255,255:62,1,0 000000F 478 . C <*> 0 . DP=65;I16=34,29,0,0,2376,94566,0,0,3780,226800,0,0,1381,32925,0,0;QS=1,0;MQ0F=0 PL:AD 0,190,255:63,0 -000000F 479 . T G,<*> 0 . DP=68;I16=36,29,0,1,2467,98357,12,144,3900,234000,60,3600,1416,33712,21,441;QS=0.995159,0.00484066,0;SGB=-0.379885;RPBZ=-0.787921;MQBZ=0;MQSBZ=0;BQBZ=-1.86106;NMBZ=-1.44958;SCBZ=-0.927109;FS=0;MQ0F=0 PL:AD 0,180,255,196,255,255:65,1,0 +000000F 479 . T G,<*> 0 . DP=68;I16=36,29,0,1,2467,98357,12,144,3900,234000,60,3600,1416,33712,21,441;QS=0.995159,0.00484066,0;SGB=-0.379885;RPBZ=-0.787962;MQBZ=0;MQSBZ=0;BQBZ=-1.86106;NMBZ=-1.44958;SCBZ=-0.927153;FS=0;MQ0F=0 PL:AD 0,180,255,196,255,255:65,1,0 000000F 480 . G <*> 0 . DP=70;I16=38,30,0,0,2563,101527,0,0,4080,244800,0,0,1495,35435,0,0;QS=1,0;MQ0F=0 PL:AD 0,205,255:68,0 000000F 481 . T <*> 0 . DP=70;I16=38,30,0,0,2521,98551,0,0,4080,244800,0,0,1514,35994,0,0;QS=1,0;MQ0F=0 PL:AD 0,205,255:68,0 -000000F 482 . T G,<*> 0 . DP=70;I16=37,30,1,0,2575,103005,12,144,4020,241200,60,3600,1518,36344,14,196;QS=0.995361,0.00463858,0;SGB=-0.379885;RPBZ=-0.917549;MQBZ=0;MQSBZ=0;BQBZ=-1.93937;NMBZ=-0.332412;SCBZ=-0.948353;FS=0;MQ0F=0 PL:AD 0,186,255,202,255,255:67,1,0 +000000F 482 . T G,<*> 0 . DP=70;I16=37,30,1,0,2575,103005,12,144,4020,241200,60,3600,1518,36344,14,196;QS=0.995361,0.00463858,0;SGB=-0.379885;RPBZ=-0.892198;MQBZ=0;MQSBZ=0;BQBZ=-1.93937;NMBZ=-0.332412;SCBZ=-0.948507;FS=0;MQ0F=0 PL:AD 0,186,255,202,255,255:67,1,0 000000F 483 . T <*> 0 . DP=70;I16=38,30,0,0,2646,106206,0,0,4080,244800,0,0,1549,37071,0,0;QS=1,0;MQ0F=0 PL:AD 0,205,255:68,0 000000F 484 . G <*> 0 . DP=70;I16=38,30,0,0,2659,107225,0,0,4080,244800,0,0,1565,37585,0,0;QS=1,0;MQ0F=0 PL:AD 0,205,255:68,0 000000F 485 . T <*> 0 . DP=70;I16=38,30,0,0,2618,104932,0,0,4080,244800,0,0,1578,37978,0,0;QS=1,0;MQ0F=0 PL:AD 0,205,255:68,0 000000F 486 . T <*> 0 . DP=70;I16=38,30,0,0,2589,103545,0,0,4080,244800,0,0,1589,38295,0,0;QS=1,0;MQ0F=0 PL:AD 0,205,255:68,0 000000F 487 . T <*> 0 . DP=73;I16=38,33,0,0,2694,107284,0,0,4260,255600,0,0,1599,38583,0,0;QS=1,0;MQ0F=0 PL:AD 0,214,255:71,0 -000000F 488 . A G,<*> 0 . DP=76;I16=41,32,0,1,2640,102296,8,64,4380,262800,60,3600,1679,40447,1,1;QS=0.996979,0.00302115,0;SGB=-0.379885;RPBZ=-1.52232;MQBZ=0;MQSBZ=0;BQBZ=-1.89405;NMBZ=-0.328825;SCBZ=-0.946346;FS=0;MQ0F=0 PL:AD 0,204,255,220,255,255:73,1,0 -000000F 489 . C A,<*> 0 . DP=79;I16=43,33,0,1,2694,103126,12,144,4560,273600,60,3600,1715,41273,25,625;QS=0.995565,0.00443459,0;SGB=-0.379885;RPBZ=-0.49518;MQBZ=0;MQSBZ=0;BQBZ=-1.58784;NMBZ=-0.135403;SCBZ=-0.974284;FS=0;MQ0F=0 PL:AD 0,213,255,229,255,255:76,1,0 +000000F 488 . A G,<*> 0 . DP=76;I16=41,32,0,1,2640,102296,8,64,4380,262800,60,3600,1679,40447,1,1;QS=0.996979,0.00302115,0;SGB=-0.379885;RPBZ=-1.52228;MQBZ=0;MQSBZ=0;BQBZ=-1.89405;NMBZ=-0.328825;SCBZ=-0.946449;FS=0;MQ0F=0 PL:AD 0,204,255,220,255,255:73,1,0 +000000F 489 . C A,<*> 0 . DP=79;I16=43,33,0,1,2694,103126,12,144,4560,273600,60,3600,1715,41273,25,625;QS=0.995565,0.00443459,0;SGB=-0.379885;RPBZ=-0.495167;MQBZ=0;MQSBZ=0;BQBZ=-1.58784;NMBZ=-0.135403;SCBZ=-0.974263;FS=0;MQ0F=0 PL:AD 0,213,255,229,255,255:76,1,0 000000F 490 . C <*> 0 . DP=80;I16=43,35,0,0,2796,107040,0,0,4680,280800,0,0,1782,43020,0,0;QS=1,0;MQ0F=0 PL:AD 0,235,255:78,0 000000F 491 . T <*> 0 . DP=80;I16=43,35,0,0,2910,113818,0,0,4680,280800,0,0,1798,43500,0,0;QS=1,0;MQ0F=0 PL:AD 0,235,255:78,0 000000F 492 . G <*> 0 . DP=81;I16=43,35,0,0,3089,125687,0,0,4680,280800,0,0,1814,44012,0,0;QS=1,0;MQ0F=0 PL:AD 0,235,255:78,0 @@ -128,83 +128,83 @@ 000000F 496 . T <*> 0 . DP=87;I16=47,37,0,0,3238,128760,0,0,5040,302400,0,0,1917,46777,0,0;QS=1,0;MQ0F=0 PL:AD 0,253,255:84,0 000000F 497 . G <*> 0 . DP=87;I16=47,37,0,0,3280,132640,0,0,5040,302400,0,0,1933,47227,0,0;QS=1,0;MQ0F=0 PL:AD 0,253,255:84,0 000000F 498 . T <*> 0 . DP=88;I16=48,37,0,0,3081,120187,0,0,5100,306000,0,0,1971,48181,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:85,0 -000000F 499 . T C,<*> 0 . DP=89;I16=48,36,0,1,3190,126958,8,64,5040,302400,60,3600,1957,47809,25,625;QS=0.997498,0.00250156,0;SGB=-0.379885;RPBZ=-0.285431;MQBZ=0;MQSBZ=0;BQBZ=-1.95559;NMBZ=-0.286188;SCBZ=-1.05764;FS=0;MQ0F=0 PL:AD 0,237,255,253,255,255:84,1,0 -000000F 500 . T G,A,<*> 0 . DP=92;I16=50,37,1,1,3308,133104,24,288,5220,313200,120,7200,1986,48376,50,1250;QS=0.992797,0.00360144,0.00360144,0;VDB=0.32;SGB=-0.453602;RPBZ=0.373842;MQBZ=0;MQSBZ=0;BQBZ=-2.60206;NMBZ=-0.583258;SCBZ=-1.00091;FS=0;MQ0F=0 PL:AD 0,245,255,245,255,255,255,255,255,255:87,1,1,0 +000000F 499 . T C,<*> 0 . DP=89;I16=48,36,0,1,3190,126958,8,64,5040,302400,60,3600,1957,47809,25,625;QS=0.997498,0.00250156,0;SGB=-0.379885;RPBZ=-0.305833;MQBZ=0;MQSBZ=0;BQBZ=-1.95559;NMBZ=-0.286188;SCBZ=-1.05778;FS=0;MQ0F=0 PL:AD 0,237,255,253,255,255:84,1,0 +000000F 500 . T G,A,<*> 0 . DP=92;I16=50,37,1,1,3308,133104,24,288,5220,313200,120,7200,1986,48376,50,1250;QS=0.992797,0.00360144,0.00360144,0;VDB=0.32;SGB=-0.453602;RPBZ=0.41539;MQBZ=0;MQSBZ=0;BQBZ=-2.60206;NMBZ=-0.583258;SCBZ=-1.0009;FS=0;MQ0F=0 PL:AD 0,245,255,245,255,255,255,255,255,255:87,1,1,0 000000F 501 . G <*> 0 . DP=97;I16=53,40,0,0,3485,138049,0,0,5580,334800,0,0,2050,49962,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:93,0 -000000F 502 . T A,<*> 0 . DP=98;I16=53,40,1,0,3391,132771,12,144,5580,334800,60,3600,2065,50183,25,625;QS=0.996476,0.00352423,0;SGB=-0.379885;RPBZ=1.67746;MQBZ=0;MQSBZ=0;BQBZ=-1.7355;NMBZ=0.221736;SCBZ=0.818516;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:93,1,0 +000000F 502 . T A,<*> 0 . DP=98;I16=53,40,1,0,3391,132771,12,144,5580,334800,60,3600,2065,50183,25,625;QS=0.996476,0.00352423,0;SGB=-0.379885;RPBZ=1.67751;MQBZ=0;MQSBZ=0;BQBZ=-1.7355;NMBZ=0.221736;SCBZ=0.856937;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:93,1,0 000000F 503 . G <*> 0 . DP=98;I16=54,40,0,0,3540,140610,0,0,5640,338400,0,0,2108,51206,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:94,0 -000000F 504 . T C,A,<*> 0 . DP=102;I16=53,42,1,1,3464,137680,20,208,5700,342000,120,7200,2099,50913,25,625;QS=0.994259,0.00344432,0.00229621,0;VDB=0.94;SGB=-0.453602;RPBZ=0.0126971;MQBZ=0;MQSBZ=0;BQBZ=-2.43319;NMBZ=1.20903;SCBZ=0.499278;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:95,1,1,0 +000000F 504 . T C,A,<*> 0 . DP=102;I16=53,42,1,1,3464,137680,20,208,5700,342000,120,7200,2099,50913,25,625;QS=0.994259,0.00344432,0.00229621,0;VDB=0.92;SGB=-0.453602;RPBZ=0.0126977;MQBZ=0;MQSBZ=0;BQBZ=-2.43319;NMBZ=1.20903;SCBZ=0.512446;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:95,1,1,0 000000F 505 . G <*> 0 . DP=102;I16=54,43,0,0,3640,144678,0,0,5820,349200,0,0,2141,51803,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:97,0 -000000F 506 . C G,<*> 0 . DP=103;I16=54,43,0,1,3621,145273,12,144,5820,349200,60,3600,2138,51502,25,625;QS=0.996697,0.00330306,0;SGB=-0.379885;RPBZ=0.265207;MQBZ=0;MQSBZ=0;BQBZ=-1.75415;NMBZ=-0.425375;SCBZ=-1.07824;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:97,1,0 +000000F 506 . C G,<*> 0 . DP=103;I16=54,43,0,1,3621,145273,12,144,5820,349200,60,3600,2138,51502,25,625;QS=0.996697,0.00330306,0;SGB=-0.379885;RPBZ=0.194473;MQBZ=0;MQSBZ=0;BQBZ=-1.75415;NMBZ=-0.425375;SCBZ=-1.07827;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:97,1,0 000000F 507 . T <*> 0 . DP=103;I16=54,44,0,0,3520,139202,0,0,5880,352800,0,0,2181,52471,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:98,0 -000000F 508 . C T,<*> 0 . DP=103;I16=54,43,0,1,3476,137498,12,144,5820,349200,60,3600,2174,52226,25,625;QS=0.99656,0.00344037,0;SGB=-0.379885;RPBZ=0.212168;MQBZ=0;MQSBZ=0;BQBZ=-1.63996;NMBZ=-0.425375;SCBZ=-1.07824;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:97,1,0 +000000F 508 . C T,<*> 0 . DP=103;I16=54,43,0,1,3476,137498,12,144,5820,349200,60,3600,2174,52226,25,625;QS=0.99656,0.00344037,0;SGB=-0.379885;RPBZ=0.265217;MQBZ=0;MQSBZ=0;BQBZ=-1.63996;NMBZ=-0.425375;SCBZ=-1.07818;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:97,1,0 000000F 509 . C <*> 0 . DP=103;I16=54,44,0,0,3580,142206,0,0,5880,352800,0,0,2217,53267,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:98,0 -000000F 510 . C A,G,<*> 0 . DP=106;I16=54,43,1,2,3646,145190,42,692,5820,349200,180,10800,2189,52645,67,1515;QS=0.988612,0.00921909,0.0021692,0;VDB=0.421281;SGB=-0.511536;RPBZ=-0.717482;MQBZ=0;MQSBZ=0;BQBZ=-3.02794;NMBZ=-0.678755;SCBZ=-0.888334;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:97,2,1,0 -000000F 511 . T A,<*> 0 . DP=107;I16=55,45,0,1,3663,144413,12,144,6000,360000,60,3600,2251,54067,25,625;QS=0.996735,0.00326531,0;SGB=-0.379885;RPBZ=-0.0171549;MQBZ=0;MQSBZ=0;BQBZ=-1.71065;NMBZ=-0.343991;SCBZ=-1.08127;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:100,1,0 -000000F 512 . C A,G,<*> 0 . DP=107;I16=55,43,1,3,3657,146609,54,836,5880,352800,240,14400,2238,53902,83,1939;QS=0.985449,0.0123956,0.00215575,0;VDB=0.692431;SGB=-0.556411;RPBZ=-0.474202;MQBZ=0;MQSBZ=0;BQBZ=-3.45917;NMBZ=0.121004;SCBZ=-0.685395;FS=0;MQ0F=0 PL:AD 0,248,255,255,255,255,255,255,255,255:98,3,1,0 -000000F 513 . T G,<*> 0 . DP=108;I16=56,46,0,1,3774,150038,7,49,6120,367200,60,3600,2340,56352,0,0;QS=0.998149,0.00185136,0;SGB=-0.379885;RPBZ=-1.71578;MQBZ=0;MQSBZ=0;BQBZ=-1.90666;NMBZ=-0.303554;SCBZ=-1.07826;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:102,1,0 -000000F 514 . G T,<*> 0 . DP=110;I16=56,47,1,1,3763,148539,20,208,6180,370800,120,7200,2348,56422,25,625;QS=0.994713,0.00528681,0;VDB=0.44;SGB=-0.453602;RPBZ=-1.58283;MQBZ=0;MQSBZ=0;BQBZ=-2.48498;NMBZ=0.481867;SCBZ=-0.0121275;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:103,2,0 -000000F 515 . C G,<*> 0 . DP=110;I16=57,47,0,1,3848,153002,12,144,6240,374400,60,3600,2367,56887,25,625;QS=0.996891,0.00310881,0;SGB=-0.379885;RPBZ=0.330015;MQBZ=0;MQSBZ=0;BQBZ=-1.75323;NMBZ=-0.446607;SCBZ=-1.07566;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:104,1,0 -000000F 516 . G T,<*> 0 . DP=111;I16=57,48,0,1,3969,158573,12,144,6300,378000,60,3600,2411,58015,0,0;QS=0.996986,0.00301432,0;SGB=-0.379885;RPBZ=-1.71622;MQBZ=0;MQSBZ=0;BQBZ=-1.8341;NMBZ=-0.409591;SCBZ=-1.06701;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:105,1,0 -000000F 517 . T C,<*> 0 . DP=112;I16=56,50,1,0,3850,151946,12,144,6360,381600,60,3600,2408,58016,21,441;QS=0.996893,0.0031072,0;SGB=-0.379885;RPBZ=-0.777206;MQBZ=0;MQSBZ=0;BQBZ=-1.67048;NMBZ=1.60672;SCBZ=0.840015;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:106,1,0 +000000F 510 . C A,G,<*> 0 . DP=106;I16=54,43,1,2,3646,145190,42,692,5820,349200,180,10800,2189,52645,67,1515;QS=0.988612,0.00921909,0.0021692,0;VDB=0.401962;SGB=-0.511536;RPBZ=-0.707412;MQBZ=0;MQSBZ=0;BQBZ=-3.02794;NMBZ=-0.678755;SCBZ=-0.99293;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:97,2,1,0 +000000F 511 . T A,<*> 0 . DP=107;I16=55,45,0,1,3663,144413,12,144,6000,360000,60,3600,2251,54067,25,625;QS=0.996735,0.00326531,0;SGB=-0.379885;RPBZ=-0.0343102;MQBZ=0;MQSBZ=0;BQBZ=-1.71065;NMBZ=-0.343991;SCBZ=-1.08137;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:100,1,0 +000000F 512 . C A,G,<*> 0 . DP=107;I16=55,43,1,3,3657,146609,54,836,5880,352800,240,14400,2238,53902,83,1939;QS=0.985449,0.0123956,0.00215575,0;VDB=0.681156;SGB=-0.556411;RPBZ=-0.465574;MQBZ=0;MQSBZ=0;BQBZ=-3.45917;NMBZ=0.121004;SCBZ=-0.667699;FS=0;MQ0F=0 PL:AD 0,248,255,255,255,255,255,255,255,255:98,3,1,0 +000000F 513 . T G,<*> 0 . DP=108;I16=56,46,0,1,3774,150038,7,49,6120,367200,60,3600,2340,56352,0,0;QS=0.998149,0.00185136,0;SGB=-0.379885;RPBZ=-1.71577;MQBZ=0;MQSBZ=0;BQBZ=-1.90666;NMBZ=-0.303554;SCBZ=-1.07835;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:102,1,0 +000000F 514 . G T,<*> 0 . DP=110;I16=56,47,1,1,3763,148539,20,208,6180,370800,120,7200,2348,56422,25,625;QS=0.994713,0.00528681,0;VDB=0.44;SGB=-0.453602;RPBZ=-1.58286;MQBZ=0;MQSBZ=0;BQBZ=-2.48498;NMBZ=0.481867;SCBZ=0.0121282;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:103,2,0 +000000F 515 . C G,<*> 0 . DP=110;I16=57,47,0,1,3848,153002,12,144,6240,374400,60,3600,2367,56887,25,625;QS=0.996891,0.00310881,0;SGB=-0.379885;RPBZ=0.263997;MQBZ=0;MQSBZ=0;BQBZ=-1.75323;NMBZ=-0.446607;SCBZ=-1.07538;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:104,1,0 +000000F 516 . G T,<*> 0 . DP=111;I16=57,48,0,1,3969,158573,12,144,6300,378000,60,3600,2411,58015,0,0;QS=0.996986,0.00301432,0;SGB=-0.379885;RPBZ=-1.71626;MQBZ=0;MQSBZ=0;BQBZ=-1.8341;NMBZ=-0.409591;SCBZ=-1.06697;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:105,1,0 +000000F 517 . T C,<*> 0 . DP=112;I16=56,50,1,0,3850,151946,12,144,6360,381600,60,3600,2408,58016,21,441;QS=0.996893,0.0031072,0;SGB=-0.379885;RPBZ=-0.7772;MQBZ=0;MQSBZ=0;BQBZ=-1.67048;NMBZ=1.60672;SCBZ=0.856997;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:106,1,0 000000F 518 . G <*> 0 . DP=115;I16=59,50,0,0,3977,155237,0,0,6540,392400,0,0,2447,58891,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:109,0 -000000F 519 . C A,<*> 0 . DP=116;I16=60,49,0,1,4018,159736,12,144,6540,392400,60,3600,2443,58747,25,625;QS=0.997022,0.00297767,0;SGB=-0.379885;RPBZ=0.110248;MQBZ=0;MQSBZ=0;BQBZ=-1.72465;NMBZ=-0.268336;SCBZ=-1.03421;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:109,1,0 -000000F 520 . T G,C,A 0 . DP=116;I16=59,48,1,2,4046,162680,48,1152,6420,385200,180,10800,2436,58644,53,1259;QS=0.988276,0.00781632,0.00195408,0.00195408;VDB=0.913952;SGB=-0.511536;RPBZ=0.55986;MQBZ=0;MQSBZ=0;BQBZ=-2.88822;NMBZ=-0.570213;SCBZ=-0.3635;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:107,1,1,1 -000000F 521 . G A,T,<*> 0 . DP=118;I16=61,48,1,2,4131,166701,36,432,6540,392400,180,10800,2454,59246,53,1089;QS=0.991361,0.00575954,0.00287977,0;VDB=0.251321;SGB=-0.511536;RPBZ=-1.62229;MQBZ=0;MQSBZ=0;BQBZ=-3.05428;NMBZ=-0.614138;SCBZ=-0.836482;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:109,2,1,0 +000000F 519 . C A,<*> 0 . DP=116;I16=60,49,0,1,4018,159736,12,144,6540,392400,60,3600,2443,58747,25,625;QS=0.997022,0.00297767,0;SGB=-0.379885;RPBZ=0.110257;MQBZ=0;MQSBZ=0;BQBZ=-1.72465;NMBZ=-0.268336;SCBZ=-1.03419;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:109,1,0 +000000F 520 . T G,C,A 0 . DP=116;I16=59,48,1,2,4046,162680,48,1152,6420,385200,180,10800,2436,58644,53,1259;QS=0.988276,0.00781632,0.00195408,0.00195408;VDB=0.913952;SGB=-0.511536;RPBZ=0.578224;MQBZ=0;MQSBZ=0;BQBZ=-2.88822;NMBZ=-0.570213;SCBZ=-0.373153;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:107,1,1,1 +000000F 521 . G A,T,<*> 0 . DP=118;I16=61,48,1,2,4131,166701,36,432,6540,392400,180,10800,2454,59246,53,1089;QS=0.991361,0.00575954,0.00287977,0;VDB=0.251321;SGB=-0.511536;RPBZ=-1.60419;MQBZ=0;MQSBZ=0;BQBZ=-3.05428;NMBZ=-0.614138;SCBZ=-0.836529;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:109,2,1,0 000000F 522 . G <*> 0 . DP=118;I16=62,50,0,0,4076,161128,0,0,6720,403200,0,0,2525,60719,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:112,0 -000000F 523 . C A,<*> 0 . DP=119;I16=63,49,0,1,4174,166860,12,144,6720,403200,60,3600,2518,60530,25,625;QS=0.997133,0.0028667,0;SGB=-0.379885;RPBZ=-0.168649;MQBZ=0;MQSBZ=0;BQBZ=-1.80506;NMBZ=-0.875769;SCBZ=-1.02484;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:112,1,0 -000000F 524 . T G,<*> 0 . DP=119;I16=62,50,1,0,4191,166163,27,729,6720,403200,60,3600,2537,61019,25,625;QS=0.993599,0.00640114,0;SGB=-0.379885;RPBZ=-0.827957;MQBZ=0;MQSBZ=0;BQBZ=-1.39926;NMBZ=0.35334;SCBZ=0.0479128;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:112,1,0 -000000F 525 . A C,G,<*> 0 . DP=119;I16=62,48,1,2,4098,163296,36,432,6600,396000,180,10800,2509,60447,71,1691;QS=0.991292,0.00580552,0.00290276,0;VDB=0.199299;SGB=-0.511536;RPBZ=-1.63448;MQBZ=0;MQSBZ=0;BQBZ=-2.97339;NMBZ=1.00241;SCBZ=1.44214;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:110,2,1,0 -000000F 526 . T A,<*> 0 . DP=120;I16=63,49,0,1,4180,166064,12,144,6720,403200,60,3600,2570,61910,25,625;QS=0.997137,0.0028626,0;SGB=-0.379885;RPBZ=-1.25721;MQBZ=0;MQSBZ=0;BQBZ=-1.74833;NMBZ=-0.245826;SCBZ=0.3354;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:112,1,0 -000000F 527 . C G,A,<*> 0 . DP=120;I16=62,49,1,1,4246,172572,24,288,6660,399600,120,7200,2557,61573,48,1154;QS=0.994379,0.0028103,0.0028103,0;VDB=0.18;SGB=-0.453602;RPBZ=-1.29599;MQBZ=0;MQSBZ=0;BQBZ=-2.51884;NMBZ=2.22611;SCBZ=1.10025;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:111,1,1,0 -000000F 528 . A G,<*> 0 . DP=121;I16=62,51,1,0,4295,173733,12,144,6780,406800,60,3600,2588,62236,25,625;QS=0.997214,0.00278616,0;SGB=-0.379885;RPBZ=-0.805475;MQBZ=0;MQSBZ=0;BQBZ=-1.82642;NMBZ=0.365458;SCBZ=0.063415;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:113,1,0 -000000F 529 . T C,<*> 0 . DP=123;I16=65,50,0,1,4363,176845,8,64,6900,414000,60,3600,2639,63305,25,625;QS=0.99817,0.00183024,0;SGB=-0.379885;RPBZ=-1.03055;MQBZ=0;MQSBZ=0;BQBZ=-1.9592;NMBZ=-0.733499;SCBZ=-1.04152;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:115,1,0 +000000F 523 . C A,<*> 0 . DP=119;I16=63,49,0,1,4174,166860,12,144,6720,403200,60,3600,2518,60530,25,625;QS=0.997133,0.0028667,0;SGB=-0.379885;RPBZ=-0.13799;MQBZ=0;MQSBZ=0;BQBZ=-1.80506;NMBZ=-0.875769;SCBZ=-1.02482;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:112,1,0 +000000F 524 . T G,<*> 0 . DP=119;I16=62,50,1,0,4191,166163,27,729,6720,403200,60,3600,2537,61019,25,625;QS=0.993599,0.00640114,0;SGB=-0.379885;RPBZ=-0.82791;MQBZ=0;MQSBZ=0;BQBZ=-1.39926;NMBZ=0.35334;SCBZ=0.0480382;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:112,1,0 +000000F 525 . A C,G,<*> 0 . DP=119;I16=62,48,1,2,4098,163296,36,432,6600,396000,180,10800,2509,60447,71,1691;QS=0.991292,0.00580552,0.00290276,0;VDB=0.199299;SGB=-0.511536;RPBZ=-1.60781;MQBZ=0;MQSBZ=0;BQBZ=-2.97339;NMBZ=1.00241;SCBZ=1.45142;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:110,2,1,0 +000000F 526 . T A,<*> 0 . DP=120;I16=63,49,0,1,4180,166064,12,144,6720,403200,60,3600,2570,61910,25,625;QS=0.997137,0.0028626,0;SGB=-0.379885;RPBZ=-1.2266;MQBZ=0;MQSBZ=0;BQBZ=-1.74833;NMBZ=-0.245826;SCBZ=0.367327;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:112,1,0 +000000F 527 . C G,A,<*> 0 . DP=120;I16=62,49,1,1,4246,172572,24,288,6660,399600,120,7200,2557,61573,48,1154;QS=0.994379,0.0028103,0.0028103,0;VDB=0.18;SGB=-0.453602;RPBZ=-1.28504;MQBZ=0;MQSBZ=0;BQBZ=-2.51884;NMBZ=2.22611;SCBZ=1.10043;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:111,1,1,0 +000000F 528 . A G,<*> 0 . DP=121;I16=62,51,1,0,4295,173733,12,144,6780,406800,60,3600,2588,62236,25,625;QS=0.997214,0.00278616,0;SGB=-0.379885;RPBZ=-0.805477;MQBZ=0;MQSBZ=0;BQBZ=-1.82642;NMBZ=0.365458;SCBZ=0.0634184;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:113,1,0 +000000F 529 . T C,<*> 0 . DP=123;I16=65,50,0,1,4363,176845,8,64,6900,414000,60,3600,2639,63305,25,625;QS=0.99817,0.00183024,0;SGB=-0.379885;RPBZ=-1.04546;MQBZ=0;MQSBZ=0;BQBZ=-1.9592;NMBZ=-0.733499;SCBZ=-1.04156;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:115,1,0 000000F 530 . G <*> 0 . DP=123;I16=65,51,0,0,4357,176035,0,0,6960,417600,0,0,2672,64088,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:116,0 -000000F 531 . T A,G,<*> 0 . DP=123;I16=63,49,2,2,4199,169729,48,576,6720,403200,240,14400,2579,61741,100,2500;QS=0.988698,0.00847657,0.00282552,0;VDB=0.0587288;SGB=-0.556411;RPBZ=-0.612965;MQBZ=0;MQSBZ=0;BQBZ=-3.46139;NMBZ=0.401901;SCBZ=-0.463609;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:112,3,1,0 -000000F 532 . C A,G,<*> 0 . DP=124;I16=65,49,0,3,4352,176182,36,432,6840,410400,180,10800,2640,63492,45,897;QS=0.991796,0.00546946,0.00273473,0;VDB=0.607612;SGB=-0.511536;RPBZ=-1.54369;MQBZ=0;MQSBZ=0;BQBZ=-3.10955;NMBZ=-0.942115;SCBZ=-1.82942;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:114,2,1,0 +000000F 531 . T A,G,<*> 0 . DP=123;I16=63,49,2,2,4199,169729,48,576,6720,403200,240,14400,2579,61741,100,2500;QS=0.988698,0.00847657,0.00282552,0;VDB=0.0550934;SGB=-0.556411;RPBZ=-0.650816;MQBZ=0;MQSBZ=0;BQBZ=-3.46139;NMBZ=0.401901;SCBZ=-0.463641;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:112,3,1,0 +000000F 532 . C A,G,<*> 0 . DP=124;I16=65,49,0,3,4352,176182,36,432,6840,410400,180,10800,2640,63492,45,897;QS=0.991796,0.00546946,0.00273473,0;VDB=0.588406;SGB=-0.511536;RPBZ=-1.58686;MQBZ=0;MQSBZ=0;BQBZ=-3.10955;NMBZ=-0.942115;SCBZ=-1.82952;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:114,2,1,0 000000F 533 . A <*> 0 . DP=124;I16=65,52,0,0,4235,168199,0,0,7020,421200,0,0,2692,64582,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:117,0 -000000F 534 . G A,<*> 0 . DP=124;I16=65,51,0,1,4319,173543,12,144,6960,417600,60,3600,2677,64331,21,441;QS=0.997229,0.00277072,0;SGB=-0.379885;RPBZ=-1.33279;MQBZ=0;MQSBZ=0;BQBZ=-1.72023;NMBZ=-0.148409;SCBZ=-1.04703;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:116,1,0 -000000F 535 . G A,<*> 0 . DP=125;I16=65,52,0,1,4309,171791,12,144,7020,421200,60,3600,2679,64385,25,625;QS=0.997223,0.00277713,0;SGB=-0.379885;RPBZ=-1.14518;MQBZ=0;MQSBZ=0;BQBZ=-1.74874;NMBZ=-0.250141;SCBZ=0.0762539;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:117,1,0 -000000F 536 . T G,A,<*> 0 . DP=125;I16=65,51,0,2,4274,171298,24,288,6960,417600,120,7200,2661,64041,48,1154;QS=0.994416,0.002792,0.002792,0;VDB=0.1;SGB=-0.453602;RPBZ=-1.69957;MQBZ=0;MQSBZ=0;BQBZ=-2.39373;NMBZ=-0.292578;SCBZ=-0.714873;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:116,1,1,0 +000000F 534 . G A,<*> 0 . DP=124;I16=65,51,0,1,4319,173543,12,144,6960,417600,60,3600,2677,64331,21,441;QS=0.997229,0.00277072,0;SGB=-0.379885;RPBZ=-1.3327;MQBZ=0;MQSBZ=0;BQBZ=-1.72023;NMBZ=-0.148409;SCBZ=-1.04702;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:116,1,0 +000000F 535 . G A,<*> 0 . DP=125;I16=65,52,0,1,4309,171791,12,144,7020,421200,60,3600,2679,64385,25,625;QS=0.997223,0.00277713,0;SGB=-0.379885;RPBZ=-1.10121;MQBZ=0;MQSBZ=0;BQBZ=-1.74874;NMBZ=-0.250141;SCBZ=0.0762649;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:117,1,0 +000000F 536 . T G,A,<*> 0 . DP=125;I16=65,51,0,2,4274,171298,24,288,6960,417600,120,7200,2661,64041,48,1154;QS=0.994416,0.002792,0.002792,0;VDB=0.1;SGB=-0.453602;RPBZ=-1.74128;MQBZ=0;MQSBZ=0;BQBZ=-2.39373;NMBZ=-0.292578;SCBZ=-0.693187;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:116,1,1,0 000000F 537 . A <*> 0 . DP=125;I16=65,53,0,0,4390,175290,0,0,7080,424800,0,0,2713,65375,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:118,0 -000000F 537 . AC A 0 . INDEL;IDV=60;IMF=0.48;DP=125;I16=37,25,30,27,2480,99200,2280,91200,3720,223200,3420,205200,1399,33485,1298,31150;QS=0.260049,0.739951;VDB=0.455511;SGB=-0.693147;RPBZ=-0.543708;MQBZ=0;MQSBZ=0;BQBZ=-2.39373;NMBZ=0.469542;SCBZ=0.641853;FS=0;MQ0F=0 PL:AD 255,0,27:62,57 +000000F 537 . AC A 0 . INDEL;IDV=60;IMF=0.48;DP=125;I16=37,25,30,27,2480,99200,2280,91200,3720,223200,3420,205200,1399,33485,1298,31150;QS=0.260049,0.739951;VDB=0.383756;SGB=-0.693147;RPBZ=-0.543708;MQBZ=0;MQSBZ=0;BQBZ=-2.39373;NMBZ=0.469542;SCBZ=0.641853;FS=0;MQ0F=0 PL:AD 255,0,27:62,57 000000F 538 . C <*> 0 . DP=65;I16=36,26,0,0,2195,86349,0,0,3720,223200,0,0,1432,34600,0,0;QS=1,0;MQ0F=0 PL:AD 0,187,255:62,0 -000000F 538 . CT C 0 . INDEL;IDV=64;IMF=0.512;DP=125;I16=30,26,36,25,2240,89600,2440,97600,3360,201600,3660,219600,1279,30735,1380,33214;QS=0.218762,0.781238;VDB=0.0040309;SGB=-0.693147;RPBZ=0.242079;MQBZ=0;MQSBZ=0;BQBZ=-2.39373;NMBZ=-2.10156;SCBZ=-0.994262;FS=0;MQ0F=0 PL:AD 255,0,27:56,61 +000000F 538 . CT C 0 . INDEL;IDV=64;IMF=0.512;DP=125;I16=30,26,36,25,2240,89600,2440,97600,3360,201600,3660,219600,1279,30735,1380,33214;QS=0.218762,0.781238;VDB=0.00357075;SGB=-0.693147;RPBZ=0.242079;MQBZ=0;MQSBZ=0;BQBZ=-2.39373;NMBZ=-2.10156;SCBZ=-0.994262;FS=0;MQ0F=0 PL:AD 255,0,27:56,61 000000F 539 . T <*> 0 . DP=60;I16=29,26,0,0,2120,86238,0,0,3300,198000,0,0,1260,30374,0,0;QS=1,0;MQ0F=0 PL:AD 0,166,255:55,0 000000F 540 . G <*> 0 . DP=124;I16=64,53,0,0,4130,161310,0,0,7020,421200,0,0,2703,65511,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:117,0 000000F 541 . G <*> 0 . DP=124;I16=64,53,0,0,4143,160525,0,0,7020,421200,0,0,2705,65703,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:117,0 -000000F 542 . T G,A,<*> 0 . DP=124;I16=63,52,1,1,4035,156631,24,288,6900,414000,120,7200,2657,64685,50,1250;QS=0.994087,0.00295639,0.00295639,0;VDB=0.26;SGB=-0.453602;RPBZ=-1.46169;MQBZ=0;MQSBZ=0;BQBZ=-2.25702;NMBZ=0.136979;SCBZ=-0.905982;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:115,1,1,0 -000000F 543 . C G,A,<*> 0 . DP=122;I16=62,53,1,1,4006,154170,24,288,6900,414000,120,7200,2673,65063,50,1250;QS=0.994045,0.00297767,0.00297767,0;VDB=0.22;SGB=-0.453602;RPBZ=-0.536309;MQBZ=0;MQSBZ=0;BQBZ=-2.21926;NMBZ=0.821994;SCBZ=0.350102;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:115,1,1,0 -000000F 544 . T A,<*> 0 . DP=121;I16=62,53,0,1,4151,162625,12,144,6900,414000,60,3600,2697,65733,25,625;QS=0.997117,0.00288254,0;SGB=-0.379885;RPBZ=0.25392;MQBZ=0;MQSBZ=0;BQBZ=-1.67238;NMBZ=-0.224501;SCBZ=-1.05502;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:115,1,0 -000000F 545 . G A,<*> 0 . DP=121;I16=62,53,0,1,4078,158586,12,144,6900,414000,60,3600,2710,66228,8,64;QS=0.997066,0.00293399,0;SGB=-0.379885;RPBZ=1.61309;MQBZ=0;MQSBZ=0;BQBZ=-1.61213;NMBZ=-0.568741;SCBZ=-1.05502;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:115,1,0 -000000F 546 . G A,<*> 0 . DP=121;I16=62,53,0,1,4230,164790,12,144,6900,414000,60,3600,2689,65637,25,625;QS=0.997171,0.00282885,0;SGB=-0.379885;RPBZ=-0.970886;MQBZ=0;MQSBZ=0;BQBZ=-1.77555;NMBZ=-0.718441;SCBZ=-1.05504;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:115,1,0 -000000F 547 . A C,<*> 0 . DP=119;I16=62,51,0,1,4105,158737,12,144,6780,406800,60,3600,2686,65592,25,625;QS=0.997085,0.00291474,0;SGB=-0.379885;RPBZ=-0.89669;MQBZ=0;MQSBZ=0;BQBZ=-1.70779;NMBZ=1.50766;SCBZ=0.0314866;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:113,1,0 -000000F 548 . C G,<*> 0 . DP=119;I16=62,51,0,1,4014,154686,12,144,6780,406800,60,3600,2681,65479,25,625;QS=0.997019,0.00298063,0;SGB=-0.379885;RPBZ=-0.896616;MQBZ=0;MQSBZ=0;BQBZ=-1.67128;NMBZ=1.50766;SCBZ=0.0314869;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:113,1,0 -000000F 549 . C A,<*> 0 . DP=117;I16=33,29,29,22,2214,83510,1893,75363,3720,223200,3060,183600,1463,35977,1212,29370;QS=0.53908,0.46092,0;VDB=0.118714;SGB=-0.693147;RPBZ=-0.655016;MQBZ=0;MQSBZ=0;BQBZ=1.17837;NMBZ=0.668443;SCBZ=0.925406;FS=0;MQ0F=0 PL:AD 255,0,255,255,255,255:62,51,0 -000000F 550 . G T,<*> 0 . DP=117;I16=62,50,0,1,4113,161301,22,484,6720,403200,60,3600,2641,64473,25,625;QS=0.99468,0.00532044,0;SGB=-0.379885;RPBZ=-0.950676;MQBZ=0;MQSBZ=0;BQBZ=-1.55326;NMBZ=-0.73753;SCBZ=-1.07862;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:112,1,0 -000000F 551 . G T,A,<*> 0 . DP=116;I16=60,50,1,1,4131,164089,24,288,6600,396000,120,7200,2607,63583,50,1250;QS=0.994224,0.00288809,0.00288809,0;VDB=0.32;SGB=-0.453602;RPBZ=-1.03288;MQBZ=0;MQSBZ=0;BQBZ=-2.59034;NMBZ=0.286289;SCBZ=0.329942;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:110,1,1,0 -000000F 552 . A C,<*> 0 . DP=116;I16=60,50,1,1,3927,151331,24,288,6600,396000,120,7200,2598,63352,50,1250;QS=0.993926,0.00607441,0;VDB=0.1;SGB=-0.453602;RPBZ=-1.15369;MQBZ=0;MQSBZ=0;BQBZ=-2.37929;NMBZ=1.33204;SCBZ=-0.147932;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:110,2,0 -000000F 553 . G T,<*> 0 . DP=116;I16=60,51,1,0,4046,158108,12,144,6660,399600,60,3600,2613,63729,25,625;QS=0.997043,0.00295712,0;SGB=-0.379885;RPBZ=-0.324841;MQBZ=0;MQSBZ=0;BQBZ=-1.77886;NMBZ=0.635577;SCBZ=0.688895;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:111,1,0 +000000F 542 . T G,A,<*> 0 . DP=124;I16=63,52,1,1,4035,156631,24,288,6900,414000,120,7200,2657,64685,50,1250;QS=0.994087,0.00295639,0.00295639,0;VDB=0.26;SGB=-0.453602;RPBZ=-1.44078;MQBZ=0;MQSBZ=0;BQBZ=-2.25702;NMBZ=0.136979;SCBZ=-0.906022;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:115,1,1,0 +000000F 543 . C G,A,<*> 0 . DP=122;I16=62,53,1,1,4006,154170,24,288,6900,414000,120,7200,2673,65063,50,1250;QS=0.994045,0.00297767,0.00297767,0;VDB=0.22;SGB=-0.453602;RPBZ=-0.483734;MQBZ=0;MQSBZ=0;BQBZ=-2.21926;NMBZ=0.821994;SCBZ=0.31726;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:115,1,1,0 +000000F 544 . T A,<*> 0 . DP=121;I16=62,53,0,1,4151,162625,12,144,6900,414000,60,3600,2697,65733,25,625;QS=0.997117,0.00288254,0;SGB=-0.379885;RPBZ=0.238977;MQBZ=0;MQSBZ=0;BQBZ=-1.67238;NMBZ=-0.224501;SCBZ=-1.05505;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:115,1,0 +000000F 545 . G A,<*> 0 . DP=121;I16=62,53,0,1,4078,158586,12,144,6900,414000,60,3600,2710,66228,8,64;QS=0.997066,0.00293399,0;SGB=-0.379885;RPBZ=1.6131;MQBZ=0;MQSBZ=0;BQBZ=-1.61213;NMBZ=-0.568741;SCBZ=-1.05503;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:115,1,0 +000000F 546 . G A,<*> 0 . DP=121;I16=62,53,0,1,4230,164790,12,144,6900,414000,60,3600,2689,65637,25,625;QS=0.997171,0.00282885,0;SGB=-0.379885;RPBZ=-0.97077;MQBZ=0;MQSBZ=0;BQBZ=-1.77555;NMBZ=-0.718441;SCBZ=-1.0549;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:115,1,0 +000000F 547 . A C,<*> 0 . DP=119;I16=62,51,0,1,4105,158737,12,144,6780,406800,60,3600,2686,65592,25,625;QS=0.997085,0.00291474,0;SGB=-0.379885;RPBZ=-0.896646;MQBZ=0;MQSBZ=0;BQBZ=-1.70779;NMBZ=1.50766;SCBZ=0.0314879;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:113,1,0 +000000F 548 . C G,<*> 0 . DP=119;I16=62,51,0,1,4014,154686,12,144,6780,406800,60,3600,2681,65479,25,625;QS=0.997019,0.00298063,0;SGB=-0.379885;RPBZ=-0.896728;MQBZ=0;MQSBZ=0;BQBZ=-1.67128;NMBZ=1.50766;SCBZ=0.0314876;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:113,1,0 +000000F 549 . C A,<*> 0 . DP=117;I16=33,29,29,22,2214,83510,1893,75363,3720,223200,3060,183600,1463,35977,1212,29370;QS=0.53908,0.46092,0;VDB=0.0978768;SGB=-0.693147;RPBZ=-0.600202;MQBZ=0;MQSBZ=0;BQBZ=1.17837;NMBZ=0.668443;SCBZ=0.928426;FS=0;MQ0F=0 PL:AD 255,0,255,255,255,255:62,51,0 +000000F 550 . G T,<*> 0 . DP=117;I16=62,50,0,1,4113,161301,22,484,6720,403200,60,3600,2641,64473,25,625;QS=0.99468,0.00532044,0;SGB=-0.379885;RPBZ=-0.950536;MQBZ=0;MQSBZ=0;BQBZ=-1.55326;NMBZ=-0.73753;SCBZ=-1.07862;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:112,1,0 +000000F 551 . G T,A,<*> 0 . DP=116;I16=60,50,1,1,4131,164089,24,288,6600,396000,120,7200,2607,63583,50,1250;QS=0.994224,0.00288809,0.00288809,0;VDB=0.32;SGB=-0.453602;RPBZ=-1.01088;MQBZ=0;MQSBZ=0;BQBZ=-2.59034;NMBZ=0.286289;SCBZ=0.329971;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:110,1,1,0 +000000F 552 . A C,<*> 0 . DP=116;I16=60,50,1,1,3927,151331,24,288,6600,396000,120,7200,2598,63352,50,1250;QS=0.993926,0.00607441,0;VDB=0.1;SGB=-0.453602;RPBZ=-1.12079;MQBZ=0;MQSBZ=0;BQBZ=-2.37929;NMBZ=1.33204;SCBZ=-0.136538;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:110,2,0 +000000F 553 . G T,<*> 0 . DP=116;I16=60,51,1,0,4046,158108,12,144,6660,399600,60,3600,2613,63729,25,625;QS=0.997043,0.00295712,0;SGB=-0.379885;RPBZ=-0.35579;MQBZ=0;MQSBZ=0;BQBZ=-1.77886;NMBZ=0.635577;SCBZ=0.688792;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:111,1,0 000000F 554 . A <*> 0 . DP=113;I16=60,50,0,0,4046,159278,0,0,6600,396000,0,0,2629,64087,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:110,0 000000F 555 . G <*> 0 . DP=112;I16=60,49,0,0,4016,156988,0,0,6540,392400,0,0,2600,63438,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:109,0 000000F 556 . A <*> 0 . DP=112;I16=60,49,0,0,3915,151463,0,0,6540,392400,0,0,2588,63068,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:109,0 000000F 557 . A <*> 0 . DP=112;I16=60,49,0,0,3957,151889,0,0,6540,392400,0,0,2575,62681,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:109,0 -000000F 558 . A G,<*> 0 . DP=112;I16=60,47,0,2,3726,140280,24,288,6420,385200,120,7200,2510,60980,50,1250;QS=0.9936,0.0064,0;VDB=0.22;SGB=-0.453602;RPBZ=-1.09528;MQBZ=0;MQSBZ=0;BQBZ=-2.29525;NMBZ=0.294161;SCBZ=-0.455548;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:107,2,0 -000000F 559 . C T,<*> 0 . DP=112;I16=59,49,1,0,3985,155617,12,144,6480,388800,60,3600,2518,61092,25,625;QS=0.996998,0.00300225,0;SGB=-0.379885;RPBZ=0.74705;MQBZ=0;MQSBZ=0;BQBZ=-1.78272;NMBZ=-0.36631;SCBZ=-1.08475;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:108,1,0 +000000F 558 . A G,<*> 0 . DP=112;I16=60,47,0,2,3726,140280,24,288,6420,385200,120,7200,2510,60980,50,1250;QS=0.9936,0.0064,0;VDB=0.22;SGB=-0.453602;RPBZ=-1.14043;MQBZ=0;MQSBZ=0;BQBZ=-2.29525;NMBZ=0.294161;SCBZ=-0.444037;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:107,2,0 +000000F 559 . C T,<*> 0 . DP=112;I16=59,49,1,0,3985,155617,12,144,6480,388800,60,3600,2518,61092,25,625;QS=0.996998,0.00300225,0;SGB=-0.379885;RPBZ=0.731168;MQBZ=0;MQSBZ=0;BQBZ=-1.78272;NMBZ=-0.36631;SCBZ=-1.08527;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:108,1,0 000000F 560 . T <*> 0 . DP=110;I16=59,48,0,0,3896,150870,0,0,6420,385200,0,0,2507,60841,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:107,0 000000F 561 . G <*> 0 . DP=110;I16=59,48,0,0,3921,153367,0,0,6420,385200,0,0,2492,60440,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:107,0 -000000F 562 . T C,A,<*> 0 . DP=110;I16=58,47,1,1,3748,143542,24,288,6300,378000,120,7200,2425,58723,50,1250;QS=0.993637,0.00318134,0.00318134,0;VDB=0.32;SGB=-0.453602;RPBZ=1.04684;MQBZ=0;MQSBZ=0;BQBZ=-2.35872;NMBZ=-0.461089;SCBZ=-0.476608;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:105,1,1,0 -000000F 563 . G A,<*> 0 . DP=109;I16=59,45,0,2,3881,153011,24,288,6240,374400,120,7200,2384,57712,50,1250;QS=0.993854,0.00614597,0;VDB=0.06;SGB=-0.453602;RPBZ=-1.78855;MQBZ=0;MQSBZ=0;BQBZ=-2.59069;NMBZ=-0.314161;SCBZ=-0.939463;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:104,2,0 +000000F 562 . T C,A,<*> 0 . DP=110;I16=58,47,1,1,3748,143542,24,288,6300,378000,120,7200,2425,58723,50,1250;QS=0.993637,0.00318134,0.00318134,0;VDB=0.32;SGB=-0.453602;RPBZ=1.03535;MQBZ=0;MQSBZ=0;BQBZ=-2.35872;NMBZ=-0.461089;SCBZ=-0.452888;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:105,1,1,0 +000000F 563 . G A,<*> 0 . DP=109;I16=59,45,0,2,3881,153011,24,288,6240,374400,120,7200,2384,57712,50,1250;QS=0.993854,0.00614597,0;VDB=0.06;SGB=-0.453602;RPBZ=-1.81161;MQBZ=0;MQSBZ=0;BQBZ=-2.59069;NMBZ=-0.314161;SCBZ=-0.927311;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:104,2,0 000000F 564 . G <*> 0 . DP=109;I16=59,47,0,0,3954,155218,0,0,6360,381600,0,0,2417,58561,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:106,0 -000000F 565 . A G,<*> 0 . DP=108;I16=59,44,0,2,3818,150006,24,288,6180,370800,120,7200,2351,56943,50,1250;QS=0.993753,0.00624675,0;VDB=0.52;SGB=-0.453602;RPBZ=-0.0703465;MQBZ=0;MQSBZ=0;BQBZ=-2.43017;NMBZ=0.434607;SCBZ=-0.752941;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:103,2,0 +000000F 565 . A G,<*> 0 . DP=108;I16=59,44,0,2,3818,150006,24,288,6180,370800,120,7200,2351,56943,50,1250;QS=0.993753,0.00624675,0;VDB=0.52;SGB=-0.453602;RPBZ=-0.0703536;MQBZ=0;MQSBZ=0;BQBZ=-2.43017;NMBZ=0.434607;SCBZ=-0.752998;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:103,2,0 000000F 566 . T <*> 0 . DP=108;I16=59,46,0,0,3981,157549,0,0,6300,378000,0,0,2384,57808,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:105,0 -000000F 567 . G T,C,<*> 0 . DP=108;I16=57,46,2,0,3847,151871,20,208,6180,370800,120,7200,2318,56254,48,1154;QS=0.994828,0.00310318,0.00206879,0;VDB=0.7;SGB=-0.453602;RPBZ=0.164158;MQBZ=0;MQSBZ=0;BQBZ=-2.74966;NMBZ=-0.822312;SCBZ=0.024351;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:103,1,1,0 -000000F 568 . T C,<*> 0 . DP=106;I16=56,47,1,0,3763,145559,8,64,6180,370800,60,3600,2349,56993,25,625;QS=0.997879,0.00212145,0;SGB=-0.379885;RPBZ=0.982953;MQBZ=0;MQSBZ=0;BQBZ=-1.93576;NMBZ=-1.60247;SCBZ=-1.05628;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:103,1,0 -000000F 569 . C G,A,<*> 0 . DP=104;I16=55,45,0,2,3734,146948,24,288,6000,360000,120,7200,2309,55985,50,1250;QS=0.993614,0.00319319,0.00319319,0;VDB=0.58;SGB=-0.453602;RPBZ=-0.531164;MQBZ=0;MQSBZ=0;BQBZ=-2.54989;NMBZ=-0.193493;SCBZ=-1.48367;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:100,1,1,0 +000000F 567 . G T,C,<*> 0 . DP=108;I16=57,46,2,0,3847,151871,20,208,6180,370800,120,7200,2318,56254,48,1154;QS=0.994828,0.00310318,0.00206879,0;VDB=0.7;SGB=-0.453602;RPBZ=0.128964;MQBZ=0;MQSBZ=0;BQBZ=-2.74966;NMBZ=-0.822312;SCBZ=-0.146119;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:103,1,1,0 +000000F 568 . T C,<*> 0 . DP=106;I16=56,47,1,0,3763,145559,8,64,6180,370800,60,3600,2349,56993,25,625;QS=0.997879,0.00212145,0;SGB=-0.379885;RPBZ=0.983018;MQBZ=0;MQSBZ=0;BQBZ=-1.93576;NMBZ=-1.60247;SCBZ=-1.05631;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:103,1,0 +000000F 569 . C G,A,<*> 0 . DP=104;I16=55,45,0,2,3734,146948,24,288,6000,360000,120,7200,2309,55985,50,1250;QS=0.993614,0.00319319,0.00319319,0;VDB=0.58;SGB=-0.453602;RPBZ=-0.543243;MQBZ=0;MQSBZ=0;BQBZ=-2.54989;NMBZ=-0.193493;SCBZ=-1.48352;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:100,1,1,0 000000F 570 . T <*> 0 . DP=104;I16=55,47,0,0,3862,151566,0,0,6120,367200,0,0,2342,56784,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:102,0 000000F 571 . G <*> 0 . DP=104;I16=55,47,0,0,3733,145003,0,0,6120,367200,0,0,2325,56367,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:102,0 -000000F 572 . T A,G,<*> 0 . DP=103;I16=53,46,1,1,3664,142548,34,628,5940,356400,120,7200,2259,54733,50,1250;QS=0.990806,0.00594916,0.003245,0;VDB=0.22;SGB=-0.453602;RPBZ=0.219462;MQBZ=0;MQSBZ=0;BQBZ=-2.44659;NMBZ=1.02598;SCBZ=0.20343;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:99,1,1,0 -000000F 573 . C G,<*> 0 . DP=103;I16=54,46,0,1,3749,146645,12,144,6000,360000,60,3600,2267,54957,25,625;QS=0.996809,0.00319064,0;SGB=-0.379885;RPBZ=-0.463189;MQBZ=0;MQSBZ=0;BQBZ=-1.85387;NMBZ=-0.446862;SCBZ=-1.03764;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:100,1,0 +000000F 572 . T A,G,<*> 0 . DP=103;I16=53,46,1,1,3664,142548,34,628,5940,356400,120,7200,2259,54733,50,1250;QS=0.990806,0.00594916,0.003245,0;VDB=0.22;SGB=-0.453602;RPBZ=0.219457;MQBZ=0;MQSBZ=0;BQBZ=-2.44659;NMBZ=1.02598;SCBZ=0.216127;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:99,1,1,0 +000000F 573 . C G,<*> 0 . DP=103;I16=54,46,0,1,3749,146645,12,144,6000,360000,60,3600,2267,54957,25,625;QS=0.996809,0.00319064,0;SGB=-0.379885;RPBZ=-0.428856;MQBZ=0;MQSBZ=0;BQBZ=-1.85387;NMBZ=-0.446862;SCBZ=-1.03794;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:100,1,0 000000F 574 . A <*> 0 . DP=102;I16=54,46,0,0,3671,141999,0,0,6000,360000,0,0,2275,55165,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:100,0 000000F 575 . A <*> 0 . DP=101;I16=53,46,0,0,3653,142115,0,0,5940,356400,0,0,2259,54781,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:99,0 000000F 576 . C <*> 0 . DP=99;I16=52,45,0,0,3665,144129,0,0,5820,349200,0,0,2229,54203,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:97,0 @@ -214,80 +214,80 @@ 000000F 580 . A <*> 0 . DP=98;I16=51,45,0,0,3569,139629,0,0,5760,345600,0,0,2141,51599,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:96,0 000000F 581 . C <*> 0 . DP=95;I16=49,44,0,0,3512,137782,0,0,5580,334800,0,0,2096,50392,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:93,0 000000F 582 . A <*> 0 . DP=94;I16=49,43,0,0,3411,135315,0,0,5520,331200,0,0,2073,49673,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:92,0 -000000F 583 . G C,<*> 0 . DP=90;I16=46,41,1,0,3292,129550,12,144,5220,313200,60,3600,1985,47479,25,625;QS=0.996368,0.00363196,0;SGB=-0.379885;RPBZ=0.334731;MQBZ=0;MQSBZ=0;BQBZ=-1.89321;NMBZ=-0.512824;SCBZ=-1.01113;FS=0;MQ0F=0 PL:AD 0,245,255,255,255,255:87,1,0 +000000F 583 . G C,<*> 0 . DP=90;I16=46,41,1,0,3292,129550,12,144,5220,313200,60,3600,1985,47479,25,625;QS=0.996368,0.00363196,0;SGB=-0.379885;RPBZ=0.334737;MQBZ=0;MQSBZ=0;BQBZ=-1.89321;NMBZ=-0.512824;SCBZ=-1.01118;FS=0;MQ0F=0 PL:AD 0,245,255,255,255,255:87,1,0 000000F 584 . A <*> 0 . DP=87;I16=45,40,0,0,3152,123280,0,0,5100,306000,0,0,1940,46204,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:85,0 000000F 585 . A <*> 0 . DP=88;I16=44,40,0,0,3202,127432,0,0,5040,302400,0,0,1914,45520,0,0;QS=1,0;MQ0F=0 PL:AD 0,253,255:84,0 -000000F 586 . A G,<*> 0 . DP=88;I16=43,40,1,0,2964,114852,12,144,4980,298800,60,3600,1875,44509,16,256;QS=0.995968,0.00403226,0;SGB=-0.379885;RPBZ=0.887054;MQBZ=0;MQSBZ=0;BQBZ=-1.73561;NMBZ=1.61188;SCBZ=1.05463;FS=0;MQ0F=0 PL:AD 0,234,255,250,255,255:83,1,0 -000000F 587 . A C,<*> 0 . DP=88;I16=45,40,0,1,2997,115249,12,144,5100,306000,60,3600,1891,44583,25,625;QS=0.996012,0.00398804,0;SGB=-0.379885;RPBZ=-0.584357;MQBZ=0;MQSBZ=0;BQBZ=-1.64438;NMBZ=1.51363;SCBZ=0.548818;FS=0;MQ0F=0 PL:AD 0,240,255,255,255,255:85,1,0 +000000F 586 . A G,<*> 0 . DP=88;I16=43,40,1,0,2964,114852,12,144,4980,298800,60,3600,1875,44509,16,256;QS=0.995968,0.00403226,0;SGB=-0.379885;RPBZ=0.866495;MQBZ=0;MQSBZ=0;BQBZ=-1.73561;NMBZ=1.61188;SCBZ=1.14098;FS=0;MQ0F=0 PL:AD 0,234,255,250,255,255:83,1,0 +000000F 587 . A C,<*> 0 . DP=88;I16=45,40,0,1,2997,115249,12,144,5100,306000,60,3600,1891,44583,25,625;QS=0.996012,0.00398804,0;SGB=-0.379885;RPBZ=-0.584321;MQBZ=0;MQSBZ=0;BQBZ=-1.64438;NMBZ=1.51363;SCBZ=0.548806;FS=0;MQ0F=0 PL:AD 0,240,255,255,255,255:85,1,0 000000F 588 . A <*> 0 . DP=87;I16=45,40,0,0,2971,113817,0,0,5100,306000,0,0,1891,44401,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:85,0 -000000F 589 . G A,<*> 0 . DP=87;I16=44,40,1,0,3059,117323,12,144,5040,302400,60,3600,1840,42970,25,625;QS=0.996092,0.00390752,0;SGB=-0.379885;RPBZ=0.550504;MQBZ=0;MQSBZ=0;BQBZ=-1.79452;NMBZ=1.61324;SCBZ=1.6633;FS=0;MQ0F=0 PL:AD 0,237,255,253,255,255:84,1,0 +000000F 589 . G A,<*> 0 . DP=87;I16=44,40,1,0,3059,117323,12,144,5040,302400,60,3600,1840,42970,25,625;QS=0.996092,0.00390752,0;SGB=-0.379885;RPBZ=0.550542;MQBZ=0;MQSBZ=0;BQBZ=-1.79452;NMBZ=1.61324;SCBZ=1.68471;FS=0;MQ0F=0 PL:AD 0,237,255,253,255,255:84,1,0 000000F 590 . T <*> 0 . DP=87;I16=45,40,0,0,3019,114421,0,0,5100,306000,0,0,1839,42841,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:85,0 -000000F 591 . G C,<*> 0 . DP=86;I16=43,40,1,0,3033,117015,12,144,4980,298800,60,3600,1807,42121,3,9;QS=0.996059,0.00394089,0;SGB=-0.379885;RPBZ=1.67115;MQBZ=0;MQSBZ=0;BQBZ=-1.80181;NMBZ=-1.0334;SCBZ=-1.01595;FS=0;MQ0F=0 PL:AD 0,234,255,250,255,255:83,1,0 -000000F 592 . A C,<*> 0 . DP=85;I16=44,38,0,2,2821,106231,24,288,4920,295200,120,7200,1748,40690,36,746;QS=0.991564,0.00843585,0;VDB=0.5;SGB=-0.453602;RPBZ=0.469689;MQBZ=0;MQSBZ=0;BQBZ=-2.1998;NMBZ=0.823216;SCBZ=-0.107629;FS=0;MQ0F=0 PL:AD 0,217,255,247,255,255:82,2,0 -000000F 593 . C G,A,<*> 0 . DP=84;I16=42,39,1,1,2912,110366,24,288,4860,291600,120,7200,1709,39543,50,1250;QS=0.991826,0.00408719,0.00408719,0;VDB=0.36;SGB=-0.453602;RPBZ=-0.0594179;MQBZ=0;MQSBZ=0;BQBZ=-2.57106;NMBZ=0.699311;SCBZ=-0.108759;FS=0;MQ0F=0 PL:AD 0,228,255,228,255,255,244,255,255,255:81,1,1,0 +000000F 591 . G C,<*> 0 . DP=86;I16=43,40,1,0,3033,117015,12,144,4980,298800,60,3600,1807,42121,3,9;QS=0.996059,0.00394089,0;SGB=-0.379885;RPBZ=1.67089;MQBZ=0;MQSBZ=0;BQBZ=-1.80181;NMBZ=-1.0334;SCBZ=-1.01597;FS=0;MQ0F=0 PL:AD 0,234,255,250,255,255:83,1,0 +000000F 592 . A C,<*> 0 . DP=85;I16=44,38,0,2,2821,106231,24,288,4920,295200,120,7200,1748,40690,36,746;QS=0.991564,0.00843585,0;VDB=0.5;SGB=-0.453602;RPBZ=0.484389;MQBZ=0;MQSBZ=0;BQBZ=-2.1998;NMBZ=0.823216;SCBZ=-0.0922779;FS=0;MQ0F=0 PL:AD 0,217,255,247,255,255:82,2,0 +000000F 593 . C G,A,<*> 0 . DP=84;I16=42,39,1,1,2912,110366,24,288,4860,291600,120,7200,1709,39543,50,1250;QS=0.991826,0.00408719,0.00408719,0;VDB=0.36;SGB=-0.453602;RPBZ=-0.0891287;MQBZ=0;MQSBZ=0;BQBZ=-2.57106;NMBZ=0.699311;SCBZ=-0.108692;FS=0;MQ0F=0 PL:AD 0,228,255,228,255,255,244,255,255,255:81,1,1,0 000000F 594 . T <*> 0 . DP=84;I16=43,40,0,0,2911,110919,0,0,4980,298800,0,0,1733,40151,0,0;QS=1,0;MQ0F=0 PL:AD 0,250,255:83,0 000000F 595 . G <*> 0 . DP=82;I16=42,39,0,0,2849,108157,0,0,4860,291600,0,0,1681,38837,0,0;QS=1,0;MQ0F=0 PL:AD 0,244,255:81,0 -000000F 596 . A C,<*> 0 . DP=81;I16=42,37,0,1,2846,108902,12,144,4740,284400,60,3600,1613,37303,25,625;QS=0.995801,0.00419874,0;SGB=-0.379885;RPBZ=-0.974789;MQBZ=0;MQSBZ=0;BQBZ=-1.73819;NMBZ=0.130213;SCBZ=0.227818;FS=0;MQ0F=0 PL:AD 0,222,255,238,255,255:79,1,0 -000000F 597 . T G,<*> 0 . DP=80;I16=42,36,0,1,2742,102116,12,144,4680,280800,60,3600,1574,36614,15,225;QS=0.995643,0.0043573,0;SGB=-0.379885;RPBZ=0.833692;MQBZ=0;MQSBZ=0;BQBZ=-1.70797;NMBZ=-0.131854;SCBZ=0.254289;FS=0;MQ0F=0 PL:AD 0,219,255,235,255,255:78,1,0 +000000F 596 . A C,<*> 0 . DP=81;I16=42,37,0,1,2846,108902,12,144,4740,284400,60,3600,1613,37303,25,625;QS=0.995801,0.00419874,0;SGB=-0.379885;RPBZ=-0.9748;MQBZ=0;MQSBZ=0;BQBZ=-1.73819;NMBZ=0.130213;SCBZ=0.250526;FS=0;MQ0F=0 PL:AD 0,222,255,238,255,255:79,1,0 +000000F 597 . T G,<*> 0 . DP=80;I16=42,36,0,1,2742,102116,12,144,4680,280800,60,3600,1574,36614,15,225;QS=0.995643,0.0043573,0;SGB=-0.379885;RPBZ=0.833621;MQBZ=0;MQSBZ=0;BQBZ=-1.70797;NMBZ=-0.131854;SCBZ=0.254296;FS=0;MQ0F=0 PL:AD 0,219,255,235,255,255:78,1,0 000000F 598 . T <*> 0 . DP=79;I16=41,37,0,0,2839,109553,0,0,4680,280800,0,0,1562,36238,0,0;QS=1,0;MQ0F=0 PL:AD 0,235,255:78,0 000000F 599 . A <*> 0 . DP=77;I16=40,36,0,0,2770,106710,0,0,4560,273600,0,0,1528,35518,0,0;QS=1,0;MQ0F=0 PL:AD 0,229,255:76,0 000000F 600 . G <*> 0 . DP=77;I16=40,36,0,0,2714,103152,0,0,4560,273600,0,0,1498,34792,0,0;QS=1,0;MQ0F=0 PL:AD 0,229,255:76,0 -000000F 601 . T G,C,<*> 0 . DP=77;I16=39,35,1,1,2583,97801,24,288,4440,266400,120,7200,1417,32827,50,1250;QS=0.990798,0.00460123,0.00460123,0;VDB=0.1;SGB=-0.453602;RPBZ=-0.795645;MQBZ=0;MQSBZ=0;BQBZ=-2.28816;NMBZ=0.569195;SCBZ=0.0680038;FS=0;MQ0F=0 PL:AD 0,207,255,207,255,255,223,255,255,255:74,1,1,0 -000000F 602 . T A,C,<*> 0 . DP=74;I16=37,33,1,2,2416,90472,61,1657,4200,252000,180,10800,1357,31631,60,1350;QS=0.975373,0.019782,0.00484457,0;VDB=0.568985;SGB=-0.511536;RPBZ=0.33372;MQBZ=0;MQSBZ=0;BQBZ=-2.13242;NMBZ=0.306281;SCBZ=0.85994;FS=0;MQ0F=0 PL:AD 0,164,255,195,255,255,211,255,255,255:70,2,1,0 -000000F 603 . A C,<*> 0 . DP=68;I16=35,30,1,0,2312,88408,12,144,3900,234000,60,3600,1347,31297,25,625;QS=0.994837,0.00516351,0;SGB=-0.379885;RPBZ=-0.131306;MQBZ=0;MQSBZ=0;BQBZ=-1.66952;NMBZ=0.526139;SCBZ=-1.04313;FS=0;MQ0F=0 PL:AD 0,180,255,196,255,255:65,1,0 +000000F 601 . T G,C,<*> 0 . DP=77;I16=39,35,1,1,2583,97801,24,288,4440,266400,120,7200,1417,32827,50,1250;QS=0.990798,0.00460123,0.00460123,0;VDB=0.1;SGB=-0.453602;RPBZ=-0.795612;MQBZ=0;MQSBZ=0;BQBZ=-2.28816;NMBZ=0.569195;SCBZ=0.0680273;FS=0;MQ0F=0 PL:AD 0,207,255,207,255,255,223,255,255,255:74,1,1,0 +000000F 602 . T A,C,<*> 0 . DP=74;I16=37,33,1,2,2416,90472,61,1657,4200,252000,180,10800,1357,31631,60,1350;QS=0.975373,0.019782,0.00484457,0;VDB=0.568985;SGB=-0.511536;RPBZ=0.333732;MQBZ=0;MQSBZ=0;BQBZ=-2.13242;NMBZ=0.306281;SCBZ=0.845379;FS=0;MQ0F=0 PL:AD 0,164,255,195,255,255,211,255,255,255:70,2,1,0 +000000F 603 . A C,<*> 0 . DP=68;I16=35,30,1,0,2312,88408,12,144,3900,234000,60,3600,1347,31297,25,625;QS=0.994837,0.00516351,0;SGB=-0.379885;RPBZ=-0.131301;MQBZ=0;MQSBZ=0;BQBZ=-1.66952;NMBZ=0.526139;SCBZ=-1.04349;FS=0;MQ0F=0 PL:AD 0,180,255,196,255,255:65,1,0 000000F 604 . G <*> 0 . DP=67;I16=36,30,0,0,2403,93039,0,0,3960,237600,0,0,1349,31351,0,0;QS=1,0;MQ0F=0 PL:AD 0,199,255:66,0 -000000F 605 . A G,<*> 0 . DP=66;I16=35,28,1,1,2254,85780,24,288,3780,226800,120,7200,1292,30038,33,689;QS=0.989464,0.0105356,0;VDB=0.36;SGB=-0.453602;RPBZ=0.589067;MQBZ=0;MQSBZ=0;BQBZ=-2.37279;NMBZ=2.34191;SCBZ=1.58673;FS=0;MQ0F=0 PL:AD 0,162,255,190,255,255:63,2,0 +000000F 605 . A G,<*> 0 . DP=66;I16=35,28,1,1,2254,85780,24,288,3780,226800,120,7200,1292,30038,33,689;QS=0.989464,0.0105356,0;VDB=0.36;SGB=-0.453602;RPBZ=0.589131;MQBZ=0;MQSBZ=0;BQBZ=-2.37279;NMBZ=2.34191;SCBZ=1.62638;FS=0;MQ0F=0 PL:AD 0,162,255,190,255,255:63,2,0 000000F 606 . T G,<*> 0 . DP=65;I16=34,29,1,0,2247,87073,22,484,3780,226800,60,3600,1287,29883,13,169;QS=0.990304,0.0096959,0;SGB=-0.379885;RPBZ=1.00206;MQBZ=0;MQSBZ=0;BQBZ=-1.38823;NMBZ=-0.596984;SCBZ=-1.04683;FS=0;MQ0F=0 PL:AD 0,170,255,190,255,255:63,1,0 000000F 607 . G <*> 0 . DP=64;I16=35,28,0,0,2255,86451,0,0,3780,226800,0,0,1255,29027,0,0;QS=1,0;MQ0F=0 PL:AD 0,190,255:63,0 -000000F 608 . T G,<*> 0 . DP=62;I16=33,27,1,0,2177,84023,8,64,3600,216000,60,3600,1182,27240,25,625;QS=0.996339,0.00366133,0;SGB=-0.379885;RPBZ=-0.0284158;MQBZ=0;MQSBZ=0;BQBZ=-1.89659;NMBZ=0.540939;SCBZ=-1.04114;FS=0;MQ0F=0 PL:AD 0,166,255,181,255,255:60,1,0 -000000F 609 . A G,<*> 0 . DP=60;I16=33,25,0,1,2036,77468,12,144,3480,208800,60,3600,1139,26307,25,625;QS=0.994141,0.00585938,0;SGB=-0.379885;RPBZ=-0.0881423;MQBZ=0;MQSBZ=0;BQBZ=-1.68674;NMBZ=1.64902;SCBZ=1.23648;FS=0;MQ0F=0 PL:AD 0,160,255,175,255,255:58,1,0 +000000F 608 . T G,<*> 0 . DP=62;I16=33,27,1,0,2177,84023,8,64,3600,216000,60,3600,1182,27240,25,625;QS=0.996339,0.00366133,0;SGB=-0.379885;RPBZ=0.0852552;MQBZ=0;MQSBZ=0;BQBZ=-1.89659;NMBZ=0.540939;SCBZ=-1.04111;FS=0;MQ0F=0 PL:AD 0,166,255,181,255,255:60,1,0 +000000F 609 . A G,<*> 0 . DP=60;I16=33,25,0,1,2036,77468,12,144,3480,208800,60,3600,1139,26307,25,625;QS=0.994141,0.00585938,0;SGB=-0.379885;RPBZ=-0.0881423;MQBZ=0;MQSBZ=0;BQBZ=-1.68674;NMBZ=1.64902;SCBZ=1.23654;FS=0;MQ0F=0 PL:AD 0,160,255,175,255,255:58,1,0 000000F 610 . A <*> 0 . DP=59;I16=33,25,0,0,2025,77505,0,0,3480,208800,0,0,1144,26524,0,0;QS=1,0;MQ0F=0 PL:AD 0,175,255:58,0 -000000F 611 . C T,<*> 0 . DP=55;I16=14,12,16,12,990,39320,1009,38281,1560,93600,1680,100800,576,13946,550,12206;QS=0.495248,0.504752,0;VDB=2.36399e-06;SGB=-0.693054;RPBZ=1.73241;MQBZ=0;MQSBZ=0;BQBZ=-0.270305;NMBZ=-0.720132;SCBZ=-0.605207;FS=0;MQ0F=0 PL:AD 255,0,255,255,255,255:26,28,0 +000000F 611 . C T,<*> 0 . DP=55;I16=14,12,16,12,990,39320,1009,38281,1560,93600,1680,100800,576,13946,550,12206;QS=0.495248,0.504752,0;VDB=1.84196e-06;SGB=-0.693054;RPBZ=1.75927;MQBZ=0;MQSBZ=0;BQBZ=-0.270305;NMBZ=-0.720132;SCBZ=-0.614376;FS=0;MQ0F=0 PL:AD 255,0,255,255,255,255:26,28,0 000000F 612 . T <*> 0 . DP=54;I16=29,24,0,0,1898,72790,0,0,3180,190800,0,0,1111,25815,0,0;QS=1,0;MQ0F=0 PL:AD 0,160,255:53,0 -000000F 613 . A G,C,<*> 0 . DP=54;I16=27,24,2,0,1946,77058,24,288,3060,183600,120,7200,1046,24258,50,1250;QS=0.987817,0.00609137,0.00609137,0;VDB=0.06;SGB=-0.453602;RPBZ=0.584004;MQBZ=0;MQSBZ=0;BQBZ=-2.67554;NMBZ=0.842481;SCBZ=0.495456;FS=0;MQ0F=0 PL:AD 0,139,255,139,255,255,154,255,255,255:51,1,1,0 +000000F 613 . A G,C,<*> 0 . DP=54;I16=27,24,2,0,1946,77058,24,288,3060,183600,120,7200,1046,24258,50,1250;QS=0.987817,0.00609137,0.00609137,0;VDB=0.06;SGB=-0.453602;RPBZ=0.537207;MQBZ=0;MQSBZ=0;BQBZ=-2.67554;NMBZ=0.842481;SCBZ=0.495445;FS=0;MQ0F=0 PL:AD 0,139,255,139,255,255,154,255,255,255:51,1,1,0 000000F 614 . A C,<*> 0 . DP=53;I16=28,23,0,1,1870,73000,12,144,3060,183600,60,3600,1054,24458,25,625;QS=0.993624,0.0063762,0;SGB=-0.379885;RPBZ=0.033359;MQBZ=0;MQSBZ=0;BQBZ=-1.88;NMBZ=1.70474;SCBZ=1.24225;FS=0;MQ0F=0 PL:AD 0,139,255,154,255,255:51,1,0 000000F 615 . T <*> 0 . DP=53;I16=28,24,0,0,1924,74686,0,0,3120,187200,0,0,1061,24643,0,0;QS=1,0;MQ0F=0 PL:AD 0,157,255:52,0 -000000F 616 . T G,<*> 0 . DP=53;I16=28,23,0,1,1815,69225,12,144,3060,183600,60,3600,1017,23565,25,625;QS=0.993432,0.00656814,0;SGB=-0.379885;RPBZ=-0.833672;MQBZ=0;MQSBZ=0;BQBZ=-1.66586;NMBZ=-0.200558;SCBZ=0.352496;FS=0;MQ0F=0 PL:AD 0,139,255,154,255,255:51,1,0 +000000F 616 . T G,<*> 0 . DP=53;I16=28,23,0,1,1815,69225,12,144,3060,183600,60,3600,1017,23565,25,625;QS=0.993432,0.00656814,0;SGB=-0.379885;RPBZ=-0.833529;MQBZ=0;MQSBZ=0;BQBZ=-1.66586;NMBZ=-0.200558;SCBZ=0.352496;FS=0;MQ0F=0 PL:AD 0,139,255,154,255,255:51,1,0 000000F 617 . T <*> 0 . DP=52;I16=27,24,0,0,1844,70962,0,0,3060,183600,0,0,1024,23774,0,0;QS=1,0;MQ0F=0 PL:AD 0,154,255:51,0 000000F 618 . C <*> 0 . DP=52;I16=27,24,0,0,1782,67390,0,0,3060,183600,0,0,1005,23345,0,0;QS=1,0;MQ0F=0 PL:AD 0,154,255:51,0 -000000F 619 . A C,<*> 0 . DP=52;I16=26,24,1,0,1756,66842,12,144,3000,180000,60,3600,961,22329,25,625;QS=0.993213,0.00678733,0;SGB=-0.379885;RPBZ=0.612067;MQBZ=0;MQSBZ=0;BQBZ=-1.58836;NMBZ=0.647334;SCBZ=1.65865;FS=0;MQ0F=0 PL:AD 0,136,255,151,255,255:50,1,0 +000000F 619 . A C,<*> 0 . DP=52;I16=26,24,1,0,1756,66842,12,144,3000,180000,60,3600,961,22329,25,625;QS=0.993213,0.00678733,0;SGB=-0.379885;RPBZ=0.612053;MQBZ=0;MQSBZ=0;BQBZ=-1.58836;NMBZ=0.647334;SCBZ=1.65684;FS=0;MQ0F=0 PL:AD 0,136,255,151,255,255:50,1,0 000000F 620 . A <*> 0 . DP=50;I16=25,24,0,0,1670,63616,0,0,2940,176400,0,0,969,22599,0,0;QS=1,0;MQ0F=0 PL:AD 0,148,255:49,0 000000F 621 . C <*> 0 . DP=49;I16=24,24,0,0,1738,67580,0,0,2880,172800,0,0,953,22277,0,0;QS=1,0;MQ0F=0 PL:AD 0,144,255:48,0 000000F 622 . T <*> 0 . DP=47;I16=23,23,0,0,1642,63060,0,0,2760,165600,0,0,921,21681,0,0;QS=1,0;MQ0F=0 PL:AD 0,138,255:46,0 -000000F 623 . A G,C,<*> 0 . DP=46;I16=22,21,1,1,1593,61369,24,288,2580,154800,120,7200,862,20368,44,986;QS=0.985158,0.00742115,0.00742115,0;VDB=0.28;SGB=-0.453602;RPBZ=0.027578;MQBZ=0;MQSBZ=0;BQBZ=-2.46441;NMBZ=0.552785;SCBZ=-0.437307;FS=0;MQ0F=0 PL:AD 0,116,255,116,255,255,129,255,255,255:43,1,1,0 +000000F 623 . A G,C,<*> 0 . DP=46;I16=22,21,1,1,1593,61369,24,288,2580,154800,120,7200,862,20368,44,986;QS=0.985158,0.00742115,0.00742115,0;VDB=0.28;SGB=-0.453602;RPBZ=0.110272;MQBZ=0;MQSBZ=0;BQBZ=-2.46441;NMBZ=0.552785;SCBZ=-0.699329;FS=0;MQ0F=0 PL:AD 0,116,255,116,255,255,129,255,255,255:43,1,1,0 000000F 624 . T <*> 0 . DP=45;I16=22,22,0,0,1522,57304,0,0,2640,158400,0,0,892,21056,0,0;QS=1,0;MQ0F=0 PL:AD 0,132,255:44,0 000000F 625 . C <*> 0 . DP=43;I16=20,23,0,0,1462,54230,0,0,2580,154800,0,0,905,21409,0,0;QS=1,0;MQ0F=0 PL:AD 0,129,255:43,0 -000000F 626 . T A,<*> 0 . DP=42;I16=19,22,0,1,1407,52739,12,144,2460,147600,60,3600,869,20535,25,625;QS=0.991543,0.00845666,0;SGB=-0.379885;RPBZ=0.0826327;MQBZ=0;MQSBZ=0;BQBZ=-1.63079;NMBZ=-0.0413668;SCBZ=-0.997981;FS=0;MQ0F=0 PL:AD 0,110,255,123,255,255:41,1,0 +000000F 626 . T A,<*> 0 . DP=42;I16=19,22,0,1,1407,52739,12,144,2460,147600,60,3600,869,20535,25,625;QS=0.991543,0.00845666,0;SGB=-0.379885;RPBZ=0.0826192;MQBZ=0;MQSBZ=0;BQBZ=-1.63079;NMBZ=-0.0413668;SCBZ=-0.998652;FS=0;MQ0F=0 PL:AD 0,110,255,123,255,255:41,1,0 000000F 627 . A <*> 0 . DP=42;I16=19,23,0,0,1458,54660,0,0,2520,151200,0,0,880,20786,0,0;QS=1,0;MQ0F=0 PL:AD 0,126,255:42,0 -000000F 628 . G C,<*> 0 . DP=41;I16=17,23,1,0,1491,57863,12,144,2400,144000,60,3600,838,19618,24,576;QS=0.992016,0.00798403,0;SGB=-0.379885;RPBZ=0.33846;MQBZ=0;MQSBZ=0;BQBZ=-1.99912;NMBZ=-0.720676;SCBZ=-0.981384;FS=0;MQ0F=0 PL:AD 0,107,255,120,255,255:40,1,0 +000000F 628 . G C,<*> 0 . DP=41;I16=17,23,1,0,1491,57863,12,144,2400,144000,60,3600,838,19618,24,576;QS=0.992016,0.00798403,0;SGB=-0.379885;RPBZ=0.296217;MQBZ=0;MQSBZ=0;BQBZ=-1.99912;NMBZ=-0.720676;SCBZ=-0.981384;FS=0;MQ0F=0 PL:AD 0,107,255,120,255,255:40,1,0 000000F 629 . T <*> 0 . DP=40;I16=18,22,0,0,1452,55272,0,0,2400,144000,0,0,827,19349,0,0;QS=1,0;MQ0F=0 PL:AD 0,120,255:40,0 000000F 630 . C <*> 0 . DP=38;I16=16,22,0,0,1338,50174,0,0,2280,136800,0,0,812,18860,0,0;QS=1,0;MQ0F=0 PL:AD 0,114,255:38,0 -000000F 631 . T G,<*> 0 . DP=37;I16=14,22,1,0,1280,48224,32,1024,2160,129600,60,3600,783,18083,11,121;QS=0.97561,0.0243902,0;SGB=-0.379885;RPBZ=1.36152;MQBZ=0;MQSBZ=0;BQBZ=-1.06419;NMBZ=0.939374;SCBZ=-0.906827;FS=0;MQ0F=0 PL:AD 0,79,255,108,255,255:36,1,0 +000000F 631 . T G,<*> 0 . DP=37;I16=14,22,1,0,1280,48224,32,1024,2160,129600,60,3600,783,18083,11,121;QS=0.97561,0.0243902,0;SGB=-0.379885;RPBZ=1.36088;MQBZ=0;MQSBZ=0;BQBZ=-1.06419;NMBZ=0.939374;SCBZ=-0.906765;FS=0;MQ0F=0 PL:AD 0,79,255,108,255,255:36,1,0 000000F 632 . T <*> 0 . DP=36;I16=15,21,0,0,1320,50548,0,0,2160,129600,0,0,761,17359,0,0;QS=1,0;MQ0F=0 PL:AD 0,108,255:36,0 -000000F 633 . C A,<*> 0 . DP=35;I16=14,19,0,2,1183,44803,24,288,1980,118800,120,7200,678,15322,47,1109;QS=0.980116,0.019884,0;VDB=0.26;SGB=-0.453602;RPBZ=0.534802;MQBZ=0;MQSBZ=0;BQBZ=-2.3085;NMBZ=1.56853;SCBZ=1.47371;FS=0;MQ0F=0 PL:AD 0,76,255,99,255,255:33,2,0 +000000F 633 . C A,<*> 0 . DP=35;I16=14,19,0,2,1183,44803,24,288,1980,118800,120,7200,678,15322,47,1109;QS=0.980116,0.019884,0;VDB=0.26;SGB=-0.453602;RPBZ=0.463397;MQBZ=0;MQSBZ=0;BQBZ=-2.3085;NMBZ=1.56853;SCBZ=1.47371;FS=0;MQ0F=0 PL:AD 0,76,255,99,255,255:33,2,0 000000F 634 . C <*> 0 . DP=35;I16=14,21,0,0,1290,49572,0,0,2100,126000,0,0,708,15898,0,0;QS=1,0;MQ0F=0 PL:AD 0,105,255:35,0 000000F 635 . T <*> 0 . DP=35;I16=14,21,0,0,1242,47888,0,0,2100,126000,0,0,691,15399,0,0;QS=1,0;MQ0F=0 PL:AD 0,105,255:35,0 -000000F 636 . C T,<*> 0 . DP=34;I16=13,20,1,0,1163,44105,12,144,1980,118800,60,3600,643,14453,16,256;QS=0.989787,0.0102128,0;SGB=-0.379885;RPBZ=0.665292;MQBZ=0;MQSBZ=0;BQBZ=-1.57615;NMBZ=-0.511566;SCBZ=-0.841547;FS=0;MQ0F=0 PL:AD 0,87,255,99,255,255:33,1,0 +000000F 636 . C T,<*> 0 . DP=34;I16=13,20,1,0,1163,44105,12,144,1980,118800,60,3600,643,14453,16,256;QS=0.989787,0.0102128,0;SGB=-0.379885;RPBZ=0.66524;MQBZ=0;MQSBZ=0;BQBZ=-1.57615;NMBZ=-0.511566;SCBZ=-0.84147;FS=0;MQ0F=0 PL:AD 0,87,255,99,255,255:33,1,0 000000F 637 . T <*> 0 . DP=33;I16=14,19,0,0,1151,43717,0,0,1980,118800,0,0,627,14033,0,0;QS=1,0;MQ0F=0 PL:AD 0,99,255:33,0 000000F 638 . A <*> 0 . DP=32;I16=13,19,0,0,1113,41153,0,0,1920,115200,0,0,605,13531,0,0;QS=1,0;MQ0F=0 PL:AD 0,96,255:32,0 -000000F 639 . A T,<*> 0 . DP=30;I16=13,16,0,1,965,34529,12,144,1740,104400,60,3600,577,12917,13,169;QS=0.987718,0.0122825,0;SGB=-0.379885;RPBZ=0.988885;MQBZ=0;MQSBZ=0;BQBZ=-1.63451;NMBZ=0.405999;SCBZ=-0.878438;FS=0;MQ0F=0 PL:AD 0,75,255,87,255,255:29,1,0 +000000F 639 . A T,<*> 0 . DP=30;I16=13,16,0,1,965,34529,12,144,1740,104400,60,3600,577,12917,13,169;QS=0.987718,0.0122825,0;SGB=-0.379885;RPBZ=0.988773;MQBZ=0;MQSBZ=0;BQBZ=-1.63451;NMBZ=0.405999;SCBZ=-0.878553;FS=0;MQ0F=0 PL:AD 0,75,255,87,255,255:29,1,0 000000F 640 . A <*> 0 . DP=29;I16=12,17,0,0,994,36924,0,0,1740,104400,0,0,575,12621,0,0;QS=1,0;MQ0F=0 PL:AD 0,87,255:29,0 000000F 641 . G T,<*> 0 . DP=27;I16=11,15,0,1,869,31995,12,144,1560,93600,60,3600,529,11623,11,121;QS=0.986379,0.0136209,0;SGB=-0.379885;RPBZ=1.35554;MQBZ=0;MQSBZ=0;BQBZ=-1.5086;NMBZ=-0.322848;SCBZ=-0.793551;FS=0;MQ0F=0 PL:AD 0,66,255,78,255,255:26,1,0 -000000F 642 . A C,<*> 0 . DP=26;I16=11,14,0,1,850,31010,22,484,1500,90000,60,3600,504,11078,9,81;QS=0.974771,0.0252294,0;SGB=-0.379885;RPBZ=1.4198;MQBZ=0;MQSBZ=0;BQBZ=-1.18957;NMBZ=1.27431;SCBZ=0.532674;FS=0;MQ0F=0 PL:AD 0,56,255,75,255,255:25,1,0 +000000F 642 . A C,<*> 0 . DP=26;I16=11,14,0,1,850,31010,22,484,1500,90000,60,3600,504,11078,9,81;QS=0.974771,0.0252294,0;SGB=-0.379885;RPBZ=1.41458;MQBZ=0;MQSBZ=0;BQBZ=-1.18957;NMBZ=1.27431;SCBZ=0.532911;FS=0;MQ0F=0 PL:AD 0,56,255,75,255,255:25,1,0 000000F 643 . C <*> 0 . DP=26;I16=11,15,0,0,912,34334,0,0,1560,93600,0,0,499,10747,0,0;QS=1,0;MQ0F=0 PL:AD 0,78,255:26,0 -000000F 644 . C A,<*> 0 . DP=26;I16=11,14,0,1,869,31707,12,144,1500,90000,60,3600,464,9914,20,400;QS=0.986379,0.0136209,0;SGB=-0.379885;RPBZ=0.335056;MQBZ=0;MQSBZ=0;BQBZ=-1.6731;NMBZ=1.00586;SCBZ=0.989252;FS=0;MQ0F=0 PL:AD 0,63,255,75,255,255:25,1,0 +000000F 644 . C A,<*> 0 . DP=26;I16=11,14,0,1,869,31707,12,144,1500,90000,60,3600,464,9914,20,400;QS=0.986379,0.0136209,0;SGB=-0.379885;RPBZ=0.268045;MQBZ=0;MQSBZ=0;BQBZ=-1.6731;NMBZ=1.00586;SCBZ=0.989693;FS=0;MQ0F=0 PL:AD 0,63,255,75,255,255:25,1,0 000000F 645 . C <*> 0 . DP=26;I16=11,15,0,0,911,33421,0,0,1560,93600,0,0,466,9764,0,0;QS=1,0;MQ0F=0 PL:AD 0,78,255:26,0 000000F 646 . C <*> 0 . DP=26;I16=11,15,0,0,850,29718,0,0,1560,93600,0,0,447,9201,0,0;QS=1,0;MQ0F=0 PL:AD 0,78,255:26,0 000000F 647 . T C,<*> 0 . DP=26;I16=11,14,0,1,898,34076,12,144,1500,90000,60,3600,423,8651,5,25;QS=0.986813,0.0131868,0;SGB=-0.379885;RPBZ=1.14097;MQBZ=0;MQSBZ=0;BQBZ=-1.57982;NMBZ=0.737633;SCBZ=-0.760963;FS=0;MQ0F=0 PL:AD 0,63,255,75,255,255:25,1,0 000000F 648 . A <*> 0 . DP=26;I16=11,15,0,0,870,32110,0,0,1560,93600,0,0,407,8091,0,0;QS=1,0;MQ0F=0 PL:AD 0,78,255:26,0 000000F 649 . C <*> 0 . DP=26;I16=11,15,0,0,928,35102,0,0,1560,93600,0,0,386,7548,0,0;QS=1,0;MQ0F=0 PL:AD 0,78,255:26,0 -000000F 650 . T C,<*> 0 . DP=26;I16=11,14,0,1,897,33867,12,144,1500,90000,60,3600,359,6973,5,25;QS=0.986799,0.0132013,0;SGB=-0.379885;RPBZ=0.873411;MQBZ=0;MQSBZ=0;BQBZ=-1.67266;NMBZ=-1.4745;SCBZ=-0.760963;FS=0;MQ0F=0 PL:AD 0,63,255,75,255,255:25,1,0 +000000F 650 . T C,<*> 0 . DP=26;I16=11,14,0,1,897,33867,12,144,1500,90000,60,3600,359,6973,5,25;QS=0.986799,0.0132013,0;SGB=-0.379885;RPBZ=0.874779;MQBZ=0;MQSBZ=0;BQBZ=-1.67266;NMBZ=-1.4745;SCBZ=-0.760963;FS=0;MQ0F=0 PL:AD 0,63,255,75,255,255:25,1,0 000000F 651 . T <*> 0 . DP=26;I16=11,15,0,0,905,33255,0,0,1560,93600,0,0,342,6492,0,0;QS=1,0;MQ0F=0 PL:AD 0,78,255:26,0 000000F 652 . T <*> 0 . DP=25;I16=11,14,0,0,891,32693,0,0,1500,90000,0,0,321,6029,0,0;QS=1,0;MQ0F=0 PL:AD 0,75,255:25,0 000000F 653 . A <*> 0 . DP=21;I16=9,12,0,0,804,31130,0,0,1260,75600,0,0,303,5555,0,0;QS=1,0;MQ0F=0 PL:AD 0,63,255:21,0 000000F 654 . A <*> 0 . DP=21;I16=9,12,0,0,659,22061,0,0,1260,75600,0,0,285,5117,0,0;QS=1,0;MQ0F=0 PL:AD 0,63,255:21,0 000000F 655 . C <*> 0 . DP=21;I16=9,12,0,0,664,22342,0,0,1260,75600,0,0,266,4666,0,0;QS=1,0;MQ0F=0 PL:AD 0,63,255:21,0 -000000F 655 . CACAATACAA CACAA 0 . INDEL;IDV=6;IMF=0.285714;DP=21;I16=0,2,5,1,240,28800,720,86400,120,7200,360,21600,46,1060,100,1788;QS=0.0977444,0.902256;VDB=0.00211394;SGB=-0.616816;RPBZ=-2.81289;MQBZ=0;MQSBZ=0;BQBZ=-1.67266;NMBZ=-2.1454;SCBZ=-2.52262;FS=0;MQ0F=0 PL:AD 159,0,2:2,6 +000000F 655 . CACAATACAA CACAA 0 . INDEL;IDV=6;IMF=0.285714;DP=21;I16=0,2,5,1,240,28800,720,86400,120,7200,360,21600,46,1060,100,1788;QS=0.0977444,0.902256;VDB=0.00189453;SGB=-0.616816;RPBZ=-2.81289;MQBZ=0;MQSBZ=0;BQBZ=-1.67266;NMBZ=-2.1454;SCBZ=-2.52262;FS=0;MQ0F=0 PL:AD 159,0,2:2,6 000000F 656 . A <*> 0 . DP=11;I16=4,7,0,0,404,15690,0,0,660,39600,0,0,141,2411,0,0;QS=1,0;MQ0F=0 PL:AD 0,33,255:11,0 000000F 657 . C <*> 0 . DP=11;I16=4,7,0,0,413,15607,0,0,660,39600,0,0,131,2189,0,0;QS=1,0;MQ0F=0 PL:AD 0,33,255:11,0 000000F 658 . A <*> 0 . DP=10;I16=3,7,0,0,121,1651,0,0,600,36000,0,0,122,1986,0,0;QS=1,0;MQ0F=0 PL:AD 0,30,79:10,0 diff --git a/test/mpileup/indel-AD.2.out b/test/mpileup/indel-AD.2.out index 649c3db6e..42715d8b2 100644 --- a/test/mpileup/indel-AD.2.out +++ b/test/mpileup/indel-AD.2.out @@ -22,4 +22,4 @@ ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample 11 75 . G <*> 0 . DP=68;I16=6,62,0,0,2437,87909,0,0,3770,217210,0,0,838,15940,0,0;QS=1,0;MQ0F=0 PL:AD 0,205,255:68,0 -11 75 . GTAAAATAAAATAAAATAAAATAAA GTAAAATAAAATAAAATAAAATAAAATAAA 0 . INDEL;IDV=6;IMF=0.0882353;DP=68;I16=5,9,1,5,1680,201600,720,86400,840,50400,174,5046,244,5778,147,3609;QS=0.730233,0.269767;VDB=0.00476095;SGB=-0.616816;RPBZ=-3.24592;MQBZ=-6.13241;MQSBZ=0;BQBZ=0;NMBZ=0;SCBZ=-0.546919;FS=0;MQ0F=0 PL:AD 83,0,244:14,6 +11 75 . GTAAAATAAAATAAAATAAAATAAA GTAAAATAAAATAAAATAAAATAAAATAAA 0 . INDEL;IDV=6;IMF=0.0882353;DP=68;I16=5,9,1,5,1680,201600,720,86400,840,50400,174,5046,244,5778,147,3609;QS=0.730233,0.269767;VDB=0.00452698;SGB=-0.616816;RPBZ=-3.24592;MQBZ=-6.13241;MQSBZ=0;BQBZ=0;NMBZ=0;SCBZ=-0.546919;FS=0;MQ0F=0 PL:AD 83,0,244:14,6 diff --git a/test/mpileup/indel-AD.3.out b/test/mpileup/indel-AD.3.out index 3d4e60257..73020c8e3 100644 --- a/test/mpileup/indel-AD.3.out +++ b/test/mpileup/indel-AD.3.out @@ -22,4 +22,4 @@ ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample 11 75 . G <*> 0 . DP=68;I16=6,62,0,0,2437,87909,0,0,3770,217210,0,0,838,15940,0,0;QS=1,0;MQ0F=0 PL:AD 0,205,255:68,0 -11 75 . GTAAAATAAAATAAAATAAAATAAA GTAAAATAAAATAAAATAAAATAAAATAAA 0 . INDEL;IDV=6;IMF=0.0882353;DP=68;I16=5,9,1,5,1680,201600,720,86400,840,50400,174,5046,244,5778,147,3609;QS=0.730233,0.269767;VDB=0.00476095;SGB=-0.616816;RPBZ=-3.24592;MQBZ=-6.13241;MQSBZ=0;BQBZ=0;NMBZ=0;SCBZ=-0.546919;FS=0;MQ0F=0 PL:AD 83,0,244:45,23 +11 75 . GTAAAATAAAATAAAATAAAATAAA GTAAAATAAAATAAAATAAAATAAAATAAA 0 . INDEL;IDV=6;IMF=0.0882353;DP=68;I16=5,9,1,5,1680,201600,720,86400,840,50400,174,5046,244,5778,147,3609;QS=0.730233,0.269767;VDB=0.00452698;SGB=-0.616816;RPBZ=-3.24592;MQBZ=-6.13241;MQSBZ=0;BQBZ=0;NMBZ=0;SCBZ=-0.546919;FS=0;MQ0F=0 PL:AD 83,0,244:45,23 diff --git a/test/mpileup/indel-AD.4.out b/test/mpileup/indel-AD.4.out index 7d2afac71..6d8f1bf8d 100644 --- a/test/mpileup/indel-AD.4.out +++ b/test/mpileup/indel-AD.4.out @@ -22,4 +22,4 @@ ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample 11 75 . G <*> 0 . DP=68;I16=6,62,0,0,2437,87909,0,0,3770,217210,0,0,838,15940,0,0;QS=1,0;MQ0F=0 PL:AD 0,205,255:68,0 -11 75 . GTAAAATAAAATAAAATAAAATAAA GTAAAATAAAATAAAATAAAATAAAATAAA 0 . INDEL;IDV=6;IMF=0.0882353;DP=68;I16=5,9,1,5,1680,201600,720,86400,840,50400,174,5046,244,5778,147,3609;QS=0.730233,0.269767;VDB=0.00476095;SGB=-0.616816;RPBZ=-3.24592;MQBZ=-6.13241;MQSBZ=0;BQBZ=0;NMBZ=0;SCBZ=-0.546919;FS=0;MQ0F=0 PL:AD 83,0,244:62,6 +11 75 . GTAAAATAAAATAAAATAAAATAAA GTAAAATAAAATAAAATAAAATAAAATAAA 0 . INDEL;IDV=6;IMF=0.0882353;DP=68;I16=5,9,1,5,1680,201600,720,86400,840,50400,174,5046,244,5778,147,3609;QS=0.730233,0.269767;VDB=0.00452698;SGB=-0.616816;RPBZ=-3.24592;MQBZ=-6.13241;MQSBZ=0;BQBZ=0;NMBZ=0;SCBZ=-0.546919;FS=0;MQ0F=0 PL:AD 83,0,244:62,6 diff --git a/test/mpileup/mpileup-SCR.out b/test/mpileup/mpileup-SCR.out index 26af1fbb0..91b7b7e9f 100644 --- a/test/mpileup/mpileup-SCR.out +++ b/test/mpileup/mpileup-SCR.out @@ -33,7 +33,7 @@ 1 72 . C <*> 0 . DP=9;SCR=3;I16=6,3,0,0,318,11254,0,0,456,24672,0,0,82,1074,0,0;QS=1,0;MQ0F=0 PL:SCR 0,27,216:3 1 73 . C <*> 0 . DP=10;SCR=3;I16=7,3,0,0,348,12146,0,0,516,28272,0,0,91,1247,0,0;QS=1,0;MQ0F=0 PL:SCR 0,30,224:3 1 74 . C <*> 0 . DP=10;SCR=3;I16=7,3,0,0,350,12278,0,0,516,28272,0,0,100,1388,0,0;QS=1,0;MQ0F=0 PL:SCR 0,30,228:3 -1 75 . C G,<*> 0 . DP=12;SCR=4;I16=6,2,3,1,274,9444,132,4392,480,28800,119,3601,55,501,54,1046;QS=0.697201,0.302799,0;VDB=0.0483573;SGB=-0.556411;RPBZ=1.71346;MQBZ=-3.26599;MQSBZ=0.111111;BQBZ=-0.515877;NMBZ=3.31662;SCBZ=3.23349;FS=0;MQ0F=0 PL:SCR 73,0,170,97,182,252:4 +1 75 . C G,<*> 0 . DP=12;SCR=4;I16=6,2,3,1,274,9444,132,4392,480,28800,119,3601,55,501,54,1046;QS=0.697201,0.302799,0;VDB=0.0533436;SGB=-0.556411;RPBZ=1.63069;MQBZ=-3.26599;MQSBZ=0.111111;BQBZ=-0.515877;NMBZ=3.31662;SCBZ=3.23349;FS=0;MQ0F=0 PL:SCR 73,0,170,97,182,252:4 1 76 . C <*> 0 . DP=12;SCR=4;I16=9,3,0,0,410,14076,0,0,599,32401,0,0,120,1726,0,0;QS=1,0;MQ0F=0 PL:SCR 0,36,233:4 1 77 . G <*> 0 . DP=12;SCR=4;I16=9,3,0,0,385,12495,0,0,599,32401,0,0,131,1927,0,0;QS=1,0;MQ0F=0 PL:SCR 0,36,225:4 1 78 . T <*> 0 . DP=12;SCR=4;I16=9,3,0,0,365,11201,0,0,599,32401,0,0,142,2150,0,0;QS=1,0;MQ0F=0 PL:SCR 0,36,213:4 diff --git a/test/mpileup/mpileup.1.out b/test/mpileup/mpileup.1.out index 48bea5ab5..3fd870e7a 100644 --- a/test/mpileup/mpileup.1.out +++ b/test/mpileup/mpileup.1.out @@ -24,7 +24,7 @@ 17 101 . C <*> 0 . DP=18;I16=16,1,0,0,630,24730,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL 0,27,182 0,9,108 0,15,132 17 102 . C <*> 0 . DP=18;I16=16,1,0,0,676,27812,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL 0,27,188 0,9,121 0,15,139 17 103 . T C,<*> 0 . DP=18;I16=15,1,1,0,668,28542,6,36,929,54841,29,841,323,7035,6,36;QS=2.98256,0.0174419,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64924;NMBZ=2.45514;SCBZ=4;FS=0;MQ0F=0 PL 0,17,184,24,187,185 0,9,118,9,118,118 0,15,147,15,147,147 -17 104 . G C,<*> 0 . DP=18;I16=15,1,1,0,601,24163,3,9,929,54841,29,841,320,6884,7,49;QS=2.98726,0.0127389,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64309;NMBZ=2.45514;SCBZ=2.91548;FS=0;MQ0F=0 PL 0,18,173,24,176,173 0,9,101,9,101,101 0,15,133,15,133,133 +17 104 . G C,<*> 0 . DP=18;I16=15,1,1,0,601,24163,3,9,929,54841,29,841,320,6884,7,49;QS=2.98726,0.0127389,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64309;NMBZ=2.45514;SCBZ=4;FS=0;MQ0F=0 PL 0,18,173,24,176,173 0,9,101,9,101,101 0,15,133,15,133,133 17 105 . G <*> 0 . DP=19;I16=17,1,0,0,603,22351,0,0,1018,59282,0,0,325,6815,0,0;QS=3,0;MQ0F=0 PL 0,30,171 0,9,106 0,15,125 17 106 . G <*> 0 . DP=19;I16=17,1,0,0,636,25058,0,0,1018,59282,0,0,324,6718,0,0;QS=3,0;MQ0F=0 PL 0,30,190 0,9,92 0,15,124 17 107 . C <*> 0 . DP=19;I16=17,1,0,0,686,27952,0,0,1018,59282,0,0,323,6643,0,0;QS=3,0;MQ0F=0 PL 0,30,192 0,9,119 0,15,136 diff --git a/test/mpileup/mpileup.10.out b/test/mpileup/mpileup.10.out index 585e06ffb..1a641fef5 100644 --- a/test/mpileup/mpileup.10.out +++ b/test/mpileup/mpileup.10.out @@ -24,7 +24,7 @@ 17 101 . C <*> 0 . DP=16;I16=14,1,0,0,567,22633,0,0,838,48482,0,0,309,7011,0,0;QS=5,0;MQ0F=0 PL 0,3,22 0,6,79 0,12,123 0,9,108 0,15,132 17 102 . C <*> 0 . DP=16;I16=14,1,0,0,602,25074,0,0,838,48482,0,0,308,6904,0,0;QS=5,0;MQ0F=0 PL 0,3,20 0,6,78 0,12,129 0,9,121 0,15,139 17 103 . T C,<*> 0 . DP=16;I16=13,1,1,0,588,25334,6,36,809,47641,29,841,301,6775,6,36;QS=4,1,0;SGB=-0.587685;RPBZ=-1.15831;MQBZ=-2.54951;MQSBZ=0.392232;BQBZ=-1.64233;NMBZ=2.31624;SCBZ=3.74166;FS=0;MQ0F=0 PL 6,3,0,6,3,6 0,6,79,6,79,79 0,12,131,12,131,131 0,9,118,9,118,118 0,15,147,15,147,147 -17 104 . G C,<*> 0 . DP=16;I16=13,1,1,0,536,21966,3,9,809,47641,29,841,298,6634,7,49;QS=4,1,0;SGB=-0.587685;RPBZ=-1.15831;MQBZ=-2.54951;MQSBZ=0.392232;BQBZ=-1.63041;NMBZ=2.31624;SCBZ=2.73861;FS=0;MQ0F=0 PL 4,3,0,4,3,4 0,6,78,6,78,78 0,12,123,12,123,123 0,9,101,9,101,101 0,15,133,15,133,133 +17 104 . G C,<*> 0 . DP=16;I16=13,1,1,0,536,21966,3,9,809,47641,29,841,298,6634,7,49;QS=4,1,0;SGB=-0.587685;RPBZ=-1.15831;MQBZ=-2.54951;MQSBZ=0.392232;BQBZ=-1.63041;NMBZ=2.31624;SCBZ=3.74166;FS=0;MQ0F=0 PL 4,3,0,4,3,4 0,6,78,6,78,78 0,12,123,12,123,123 0,9,101,9,101,101 0,15,133,15,133,133 17 105 . G <*> 0 . DP=17;I16=15,1,0,0,541,20301,0,0,898,52082,0,0,303,6571,0,0;QS=5,0;MQ0F=0 PL 0,6,35 0,6,77 0,12,106 0,9,106 0,15,125 17 106 . G <*> 0 . DP=17;I16=15,1,0,0,562,22318,0,0,898,52082,0,0,302,6476,0,0;QS=5,0;MQ0F=0 PL 0,6,44 0,6,75 0,12,130 0,9,92 0,15,124 17 107 . C <*> 0 . DP=17;I16=15,1,0,0,606,24752,0,0,898,52082,0,0,301,6399,0,0;QS=5,0;MQ0F=0 PL 0,6,36 0,6,77 0,12,130 0,9,119 0,15,136 diff --git a/test/mpileup/mpileup.11.out b/test/mpileup/mpileup.11.out index 36d61d4ae..c5d6c0c70 100644 --- a/test/mpileup/mpileup.11.out +++ b/test/mpileup/mpileup.11.out @@ -178,7 +178,7 @@ 17 156 . C <*> 0 . DP=5;I16=4,1,0,0,190,7238,0,0,269,15241,0,0,101,2311,0,0;QS=1,0;MQ0F=0 PL 0,15,150 17 157 . C <*> 0 . DP=5;I16=4,1,0,0,192,7384,0,0,269,15241,0,0,101,2341,0,0;QS=1,0;MQ0F=0 PL 0,15,149 17 158 . T <*> 0 . DP=5;I16=4,1,0,0,205,8455,0,0,269,15241,0,0,101,2375,0,0;QS=1,0;MQ0F=0 PL 0,15,159 -17 159 . A G,<*> 0 . DP=6;I16=4,1,1,0,179,6513,5,25,269,15241,60,3600,101,2413,0,0;QS=0.97076,0.0292398,0;SGB=-0.379885;RPBZ=-1.48522;MQBZ=0.447214;MQSBZ=-2.23607;BQBZ=-1.46385;NMBZ=0;SCBZ=0;FS=0;MQ0F=0 PL 0,10,129,15,132,129 +17 159 . A G,<*> 0 . DP=6;I16=4,1,1,0,179,6513,5,25,269,15241,60,3600,101,2413,0,0;QS=0.97076,0.0292398,0;SGB=-0.379885;RPBZ=-1.46385;MQBZ=0.447214;MQSBZ=-2.23607;BQBZ=-1.46385;NMBZ=0;SCBZ=0;FS=0;MQ0F=0 PL 0,10,129,15,132,129 17 160 . G <*> 0 . DP=6;I16=5,1,0,0,187,6199,0,0,329,18841,0,0,102,2456,0,0;QS=1,0;MQ0F=0 PL 0,18,139 17 161 . A <*> 0 . DP=6;I16=5,1,0,0,225,8479,0,0,329,18841,0,0,103,2505,0,0;QS=1,0;MQ0F=0 PL 0,18,162 17 162 . A <*> 0 . DP=6;I16=5,1,0,0,233,9149,0,0,329,18841,0,0,103,2509,0,0;QS=1,0;MQ0F=0 PL 0,18,167 @@ -322,7 +322,7 @@ 17 300 . A <*> 0 . DP=7;I16=2,5,0,0,296,12578,0,0,358,19682,0,0,133,3069,0,0;QS=1,0;MQ0F=0 PL 0,21,210 17 301 . G <*> 0 . DP=7;I16=2,5,0,0,274,10742,0,0,358,19682,0,0,136,3138,0,0;QS=1,0;MQ0F=0 PL 0,21,196 17 302 . T <*> 0 . DP=7;I16=2,5,0,0,283,11451,0,0,358,19682,0,0,139,3213,0,0;QS=1,0;MQ0F=0 PL 0,21,202 -17 302 . T TA 0 . INDEL;IDV=7;IMF=1;DP=7;I16=0,0,2,5,0,0,280,11200,0,0,358,19682,0,0,139,3213;QS=0,1;VDB=0.380378;SGB=-0.636426;BQBZ=-1.34164;FS=0;MQ0F=0 PL 201,21,0 +17 302 . T TA 0 . INDEL;IDV=7;IMF=1;DP=7;I16=0,0,2,5,0,0,280,11200,0,0,358,19682,0,0,139,3213;QS=0,1;VDB=0.355905;SGB=-0.636426;BQBZ=-1.34164;FS=0;MQ0F=0 PL 201,21,0 17 303 . G <*> 0 . DP=7;I16=2,5,0,0,280,11264,0,0,358,19682,0,0,144,3330,0,0;QS=1,0;MQ0F=0 PL 0,21,195 17 304 . C <*> 0 . DP=8;I16=2,6,0,0,304,11716,0,0,418,23282,0,0,146,3370,0,0;QS=1,0;MQ0F=0 PL 0,24,200 17 305 . C <*> 0 . DP=8;I16=2,6,0,0,318,12738,0,0,418,23282,0,0,149,3415,0,0;QS=1,0;MQ0F=0 PL 0,24,211 @@ -491,7 +491,7 @@ 17 468 . A <*> 0 . DP=10;I16=5,5,0,0,357,13375,0,0,515,28251,0,0,202,4604,0,0;QS=1,0;MQ0F=0 PL 0,30,251 17 469 . A <*> 0 . DP=10;I16=5,5,0,0,387,15581,0,0,515,28251,0,0,201,4563,0,0;QS=1,0;MQ0F=0 PL 0,30,255 17 470 . G <*> 0 . DP=10;I16=5,5,0,0,328,11334,0,0,515,28251,0,0,200,4532,0,0;QS=1,0;MQ0F=0 PL 0,30,238 -17 471 . T G,C,<*> 0 . DP=11;I16=5,4,0,2,319,11637,18,162,478,26882,97,4969,183,4255,16,256;QS=0.945289,0.0273556,0.0273556,0;VDB=0.96;SGB=-0.453602;RPBZ=0.237875;MQBZ=-0.451335;MQSBZ=1.04881;BQBZ=-2.14585;NMBZ=1.39841;SCBZ=0;FS=0;MQ0F=0 PL 0,19,219,19,221,219,27,222,222,221 +17 471 . T G,C,<*> 0 . DP=11;I16=5,4,0,2,319,11637,18,162,478,26882,97,4969,183,4255,16,256;QS=0.945289,0.0273556,0.0273556,0;VDB=0.96;SGB=-0.453602;RPBZ=0.23624;MQBZ=-0.451335;MQSBZ=1.04881;BQBZ=-2.14585;NMBZ=1.39841;SCBZ=0;FS=0;MQ0F=0 PL 0,19,219,19,221,219,27,222,222,221 17 472 . T <*> 0 . DP=10;I16=5,5,0,0,340,12388,0,0,515,28251,0,0,200,4500,0,0;QS=1,0;MQ0F=0 PL 0,30,241 17 473 . G <*> 0 . DP=10;I16=5,5,0,0,363,14103,0,0,515,28251,0,0,201,4499,0,0;QS=1,0;MQ0F=0 PL 0,30,250 17 474 . G <*> 0 . DP=11;I16=6,5,0,0,378,13788,0,0,575,31851,0,0,202,4508,0,0;QS=1,0;MQ0F=0 PL 0,33,255 @@ -508,7 +508,7 @@ 17 485 . G <*> 0 . DP=11;I16=6,5,0,0,419,16073,0,0,575,31851,0,0,202,4328,0,0;QS=1,0;MQ0F=0 PL 0,33,255 17 486 . A <*> 0 . DP=11;I16=6,5,0,0,452,18618,0,0,575,31851,0,0,200,4280,0,0;QS=1,0;MQ0F=0 PL 0,33,255 17 487 . G <*> 0 . DP=11;I16=6,5,0,0,403,14875,0,0,575,31851,0,0,198,4244,0,0;QS=1,0;MQ0F=0 PL 0,33,255 -17 488 . A G,<*> 0 . DP=11;I16=5,5,1,0,388,15102,4,16,546,31010,29,841,171,3595,25,625;QS=0.989474,0.0105263,0;SGB=-0.379885;RPBZ=-0.158474;MQBZ=-1.81659;MQSBZ=0.699206;BQBZ=-1.60315;NMBZ=0;SCBZ=0;FS=0;MQ0F=0 PL 0,23,255,30,255,255 +17 488 . A G,<*> 0 . DP=11;I16=5,5,1,0,388,15102,4,16,546,31010,29,841,171,3595,25,625;QS=0.989474,0.0105263,0;SGB=-0.379885;RPBZ=0;MQBZ=-1.81659;MQSBZ=0.699206;BQBZ=-1.60315;NMBZ=0;SCBZ=0;FS=0;MQ0F=0 PL 0,23,255,30,255,255 17 489 . A <*> 0 . DP=11;I16=6,5,0,0,393,14565,0,0,575,31851,0,0,194,4208,0,0;QS=1,0;MQ0F=0 PL 0,33,255 17 490 . A <*> 0 . DP=11;I16=6,5,0,0,401,14927,0,0,575,31851,0,0,192,4208,0,0;QS=1,0;MQ0F=0 PL 0,33,255 17 491 . T <*> 0 . DP=11;I16=6,5,0,0,385,13773,0,0,575,31851,0,0,190,4220,0,0;QS=1,0;MQ0F=0 PL 0,33,255 @@ -763,7 +763,7 @@ 17 740 . T <*> 0 . DP=7;I16=0,7,0,0,248,9042,0,0,358,19682,0,0,118,2610,0,0;QS=1,0;MQ0F=0 PL 0,21,155 17 741 . T <*> 0 . DP=7;I16=0,7,0,0,244,8970,0,0,358,19682,0,0,116,2548,0,0;QS=1,0;MQ0F=0 PL 0,21,151 17 742 . C <*> 0 . DP=7;I16=0,7,0,0,212,7112,0,0,358,19682,0,0,114,2494,0,0;QS=1,0;MQ0F=0 PL 0,21,138 -17 743 . A C,<*> 0 . DP=7;I16=0,6,0,1,189,6467,10,100,329,18841,29,841,87,1823,25,625;QS=0.949749,0.0502513,0;SGB=-0.379885;RPBZ=-1;MQBZ=-1.58114;BQBZ=-1.5;NMBZ=1.10335;SCBZ=1.24722;FS=0;MQ0F=0 PL 0,10,123,18,126,126 +17 743 . A C,<*> 0 . DP=7;I16=0,6,0,1,189,6467,10,100,329,18841,29,841,87,1823,25,625;QS=0.949749,0.0502513,0;SGB=-0.379885;RPBZ=-1;MQBZ=-1.58114;BQBZ=-1.5;NMBZ=1.10335;SCBZ=-0.408248;FS=0;MQ0F=0 PL 0,10,123,18,126,126 17 744 . T <*> 0 . DP=7;I16=0,7,0,0,259,9751,0,0,358,19682,0,0,110,2410,0,0;QS=1,0;MQ0F=0 PL 0,21,154 17 745 . G <*> 0 . DP=8;I16=1,7,0,0,280,10088,0,0,418,23282,0,0,108,2380,0,0;QS=1,0;MQ0F=0 PL 0,24,182 17 746 . G <*> 0 . DP=8;I16=1,7,0,0,274,9756,0,0,418,23282,0,0,107,2359,0,0;QS=1,0;MQ0F=0 PL 0,24,178 @@ -854,7 +854,7 @@ 17 831 . T <*> 0 . DP=4;I16=1,3,0,0,151,5761,0,0,240,14400,0,0,68,1462,0,0;QS=1,0;MQ0F=0 PL 0,12,133 17 832 . C <*> 0 . DP=4;I16=1,3,0,0,139,4905,0,0,240,14400,0,0,66,1428,0,0;QS=1,0;MQ0F=0 PL 0,12,123 17 833 . T <*> 0 . DP=5;I16=1,4,0,0,185,6853,0,0,300,18000,0,0,64,1398,0,0;QS=1,0;MQ0F=0 PL 0,15,149 -17 834 . G A,<*> 0 . DP=5;I16=0,0,1,4,0,0,163,5375,0,0,300,18000,0,0,63,1373;QS=0,1,0;VDB=0.89072;SGB=-0.590765;MQSBZ=0;FS=0;MQ0F=0 PL 133,15,0,133,15,133 +17 834 . G A,<*> 0 . DP=5;I16=0,0,1,4,0,0,163,5375,0,0,300,18000,0,0,63,1373;QS=0,1,0;VDB=0.877481;SGB=-0.590765;MQSBZ=0;FS=0;MQ0F=0 PL 133,15,0,133,15,133 17 835 . T <*> 0 . DP=5;I16=1,4,0,0,164,5828,0,0,300,18000,0,0,62,1354,0,0;QS=1,0;MQ0F=0 PL 0,15,138 17 836 . G <*> 0 . DP=4;I16=1,3,0,0,149,5551,0,0,240,14400,0,0,61,1291,0,0;QS=1,0;MQ0F=0 PL 0,12,131 17 837 . T <*> 0 . DP=4;I16=1,3,0,0,161,6499,0,0,240,14400,0,0,60,1234,0,0;QS=1,0;MQ0F=0 PL 0,12,143 @@ -2061,7 +2061,7 @@ 17 2038 . C <*> 0 . DP=7;I16=4,3,0,0,262,9910,0,0,420,25200,0,0,131,2667,0,0;QS=1,0;MQ0F=0 PL 0,21,211 17 2039 . A <*> 0 . DP=7;I16=4,3,0,0,265,10071,0,0,420,25200,0,0,133,2735,0,0;QS=1,0;MQ0F=0 PL 0,21,212 17 2040 . C <*> 0 . DP=7;I16=4,3,0,0,243,8635,0,0,420,25200,0,0,135,2811,0,0;QS=1,0;MQ0F=0 PL 0,21,196 -17 2041 . G A,<*> 0 . DP=7;I16=0,0,4,3,0,0,276,11066,0,0,420,25200,0,0,137,2895;QS=0,1,0;VDB=0.80233;SGB=-0.636426;MQSBZ=0;FS=0;MQ0F=0 PL 223,21,0,223,21,223 +17 2041 . G A,<*> 0 . DP=7;I16=0,0,4,3,0,0,276,11066,0,0,420,25200,0,0,137,2895;QS=0,1,0;VDB=0.792147;SGB=-0.636426;MQSBZ=0;FS=0;MQ0F=0 PL 223,21,0,223,21,223 17 2042 . G <*> 0 . DP=7;I16=4,3,0,0,256,9542,0,0,420,25200,0,0,139,2987,0,0;QS=1,0;MQ0F=0 PL 0,21,206 17 2043 . G <*> 0 . DP=7;I16=4,3,0,0,240,8782,0,0,420,25200,0,0,141,3087,0,0;QS=1,0;MQ0F=0 PL 0,21,197 17 2044 . C <*> 0 . DP=7;I16=4,3,0,0,258,9636,0,0,420,25200,0,0,143,3195,0,0;QS=1,0;MQ0F=0 PL 0,21,207 @@ -2240,7 +2240,7 @@ 17 2217 . T <*> 0 . DP=4;I16=0,4,0,0,150,5810,0,0,240,14400,0,0,89,2015,0,0;QS=1,0;MQ0F=0 PL 0,12,118 17 2218 . C <*> 0 . DP=4;I16=0,4,0,0,154,5950,0,0,240,14400,0,0,89,2023,0,0;QS=1,0;MQ0F=0 PL 0,12,119 17 2219 . C <*> 0 . DP=4;I16=0,4,0,0,159,6331,0,0,240,14400,0,0,89,2035,0,0;QS=1,0;MQ0F=0 PL 0,12,122 -17 2220 . G A,<*> 0 . DP=4;I16=0,0,0,4,0,0,170,7254,0,0,240,14400,0,0,89,2051;QS=0,1,0;VDB=0.775568;SGB=-0.556411;FS=0;MQ0F=0 PL 131,12,0,131,12,131 +17 2220 . G A,<*> 0 . DP=4;I16=0,0,0,4,0,0,170,7254,0,0,240,14400,0,0,89,2051;QS=0,1,0;VDB=0.756056;SGB=-0.556411;FS=0;MQ0F=0 PL 131,12,0,131,12,131 17 2221 . G <*> 0 . DP=4;I16=0,4,0,0,154,6054,0,0,240,14400,0,0,88,2022,0,0;QS=1,0;MQ0F=0 PL 0,12,120 17 2222 . C <*> 0 . DP=4;I16=0,4,0,0,133,4857,0,0,240,14400,0,0,86,1948,0,0;QS=1,0;MQ0F=0 PL 0,12,107 17 2223 . C <*> 0 . DP=4;I16=0,4,0,0,158,6262,0,0,240,14400,0,0,84,1878,0,0;QS=1,0;MQ0F=0 PL 0,12,122 @@ -2584,7 +2584,7 @@ 17 2561 . C <*> 0 . DP=5;I16=3,2,0,0,175,6231,0,0,300,18000,0,0,100,2144,0,0;QS=1,0;MQ0F=0 PL 0,15,153 17 2562 . T <*> 0 . DP=5;I16=3,2,0,0,190,7478,0,0,300,18000,0,0,101,2195,0,0;QS=1,0;MQ0F=0 PL 0,15,167 17 2563 . C <*> 0 . DP=5;I16=3,2,0,0,163,5483,0,0,300,18000,0,0,102,2252,0,0;QS=1,0;MQ0F=0 PL 0,15,142 -17 2564 . A G,<*> 0 . DP=5;I16=0,0,3,2,0,0,137,4729,0,0,300,18000,0,0,102,2264;QS=0,1,0;VDB=0.724679;SGB=-0.590765;MQSBZ=0;FS=0;MQ0F=0 PL 124,15,0,124,15,124 +17 2564 . A G,<*> 0 . DP=5;I16=0,0,3,2,0,0,137,4729,0,0,300,18000,0,0,102,2264;QS=0,1,0;VDB=0.709369;SGB=-0.590765;MQSBZ=0;FS=0;MQ0F=0 PL 124,15,0,124,15,124 17 2565 . A <*> 0 . DP=5;I16=3,2,0,0,191,7347,0,0,300,18000,0,0,102,2280,0,0;QS=1,0;MQ0F=0 PL 0,15,166 17 2566 . A <*> 0 . DP=5;I16=3,2,0,0,186,6998,0,0,300,18000,0,0,101,2251,0,0;QS=1,0;MQ0F=0 PL 0,15,162 17 2567 . A <*> 0 . DP=5;I16=3,2,0,0,191,7375,0,0,300,18000,0,0,100,2228,0,0;QS=1,0;MQ0F=0 PL 0,15,166 @@ -3124,7 +3124,7 @@ 17 3101 . C <*> 0 . DP=5;I16=2,3,0,0,186,6930,0,0,300,18000,0,0,78,1546,0,0;QS=1,0;MQ0F=0 PL 0,15,161 17 3102 . A <*> 0 . DP=6;I16=3,3,0,0,226,8548,0,0,360,21600,0,0,78,1560,0,0;QS=1,0;MQ0F=0 PL 0,18,189 17 3103 . T <*> 0 . DP=6;I16=3,3,0,0,223,8347,0,0,360,21600,0,0,79,1583,0,0;QS=1,0;MQ0F=0 PL 0,18,187 -17 3104 . C T,<*> 0 . DP=5;I16=1,2,2,0,114,4334,80,3202,180,10800,120,7200,41,765,40,850;QS=0.587629,0.412371,0;VDB=0.8;SGB=-0.453602;RPBZ=0.296174;MQBZ=0;MQSBZ=0;BQBZ=1.48087;NMBZ=-0.816497;SCBZ=-0.816497;FS=0;MQ0F=0 PL 59,0,93,68,99,157 +17 3104 . C T,<*> 0 . DP=5;I16=1,2,2,0,114,4334,80,3202,180,10800,120,7200,41,765,40,850;QS=0.587629,0.412371,0;VDB=0.78;SGB=-0.453602;RPBZ=0.296174;MQBZ=0;MQSBZ=0;BQBZ=1.48087;NMBZ=-0.816497;SCBZ=-0.816497;FS=0;MQ0F=0 PL 59,0,93,68,99,157 17 3105 . T <*> 0 . DP=5;I16=3,2,0,0,195,7621,0,0,300,18000,0,0,83,1655,0,0;QS=1,0;MQ0F=0 PL 0,15,169 17 3106 . G <*> 0 . DP=5;I16=3,2,0,0,193,7461,0,0,300,18000,0,0,85,1703,0,0;QS=1,0;MQ0F=0 PL 0,15,167 17 3107 . T <*> 0 . DP=6;I16=3,3,0,0,233,9067,0,0,360,21600,0,0,87,1759,0,0;QS=1,0;MQ0F=0 PL 0,18,195 @@ -3607,7 +3607,7 @@ 17 3584 . G <*> 0 . DP=7;I16=4,3,0,0,271,10633,0,0,420,25200,0,0,121,2629,0,0;QS=1,0;MQ0F=0 PL 0,21,218 17 3585 . A <*> 0 . DP=8;I16=5,3,0,0,301,11477,0,0,480,28800,0,0,121,2633,0,0;QS=1,0;MQ0F=0 PL 0,24,229 17 3586 . A <*> 0 . DP=8;I16=5,3,0,0,308,11984,0,0,480,28800,0,0,122,2646,0,0;QS=1,0;MQ0F=0 PL 0,24,234 -17 3587 . G A,<*> 0 . DP=8;I16=0,0,5,3,0,0,314,12410,0,0,480,28800,0,0,123,2669;QS=0,1,0;VDB=0.933643;SGB=-0.651104;MQSBZ=0;FS=0;MQ0F=0 PL 240,24,0,240,24,240 +17 3587 . G A,<*> 0 . DP=8;I16=0,0,5,3,0,0,314,12410,0,0,480,28800,0,0,123,2669;QS=0,1,0;VDB=0.92727;SGB=-0.651104;MQSBZ=0;FS=0;MQ0F=0 PL 240,24,0,240,24,240 17 3588 . A <*> 0 . DP=8;I16=5,3,0,0,313,12383,0,0,480,28800,0,0,123,2651,0,0;QS=1,0;MQ0F=0 PL 0,24,239 17 3589 . A <*> 0 . DP=8;I16=5,3,0,0,293,10975,0,0,480,28800,0,0,123,2641,0,0;QS=1,0;MQ0F=0 PL 0,24,224 17 3590 . A <*> 0 . DP=8;I16=5,3,0,0,296,11288,0,0,480,28800,0,0,123,2639,0,0;QS=1,0;MQ0F=0 PL 0,24,227 diff --git a/test/mpileup/mpileup.2.out b/test/mpileup/mpileup.2.out index 45cdd502e..9d52186e3 100644 --- a/test/mpileup/mpileup.2.out +++ b/test/mpileup/mpileup.2.out @@ -26,7 +26,7 @@ 17 101 . C <*> 0 . DP=18;I16=16,1,0,0,630,24730,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,182:9:0 0,9,108:3:0 0,15,132:5:0 17 102 . C <*> 0 . DP=18;I16=16,1,0,0,676,27812,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,188:9:0 0,9,121:3:0 0,15,139:5:0 17 103 . T C,<*> 0 . DP=18;I16=15,1,1,0,668,28542,6,36,929,54841,29,841,323,7035,6,36;QS=2.98256,0.0174419,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64924;NMBZ=2.45514;SCBZ=4;FS=0;MQ0F=0 PL:DP:DV 0,17,184,24,187,185:9:1 0,9,118,9,118,118:3:0 0,15,147,15,147,147:5:0 -17 104 . G C,<*> 0 . DP=18;I16=15,1,1,0,601,24163,3,9,929,54841,29,841,320,6884,7,49;QS=2.98726,0.0127389,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64309;NMBZ=2.45514;SCBZ=2.91548;FS=0;MQ0F=0 PL:DP:DV 0,18,173,24,176,173:9:1 0,9,101,9,101,101:3:0 0,15,133,15,133,133:5:0 +17 104 . G C,<*> 0 . DP=18;I16=15,1,1,0,601,24163,3,9,929,54841,29,841,320,6884,7,49;QS=2.98726,0.0127389,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64309;NMBZ=2.45514;SCBZ=4;FS=0;MQ0F=0 PL:DP:DV 0,18,173,24,176,173:9:1 0,9,101,9,101,101:3:0 0,15,133,15,133,133:5:0 17 105 . G <*> 0 . DP=19;I16=17,1,0,0,603,22351,0,0,1018,59282,0,0,325,6815,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,171:10:0 0,9,106:3:0 0,15,125:5:0 17 106 . G <*> 0 . DP=19;I16=17,1,0,0,636,25058,0,0,1018,59282,0,0,324,6718,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,190:10:0 0,9,92:3:0 0,15,124:5:0 17 107 . C <*> 0 . DP=19;I16=17,1,0,0,686,27952,0,0,1018,59282,0,0,323,6643,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,192:10:0 0,9,119:3:0 0,15,136:5:0 @@ -81,7 +81,7 @@ 17 156 . C <*> 0 . DP=14;I16=12,2,0,0,536,20884,0,0,809,47641,0,0,266,5934,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,163:7:0 0,6,84:2:0 0,15,150:5:0 17 157 . C <*> 0 . DP=14;I16=12,2,0,0,555,22081,0,0,809,47641,0,0,264,5904,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,169:7:0 0,6,85:2:0 0,15,149:5:0 17 158 . T <*> 0 . DP=14;I16=12,2,0,0,568,23154,0,0,809,47641,0,0,262,5886,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,170:7:0 0,6,84:2:0 0,15,159:5:0 -17 159 . A G,<*> 0 . DP=15;I16=12,2,1,0,519,19467,5,25,809,47641,60,3600,260,5880,0,0;QS=2.97076,0.0292398,0;SGB=-0.556633;RPBZ=-1.62163;MQBZ=0.267261;MQSBZ=-2.54951;BQBZ=-1.63041;NMBZ=0;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,21,157,21,157,157:7:0 0,6,83,6,83,83:2:0 0,10,129,15,132,129:6:1 +17 159 . A G,<*> 0 . DP=15;I16=12,2,1,0,519,19467,5,25,809,47641,60,3600,260,5880,0,0;QS=2.97076,0.0292398,0;SGB=-0.556633;RPBZ=-1.62019;MQBZ=0.267261;MQSBZ=-2.54951;BQBZ=-1.63041;NMBZ=0;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,21,157,21,157,157:7:0 0,6,83,6,83,83:2:0 0,10,129,15,132,129:6:1 17 160 . G <*> 0 . DP=15;I16=13,2,0,0,547,20633,0,0,869,51241,0,0,259,5887,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,165:7:0 0,6,85:2:0 0,18,139:6:0 17 161 . A <*> 0 . DP=15;I16=13,2,0,0,568,21610,0,0,869,51241,0,0,258,5908,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,157:7:0 0,6,83:2:0 0,18,162:6:0 17 162 . A <*> 0 . DP=15;I16=13,2,0,0,558,21206,0,0,869,51241,0,0,255,5843,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,147:7:0 0,6,87:2:0 0,18,167:6:0 @@ -145,10 +145,10 @@ 17 220 . G <*> 0 . DP=14;I16=11,3,0,0,495,18407,0,0,747,42123,0,0,267,6079,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,188:7:0 0,9,88:3:0 0,12,84:4:0 17 221 . A <*> 0 . DP=14;I16=11,3,0,0,488,17688,0,0,747,42123,0,0,267,6135,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,176:7:0 0,9,89:3:0 0,12,101:4:0 17 222 . A <*> 0 . DP=14;I16=11,3,0,0,479,17747,0,0,747,42123,0,0,267,6203,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,186:7:0 0,9,89:3:0 0,12,73:4:0 -17 223 . G T,<*> 0 . DP=13;I16=9,3,1,0,412,14782,8,64,627,34923,60,3600,243,5657,25,625;QS=2.96596,0.0340426,0;SGB=-0.556633;RPBZ=1.06904;MQBZ=0.547723;MQSBZ=-3.4641;BQBZ=-1.60577;NMBZ=-0.288675;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,11,166,18,169,167:7:1 0,6,53,6,53,53:2:0 0,12,81,12,81,81:4:0 +17 223 . G T,<*> 0 . DP=13;I16=9,3,1,0,412,14782,8,64,627,34923,60,3600,243,5657,25,625;QS=2.96596,0.0340426,0;SGB=-0.556633;RPBZ=1.07052;MQBZ=0.547723;MQSBZ=-3.4641;BQBZ=-1.60577;NMBZ=-0.288675;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,11,166,18,169,167:7:1 0,6,53,6,53,53:2:0 0,12,81,12,81,81:4:0 17 224 . G <*> 0 . DP=12;I16=9,3,0,0,379,12759,0,0,627,34923,0,0,270,6370,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,18,168:6:0 0,6,50:2:0 0,12,70:4:0 17 225 . C <*> 0 . DP=12;I16=9,3,0,0,390,13960,0,0,627,34923,0,0,272,6466,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,18,165:6:0 0,6,48:2:0 0,12,86:4:0 -17 226 . A G,C,<*> 0 . DP=13;I16=8,3,1,1,381,13669,6,18,567,31323,89,4441,248,5894,44,986;QS=2.94293,0.0392157,0.0178571,0;VDB=0.84;SGB=-2.62246;RPBZ=-0.592972;MQBZ=-0.615457;MQSBZ=-3.4641;BQBZ=-2.17723;NMBZ=2.34521;SCBZ=2.34521;FS=0;MQ0F=0 PL:DP:DV 0,18,159,12,162,159,18,159,162,159:7:1 0,6,53,6,53,53,6,53,53,53:2:0 0,5,79,9,82,80,9,82,80,80:4:1 +17 226 . A G,C,<*> 0 . DP=13;I16=8,3,1,1,381,13669,6,18,567,31323,89,4441,248,5894,44,986;QS=2.94293,0.0392157,0.0178571,0;VDB=0.84;SGB=-2.62246;RPBZ=-0.592157;MQBZ=-0.615457;MQSBZ=-3.4641;BQBZ=-2.17723;NMBZ=2.34521;SCBZ=2.34521;FS=0;MQ0F=0 PL:DP:DV 0,18,159,12,162,159,18,159,162,159:7:1 0,6,53,6,53,53,6,53,53,53:2:0 0,5,79,9,82,80,9,82,80,80:4:1 17 227 . C <*> 0 . DP=13;I16=9,4,0,0,412,14342,0,0,656,35764,0,0,292,6878,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,190:7:0 0,6,53:2:0 0,12,75:4:0 17 228 . C <*> 0 . DP=13;I16=9,4,0,0,417,14381,0,0,656,35764,0,0,292,6884,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,187:7:0 0,6,45:2:0 0,12,96:4:0 17 229 . G <*> 0 . DP=13;I16=9,4,0,0,368,11524,0,0,656,35764,0,0,292,6898,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,145:7:0 0,6,53:2:0 0,12,70:4:0 @@ -189,7 +189,7 @@ 17 264 . C <*> 0 . DP=22;I16=10,12,0,0,821,31325,0,0,1049,54897,0,0,386,8326,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,15,104:5:0 0,18,172:6:0 17 265 . A <*> 0 . DP=21;I16=9,12,0,0,800,31906,0,0,989,51297,0,0,390,8380,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,15,114:5:0 0,15,129:5:0 17 266 . G <*> 0 . DP=21;I16=9,12,0,0,754,28204,0,0,989,51297,0,0,394,8458,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,15,99:5:0 0,15,138:5:0 -17 267 . T G,<*> 0 . DP=21;I16=9,11,0,1,739,27465,8,64,960,50456,29,841,373,7935,25,625;QS=2.94203,0.057971,0;SGB=-0.556633;RPBZ=-0.330504;MQBZ=-1.23153;MQSBZ=-3.3021;BQBZ=-1.66282;NMBZ=2.4409;SCBZ=2.91633;FS=0;MQ0F=0 PL:DP:DV 0,33,254,33,254,254:11:0 0,6,93,12,96,96:5:1 0,15,149,15,149,149:5:0 +17 267 . T G,<*> 0 . DP=21;I16=9,11,0,1,739,27465,8,64,960,50456,29,841,373,7935,25,625;QS=2.94203,0.057971,0;SGB=-0.556633;RPBZ=-0.330396;MQBZ=-1.23153;MQSBZ=-3.3021;BQBZ=-1.66282;NMBZ=2.4409;SCBZ=2.91633;FS=0;MQ0F=0 PL:DP:DV 0,33,254,33,254,254:11:0 0,6,93,12,96,96:5:1 0,15,149,15,149,149:5:0 17 268 . T <*> 0 . DP=21;I16=9,12,0,0,748,27708,0,0,989,51297,0,0,402,8686,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,238:11:0 0,15,110:5:0 0,15,156:5:0 17 269 . C <*> 0 . DP=22;I16=9,13,0,0,767,28641,0,0,1018,52138,0,0,406,8836,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,15,91:5:0 0,15,154:5:0 17 270 . C <*> 0 . DP=22;I16=9,13,0,0,766,28210,0,0,1018,52138,0,0,410,8962,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,15,98:5:0 0,15,143:5:0 @@ -200,7 +200,7 @@ 17 275 . C <*> 0 . DP=20;I16=7,13,0,0,768,29994,0,0,898,44938,0,0,423,9519,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,15,114:5:0 0,12,122:4:0 17 276 . A <*> 0 . DP=20;I16=7,13,0,0,805,32931,0,0,898,44938,0,0,424,9538,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,253:11:0 0,15,122:5:0 0,12,124:4:0 17 277 . G <*> 0 . DP=20;I16=7,13,0,0,764,29732,0,0,898,44938,0,0,425,9579,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,15,114:5:0 0,12,121:4:0 -17 278 . A C,<*> 0 . DP=21;I16=6,14,1,0,722,26452,7,49,867,42179,60,3600,415,9521,11,121;QS=2.97935,0.020649,0;SGB=-0.556633;RPBZ=1.56989;MQBZ=1.0247;MQSBZ=-3.24037;BQBZ=-1.66667;NMBZ=-0.406816;SCBZ=-0.324037;FS=0;MQ0F=0 PL:DP:DV 0,22,231,30,234,231:11:1 0,18,123,18,123,123:6:0 0,12,121,12,121,121:4:0 +17 278 . A C,<*> 0 . DP=21;I16=6,14,1,0,722,26452,7,49,867,42179,60,3600,415,9521,11,121;QS=2.97935,0.020649,0;SGB=-0.556633;RPBZ=1.65198;MQBZ=1.0247;MQSBZ=-3.24037;BQBZ=-1.66667;NMBZ=-0.406816;SCBZ=-0.324037;FS=0;MQ0F=0 PL:DP:DV 0,22,231,30,234,231:11:1 0,18,123,18,123,123:6:0 0,12,121,12,121,121:4:0 17 279 . A <*> 0 . DP=22;I16=7,15,0,0,786,28694,0,0,956,46620,0,0,427,9677,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,18,123:6:0 0,12,122:4:0 17 280 . A <*> 0 . DP=22;I16=7,15,0,0,815,31561,0,0,956,46620,0,0,428,9684,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,253:12:0 0,18,130:6:0 0,12,129:4:0 17 281 . G <*> 0 . DP=22;I16=7,15,0,0,820,31416,0,0,956,46620,0,0,428,9662,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,18,122:6:0 0,12,123:4:0 @@ -225,7 +225,7 @@ 17 300 . A <*> 0 . DP=27;I16=11,15,0,0,1001,39455,0,0,1258,66538,0,0,469,10437,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,204:8:0 0,21,210:7:0 17 301 . G <*> 0 . DP=25;I16=10,14,0,0,928,36116,0,0,1169,62097,0,0,476,10632,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,255:10:0 0,21,195:7:0 0,21,196:7:0 17 302 . T <*> 0 . DP=25;I16=10,14,0,0,879,32885,0,0,1169,62097,0,0,483,10849,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,231:10:0 0,21,172:7:0 0,21,202:7:0 -17 302 . T TA 0 . INDEL;IDV=7;IMF=1;DP=25;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.539485,2.46052;VDB=0.260546;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.22749;BQBZ=-1.67542;NMBZ=-0.199304;SCBZ=-0.268121;FS=0;MQ0F=0 PL:DP:DV 161,0,99:11:6 158,0,14:7:6 201,21,0:7:7 +17 302 . T TA 0 . INDEL;IDV=7;IMF=1;DP=25;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.539485,2.46052;VDB=0.241622;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.22749;BQBZ=-1.67542;NMBZ=-0.199304;SCBZ=-0.268121;FS=0;MQ0F=0 PL:DP:DV 161,0,99:11:6 158,0,14:7:6 201,21,0:7:7 17 303 . G <*> 0 . DP=25;I16=10,15,0,0,968,37972,0,0,1229,65697,0,0,497,11181,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,21,197:7:0 0,21,195:7:0 17 304 . C <*> 0 . DP=27;I16=11,16,0,0,991,37005,0,0,1318,70138,0,0,503,11359,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,206:8:0 0,24,200:8:0 17 305 . C <*> 0 . DP=27;I16=11,16,0,0,1057,41761,0,0,1318,70138,0,0,510,11508,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,213:8:0 0,24,211:8:0 @@ -258,9 +258,9 @@ 17 332 . A <*> 0 . DP=32;I16=14,18,0,0,1156,42666,0,0,1649,90897,0,0,560,12178,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,27,214:9:0 0,33,255:11:0 17 333 . A <*> 0 . DP=32;I16=14,18,0,0,1141,41987,0,0,1649,90897,0,0,558,12064,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,27,223:9:0 0,33,255:11:0 17 334 . A <*> 0 . DP=32;I16=14,18,0,0,1162,43328,0,0,1649,90897,0,0,556,11986,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,27,221:9:0 0,33,255:11:0 -17 335 . A G,<*> 0 . DP=32;I16=13,18,1,0,1084,40336,4,16,1589,87297,60,3600,555,11943,0,0;QS=2.98919,0.0108108,0;SGB=-0.556633;RPBZ=-1.67921;MQBZ=0.622171;MQSBZ=-2.25492;BQBZ=-1.68602;NMBZ=-0.428353;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV 0,33,252,33,252,252:11:0 0,27,219,27,219,219:9:0 0,25,245,33,248,245:12:1 +17 335 . A G,<*> 0 . DP=32;I16=13,18,1,0,1084,40336,4,16,1589,87297,60,3600,555,11943,0,0;QS=2.98919,0.0108108,0;SGB=-0.556633;RPBZ=-1.67936;MQBZ=0.622171;MQSBZ=-2.25492;BQBZ=-1.68602;NMBZ=-0.428353;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV 0,33,252,33,252,252:11:0 0,27,219,27,219,219:9:0 0,25,245,33,248,245:12:1 17 336 . A <*> 0 . DP=32;I16=14,18,0,0,1094,39794,0,0,1649,90897,0,0,555,11935,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,27,212:9:0 0,36,255:12:0 -17 337 . C A,<*> 0 . DP=32;I16=14,17,0,1,1125,42481,5,25,1612,89528,37,1369,536,11590,18,324;QS=2.98113,0.0188679,0;SGB=-0.556633;RPBZ=0.812519;MQBZ=-1.03695;MQSBZ=-2.25492;BQBZ=-1.68353;NMBZ=-0.376914;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV 0,33,255,33,255,255:11:0 0,17,195,24,198,195:9:1 0,36,255,36,255,255:12:0 +17 337 . C A,<*> 0 . DP=32;I16=14,17,0,1,1125,42481,5,25,1612,89528,37,1369,536,11590,18,324;QS=2.98113,0.0188679,0;SGB=-0.556633;RPBZ=0.812593;MQBZ=-1.03695;MQSBZ=-2.25492;BQBZ=-1.68353;NMBZ=-0.376914;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV 0,33,255,33,255,255:11:0 0,17,195,24,198,195:9:1 0,36,255,36,255,255:12:0 17 338 . T <*> 0 . DP=30;I16=14,16,0,0,1190,47898,0,0,1560,86456,0,0,554,11878,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,255:10:0 0,24,226:8:0 0,36,255:12:0 17 339 . C <*> 0 . DP=31;I16=14,17,0,0,1130,43210,0,0,1589,87297,0,0,554,11874,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,185:8:0 0,36,255:12:0 17 340 . C <*> 0 . DP=31;I16=14,17,0,0,1196,47044,0,0,1589,87297,0,0,554,11852,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,221:8:0 0,36,255:12:0 @@ -282,7 +282,7 @@ 17 356 . G <*> 0 . DP=27;I16=14,13,0,0,993,37481,0,0,1465,83405,0,0,574,13174,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,228:9:0 0,24,201:8:0 0,30,255:10:0 17 357 . C <*> 0 . DP=28;I16=15,13,0,0,1026,39496,0,0,1525,87005,0,0,575,13209,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,255:10:0 0,24,205:8:0 0,30,252:10:0 17 358 . A <*> 0 . DP=28;I16=15,13,0,0,1050,40518,0,0,1525,87005,0,0,576,13216,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,254:10:0 0,24,197:8:0 0,30,255:10:0 -17 359 . G T,<*> 0 . DP=29;I16=15,13,0,1,1085,42761,10,100,1525,87005,60,3600,552,12620,25,625;QS=2.96032,0.0396825,0;SGB=-0.556633;RPBZ=-0.119567;MQBZ=0.456435;MQSBZ=-1.53333;BQBZ=-1.68246;NMBZ=3.0531;SCBZ=5.2915;FS=0;MQ0F=0 PL:DP:DV 0,30,255,30,255,255:10:0 0,13,178,21,181,180:8:1 0,33,255,33,255,255:11:0 +17 359 . G T,<*> 0 . DP=29;I16=15,13,0,1,1085,42761,10,100,1525,87005,60,3600,552,12620,25,625;QS=2.96032,0.0396825,0;SGB=-0.556633;RPBZ=-0.119611;MQBZ=0.456435;MQSBZ=-1.53333;BQBZ=-1.68246;NMBZ=3.0531;SCBZ=5.2915;FS=0;MQ0F=0 PL:DP:DV 0,30,255,30,255,255:10:0 0,13,178,21,181,180:8:1 0,33,255,33,255,255:11:0 17 360 . A <*> 0 . DP=29;I16=15,14,0,0,1111,43259,0,0,1585,90605,0,0,579,13297,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,252:10:0 0,24,220:8:0 0,33,255:11:0 17 361 . A <*> 0 . DP=29;I16=15,14,0,0,1116,43442,0,0,1585,90605,0,0,579,13273,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,252:10:0 0,24,219:8:0 0,33,255:11:0 17 362 . A <*> 0 . DP=29;I16=16,13,0,0,1104,42700,0,0,1585,90605,0,0,580,13272,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,218:8:0 0,30,255:10:0 @@ -292,13 +292,13 @@ 17 366 . A <*> 0 . DP=29;I16=16,13,0,0,1090,41562,0,0,1585,90605,0,0,581,13167,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,211:8:0 0,30,255:10:0 17 367 . T <*> 0 . DP=29;I16=16,13,0,0,1055,39149,0,0,1585,90605,0,0,579,13093,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,204:8:0 0,30,255:10:0 17 368 . A <*> 0 . DP=29;I16=16,13,0,0,1054,39632,0,0,1585,90605,0,0,576,12998,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,208:8:0 0,30,255:10:0 -17 369 . T G,<*> 0 . DP=28;I16=16,11,0,1,1037,40275,6,36,1496,86164,60,3600,548,12256,25,625;QS=2.97683,0.023166,0;SGB=-0.556633;RPBZ=0.123865;MQBZ=0.408248;MQSBZ=-1.37784;BQBZ=-1.68703;NMBZ=2.99794;SCBZ=5.19615;FS=0;MQ0F=0 PL:DP:DV 0,30,250,30,250,250:10:0 0,15,189,21,192,190:8:1 0,30,255,30,255,255:10:0 +17 369 . T G,<*> 0 . DP=28;I16=16,11,0,1,1037,40275,6,36,1496,86164,60,3600,548,12256,25,625;QS=2.97683,0.023166,0;SGB=-0.556633;RPBZ=0.12395;MQBZ=0.408248;MQSBZ=-1.37784;BQBZ=-1.68703;NMBZ=2.99794;SCBZ=5.19615;FS=0;MQ0F=0 PL:DP:DV 0,30,250,30,250,250:10:0 0,15,189,21,192,190:8:1 0,30,255,30,255,255:10:0 17 370 . C <*> 0 . DP=28;I16=16,12,0,0,1045,40219,0,0,1556,89764,0,0,570,12790,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,255:10:0 0,24,201:8:0 0,30,255:10:0 17 371 . T <*> 0 . DP=29;I16=16,13,0,0,1155,46591,0,0,1616,93364,0,0,567,12725,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,255:10:0 0,24,227:8:0 0,33,255:11:0 17 372 . C <*> 0 . DP=30;I16=16,14,0,0,1139,44019,0,0,1676,96964,0,0,564,12636,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,215:8:0 0,33,255:11:0 17 373 . A <*> 0 . DP=30;I16=16,14,0,0,1142,44118,0,0,1676,96964,0,0,561,12525,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,220:8:0 0,33,255:11:0 17 374 . T <*> 0 . DP=30;I16=16,14,0,0,1098,41180,0,0,1676,96964,0,0,556,12344,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,221:8:0 0,33,255:11:0 -17 375 . A T,<*> 0 . DP=31;I16=17,13,0,1,1138,43798,14,196,1676,96964,60,3600,547,12177,4,16;QS=2.9661,0.0338983,0;SGB=-0.556633;RPBZ=-1.45462;MQBZ=0.3849;MQSBZ=-1.26404;BQBZ=-1.68488;NMBZ=2.30253;SCBZ=-0.182574;FS=0;MQ0F=0 PL:DP:DV 0,36,255,36,255,255:12:0 0,24,218,24,218,218:8:0 0,18,255,30,255,255:11:1 +17 375 . A T,<*> 0 . DP=31;I16=17,13,0,1,1138,43798,14,196,1676,96964,60,3600,547,12177,4,16;QS=2.9661,0.0338983,0;SGB=-0.556633;RPBZ=-1.45432;MQBZ=0.3849;MQSBZ=-1.26404;BQBZ=-1.68488;NMBZ=2.30253;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,36,255,36,255,255:12:0 0,24,218,24,218,218:8:0 0,18,255,30,255,255:11:1 17 376 . G <*> 0 . DP=31;I16=17,14,0,0,1131,42581,0,0,1736,100564,0,0,547,12073,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,24,220:8:0 0,33,255:11:0 17 377 . T <*> 0 . DP=31;I16=17,14,0,0,1116,41750,0,0,1736,100564,0,0,543,11985,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,24,211:8:0 0,33,255:11:0 17 378 . T <*> 0 . DP=30;I16=18,12,0,0,1098,41066,0,0,1707,99723,0,0,541,11927,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,39,255:13:0 0,21,186:7:0 0,30,255:10:0 @@ -307,7 +307,7 @@ 17 381 . T <*> 0 . DP=29;I16=18,11,0,0,1167,47337,0,0,1678,98882,0,0,537,11729,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,21,211:7:0 0,30,255:10:0 17 382 . T <*> 0 . DP=29;I16=18,11,0,0,1062,40514,0,0,1678,98882,0,0,535,11693,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,21,182:7:0 0,30,255:10:0 17 383 . T <*> 0 . DP=29;I16=18,11,0,0,1059,39847,0,0,1678,98882,0,0,532,11638,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,21,172:7:0 0,30,255:10:0 -17 384 . A C,<*> 0 . DP=31;I16=19,11,0,1,1077,39885,4,16,1738,102482,60,3600,504,10988,25,625;QS=2.98419,0.0158103,0;SGB=-0.556633;RPBZ=0.615415;MQBZ=0.262613;MQSBZ=-0.333409;BQBZ=-1.68746;NMBZ=3.26825;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,39,255,39,255,255:13:0 0,15,171,21,174,171:8:1 0,30,255,30,255,255:10:0 +17 384 . A C,<*> 0 . DP=31;I16=19,11,0,1,1077,39885,4,16,1738,102482,60,3600,504,10988,25,625;QS=2.98419,0.0158103,0;SGB=-0.556633;RPBZ=0.615229;MQBZ=0.262613;MQSBZ=-0.333409;BQBZ=-1.68746;NMBZ=3.26825;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,39,255,39,255,255:13:0 0,15,171,21,174,171:8:1 0,30,255,30,255,255:10:0 17 385 . C <*> 0 . DP=31;I16=19,12,0,0,1118,41180,0,0,1798,106082,0,0,527,11569,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,39,255:13:0 0,24,186:8:0 0,30,255:10:0 17 386 . T <*> 0 . DP=30;I16=18,12,0,0,1158,45592,0,0,1738,102482,0,0,526,11556,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,39,255:13:0 0,21,191:7:0 0,30,255:10:0 17 387 . T <*> 0 . DP=30;I16=18,12,0,0,1105,41821,0,0,1738,102482,0,0,525,11573,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,39,255:13:0 0,21,187:7:0 0,30,255:10:0 @@ -335,7 +335,7 @@ 17 409 . T <*> 0 . DP=29;I16=17,12,0,0,1100,42734,0,0,1678,98882,0,0,525,11503,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,42,255:14:0 0,12,131:4:0 0,33,255:11:0 17 410 . T <*> 0 . DP=29;I16=17,12,0,0,1035,38325,0,0,1678,98882,0,0,524,11432,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,42,255:14:0 0,12,125:4:0 0,33,255:11:0 17 411 . T <*> 0 . DP=29;I16=17,12,0,0,1022,37928,0,0,1678,98882,0,0,522,11342,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,42,255:14:0 0,12,111:4:0 0,33,255:11:0 -17 412 . C T,<*> 0 . DP=30;I16=17,12,1,0,1094,42458,14,196,1678,98882,60,3600,495,10659,25,625;QS=2.97455,0.0254545,0;SGB=-0.556633;RPBZ=-0.404685;MQBZ=0.267261;MQSBZ=-0.293785;BQBZ=-1.6942;NMBZ=-0.267102;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,30,255,42,255,255:15:1 0,12,124,12,124,124:4:0 0,33,255,33,255,255:11:0 +17 412 . C T,<*> 0 . DP=30;I16=17,12,1,0,1094,42458,14,196,1678,98882,60,3600,495,10659,25,625;QS=2.97455,0.0254545,0;SGB=-0.556633;RPBZ=-0.40473;MQBZ=0.267261;MQSBZ=-0.293785;BQBZ=-1.6942;NMBZ=-0.267102;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,30,255,42,255,255:15:1 0,12,124,12,124,124:4:0 0,33,255,33,255,255:11:0 17 413 . A <*> 0 . DP=31;I16=18,13,0,0,1189,45985,0,0,1798,106082,0,0,520,11258,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,9,102:3:0 0,33,255:11:0 17 414 . T <*> 0 . DP=30;I16=18,12,0,0,1151,44355,0,0,1738,102482,0,0,523,11265,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,9,109:3:0 0,33,255:11:0 17 415 . G <*> 0 . DP=30;I16=18,12,0,0,1131,43175,0,0,1738,102482,0,0,526,11306,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,9,110:3:0 0,33,255:11:0 @@ -360,7 +360,7 @@ 17 434 . T <*> 0 . DP=29;I16=15,14,0,0,1036,37654,0,0,1647,96123,0,0,561,12567,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,9,98:3:0 0,30,243:10:0 17 435 . A <*> 0 . DP=29;I16=15,14,0,0,1035,38091,0,0,1647,96123,0,0,562,12596,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,9,103:3:0 0,30,237:10:0 17 436 . T <*> 0 . DP=28;I16=14,14,0,0,998,36220,0,0,1587,92523,0,0,564,12654,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,9,110:3:0 0,27,223:9:0 -17 437 . T G,<*> 0 . DP=28;I16=13,14,1,0,990,36832,6,36,1558,91682,29,841,549,12435,16,256;QS=2.9781,0.0218978,0;SGB=-0.556633;RPBZ=-1.36195;MQBZ=-2.88675;MQSBZ=0.6;BQBZ=-1.67909;NMBZ=-0.19245;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,48,255,48,255,255:16:0 0,9,109,9,109,109:3:0 0,17,200,24,203,201:9:1 +17 437 . T G,<*> 0 . DP=28;I16=13,14,1,0,990,36832,6,36,1558,91682,29,841,549,12435,16,256;QS=2.9781,0.0218978,0;SGB=-0.556633;RPBZ=-1.36214;MQBZ=-2.88675;MQSBZ=0.6;BQBZ=-1.67909;NMBZ=-0.19245;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,48,255,48,255,255:16:0 0,9,109,9,109,109:3:0 0,17,200,24,203,201:9:1 17 438 . A <*> 0 . DP=28;I16=14,14,0,0,984,35784,0,0,1587,92523,0,0,565,12707,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,9,107:3:0 0,27,220:9:0 17 439 . C <*> 0 . DP=28;I16=14,14,0,0,1055,40273,0,0,1587,92523,0,0,563,12649,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,9,107:3:0 0,27,224:9:0 17 440 . A <*> 0 . DP=28;I16=14,14,0,0,1095,43251,0,0,1587,92523,0,0,561,12615,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,9,115:3:0 0,27,247:9:0 @@ -388,7 +388,7 @@ 17 462 . G <*> 0 . DP=32;I16=18,13,0,0,1169,46001,0,0,1775,103851,0,0,577,12669,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,12,131:4:0 0,30,241:10:0 17 463 . G <*> 0 . DP=32;I16=18,13,0,0,1095,41573,0,0,1775,103851,0,0,583,12729,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,12,126:4:0 0,30,221:10:0 17 464 . A <*> 0 . DP=32;I16=18,13,0,0,1100,41724,0,0,1775,103851,0,0,589,12821,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,12,148:4:0 0,30,217:10:0 -17 465 . C T,<*> 0 . DP=33;I16=19,12,0,1,1173,45601,4,16,1775,103851,60,3600,589,12909,6,36;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.67936;MQBZ=0.321288;MQSBZ=0.341466;BQBZ=-1.68493;NMBZ=3.21288;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,51,255,51,255,255:17:0 0,15,158,15,158,158:5:0 0,20,224,27,227,224:10:1 +17 465 . C T,<*> 0 . DP=33;I16=19,12,0,1,1173,45601,4,16,1775,103851,60,3600,589,12909,6,36;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.67982;MQBZ=0.321288;MQSBZ=0.341466;BQBZ=-1.68493;NMBZ=3.21288;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,51,255,51,255,255:17:0 0,15,158,15,158,158:5:0 0,20,224,27,227,224:10:1 17 466 . A <*> 0 . DP=34;I16=20,13,0,0,1268,49686,0,0,1895,111051,0,0,602,13102,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,15,173:5:0 0,30,255:10:0 17 467 . A <*> 0 . DP=34;I16=20,13,0,0,1246,48610,0,0,1895,111051,0,0,608,13194,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,15,177:5:0 0,30,251:10:0 17 468 . A <*> 0 . DP=35;I16=21,13,0,0,1253,48095,0,0,1955,114651,0,0,613,13273,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,15,174:5:0 0,30,251:10:0 @@ -411,7 +411,7 @@ 17 485 . G <*> 0 . DP=35;I16=23,12,0,0,1329,51411,0,0,2015,118251,0,0,669,14931,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,18,160:6:0 0,33,255:11:0 17 486 . A <*> 0 . DP=34;I16=22,12,0,0,1313,51667,0,0,1955,114651,0,0,671,14989,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,18,173:6:0 0,33,255:11:0 17 487 . G <*> 0 . DP=34;I16=22,12,0,0,1300,50304,0,0,1955,114651,0,0,672,15030,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,18,169:6:0 0,33,255:11:0 -17 488 . A G,<*> 0 . DP=35;I16=22,12,1,0,1278,48412,4,16,1986,117410,29,841,646,14380,25,625;QS=2.98947,0.0105263,0;SGB=-0.556633;RPBZ=0.544734;MQBZ=-3.36505;MQSBZ=0.10737;BQBZ=-1.69552;NMBZ=-0.171499;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,54,255,54,255,255:18:0 0,18,177,18,177,177:6:0 0,23,255,30,255,255:11:1 +17 488 . A G,<*> 0 . DP=35;I16=22,12,1,0,1278,48412,4,16,1986,117410,29,841,646,14380,25,625;QS=2.98947,0.0105263,0;SGB=-0.556633;RPBZ=0.594463;MQBZ=-3.36505;MQSBZ=0.10737;BQBZ=-1.69552;NMBZ=-0.171499;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,54,255,54,255,255:18:0 0,18,177,18,177,177:6:0 0,23,255,30,255,255:11:1 17 489 . A <*> 0 . DP=35;I16=23,12,0,0,1264,46916,0,0,2015,118251,0,0,671,15015,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,18,175:6:0 0,33,255:11:0 17 490 . A <*> 0 . DP=36;I16=24,12,0,0,1332,50280,0,0,2075,121851,0,0,671,15061,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,188:7:0 0,33,255:11:0 17 491 . T <*> 0 . DP=36;I16=24,12,0,0,1284,46802,0,0,2075,121851,0,0,671,15093,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,178:7:0 0,33,255:11:0 @@ -435,9 +435,9 @@ 17 509 . C <*> 0 . DP=34;I16=24,10,0,0,1272,48272,0,0,1986,117410,0,0,640,14430,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,186:7:0 0,27,241:9:0 17 510 . A <*> 0 . DP=34;I16=23,11,0,0,1211,44827,0,0,1986,117410,0,0,638,14398,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,21,187:7:0 0,24,221:8:0 17 511 . A <*> 0 . DP=34;I16=23,11,0,0,1238,46516,0,0,1986,117410,0,0,637,14395,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,21,195:7:0 0,24,233:8:0 -17 512 . A C,<*> 0 . DP=33;I16=22,10,0,1,1133,41513,13,169,1866,110210,60,3600,628,14340,9,81;QS=2.97766,0.0223368,0;SGB=-0.556633;RPBZ=-1.47091;MQBZ=0.253876;MQSBZ=-0.461593;BQBZ=-1.68442;NMBZ=2.68627;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,39,255,51,255,255:18:1 0,21,183,21,183,183:7:0 0,24,231,24,231,231:8:0 -17 513 . A T,<*> 0 . DP=32;I16=21,10,1,0,1125,42283,12,144,1806,106610,60,3600,623,14249,15,225;QS=2.97966,0.020339,0;SGB=-0.556633;RPBZ=-1.24598;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.57376;NMBZ=2.63913;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,37,255,48,255,255:17:1 0,21,177,21,177,177:7:0 0,24,233,24,233,233:8:0 -17 514 . A T,<*> 0 . DP=32;I16=22,9,0,1,1086,40204,16,256,1806,106610,60,3600,627,14381,11,121;QS=2.97127,0.0287253,0;SGB=-0.556633;RPBZ=-1.46267;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.46657;NMBZ=2.63913;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,34,255,48,255,255:17:1 0,21,172,21,172,172:7:0 0,24,235,24,235,235:8:0 +17 512 . A C,<*> 0 . DP=33;I16=22,10,0,1,1133,41513,13,169,1866,110210,60,3600,628,14340,9,81;QS=2.97766,0.0223368,0;SGB=-0.556633;RPBZ=-1.47079;MQBZ=0.253876;MQSBZ=-0.461593;BQBZ=-1.68442;NMBZ=2.68627;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,39,255,51,255,255:18:1 0,21,183,21,183,183:7:0 0,24,231,24,231,231:8:0 +17 513 . A T,<*> 0 . DP=32;I16=21,10,1,0,1125,42283,12,144,1806,106610,60,3600,623,14249,15,225;QS=2.97966,0.020339,0;SGB=-0.556633;RPBZ=-1.24609;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.57376;NMBZ=2.63913;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,37,255,48,255,255:17:1 0,21,177,21,177,177:7:0 0,24,233,24,233,233:8:0 +17 514 . A T,<*> 0 . DP=32;I16=22,9,0,1,1086,40204,16,256,1806,106610,60,3600,627,14381,11,121;QS=2.97127,0.0287253,0;SGB=-0.556633;RPBZ=-1.4628;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.46657;NMBZ=2.63913;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,34,255,48,255,255:17:1 0,21,172,21,172,172:7:0 0,24,235,24,235,235:8:0 17 515 . C <*> 0 . DP=32;I16=22,10,0,0,1050,37704,0,0,1866,110210,0,0,638,14554,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,21,169:7:0 0,24,211:8:0 17 516 . C <*> 0 . DP=32;I16=22,10,0,0,1109,40651,0,0,1866,110210,0,0,637,14579,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,21,187:7:0 0,24,215:8:0 17 517 . T <*> 0 . DP=33;I16=23,10,0,0,1269,49995,0,0,1926,113810,0,0,636,14626,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,201:7:0 0,24,242:8:0 @@ -446,7 +446,7 @@ 17 520 . T <*> 0 . DP=36;I16=25,11,0,0,1243,45051,0,0,2106,124610,0,0,638,14818,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,63,255:21:0 0,21,180:7:0 0,24,223:8:0 17 521 . C <*> 0 . DP=34;I16=25,9,0,0,1281,49527,0,0,1986,117410,0,0,641,14875,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,60,255:20:0 0,21,191:7:0 0,21,204:7:0 17 522 . A <*> 0 . DP=32;I16=24,8,0,0,1158,43228,0,0,1897,112969,0,0,646,14960,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,60,255:20:0 0,21,185:7:0 0,15,170:5:0 -17 523 . T G,<*> 0 . DP=32;I16=23,8,1,0,1184,45708,15,225,1837,109369,60,3600,626,14446,25,625;QS=2.9794,0.0206044,0;SGB=-0.556633;RPBZ=1.13753;MQBZ=0.179605;MQSBZ=-1.73205;BQBZ=-1.68805;NMBZ=2.89159;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,44,255,57,255,255:20:1 0,21,191,21,191,191:7:0 0,15,166,15,166,166:5:0 +17 523 . T G,<*> 0 . DP=32;I16=23,8,1,0,1184,45708,15,225,1837,109369,60,3600,626,14446,25,625;QS=2.9794,0.0206044,0;SGB=-0.556633;RPBZ=1.13742;MQBZ=0.179605;MQSBZ=-1.73205;BQBZ=-1.68805;NMBZ=2.89159;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,44,255,57,255,255:20:1 0,21,191,21,191,191:7:0 0,15,166,15,166,166:5:0 17 524 . T <*> 0 . DP=32;I16=24,8,0,0,1096,39618,0,0,1897,112969,0,0,654,15108,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,60,255:20:0 0,21,194:7:0 0,15,150:5:0 17 525 . G <*> 0 . DP=32;I16=24,8,0,0,1188,45718,0,0,1897,112969,0,0,656,15120,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,60,255:20:0 0,21,188:7:0 0,15,133:5:0 17 526 . C <*> 0 . DP=32;I16=24,8,0,0,1154,44014,0,0,1897,112969,0,0,658,15156,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,60,255:20:0 0,21,185:7:0 0,15,137:5:0 @@ -458,7 +458,7 @@ 17 532 . T <*> 0 . DP=32;I16=25,7,0,0,1161,43607,0,0,1897,112969,0,0,649,14477,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,21,181:7:0 0,18,192:6:0 17 533 . C <*> 0 . DP=32;I16=25,7,0,0,1154,44084,0,0,1897,112969,0,0,644,14274,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,21,178:7:0 0,18,180:6:0 17 534 . T <*> 0 . DP=31;I16=24,7,0,0,1222,49526,0,0,1837,109369,0,0,640,14104,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,205:7:0 0,18,205:6:0 -17 535 . A G,<*> 0 . DP=31;I16=24,6,0,1,1080,39870,8,64,1777,105769,60,3600,611,13341,25,625;QS=2.98623,0.0137694,0;SGB=-0.556633;RPBZ=-0.894608;MQBZ=0.182574;MQSBZ=-1.85164;BQBZ=-1.6854;NMBZ=2.94255;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,21,194,21,194,194:7:0 0,18,189,18,189,189:6:0 +17 535 . A G,<*> 0 . DP=31;I16=24,6,0,1,1080,39870,8,64,1777,105769,60,3600,611,13341,25,625;QS=2.98623,0.0137694,0;SGB=-0.556633;RPBZ=-0.894788;MQBZ=0.182574;MQSBZ=-1.85164;BQBZ=-1.6854;NMBZ=2.94255;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,21,194,21,194,194:7:0 0,18,189,18,189,189:6:0 17 536 . C <*> 0 . DP=31;I16=24,7,0,0,1095,40551,0,0,1837,109369,0,0,631,13809,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,184:7:0 0,18,157:6:0 17 537 . C <*> 0 . DP=31;I16=24,7,0,0,1049,38677,0,0,1837,109369,0,0,626,13682,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,172:7:0 0,18,183:6:0 17 538 . A <*> 0 . DP=31;I16=24,7,0,0,1138,42478,0,0,1837,109369,0,0,620,13536,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,189:7:0 0,18,181:6:0 @@ -505,7 +505,7 @@ 17 579 . G <*> 0 . DP=30;I16=16,14,0,0,1038,38820,0,0,1769,105241,0,0,523,11335,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,24,224:8:0 0,15,144:5:0 17 580 . A C,<*> 0 . DP=30;I16=15,14,1,0,1060,39178,16,256,1709,101641,60,3600,510,11078,17,289;QS=2.97338,0.0266223,0;SGB=-0.556633;RPBZ=1.32953;MQBZ=0.185695;MQSBZ=-1.06904;BQBZ=-1.69093;NMBZ=1.86885;SCBZ=-0.267102;FS=0;MQ0F=0 PL:DP:DV 0,34,255,48,255,255:17:1 0,24,221,24,221,221:8:0 0,15,155,15,155,155:5:0 17 581 . A <*> 0 . DP=31;I16=16,15,0,0,1083,39215,0,0,1829,108841,0,0,530,11384,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,24,223:8:0 0,15,153:5:0 -17 582 . C G,<*> 0 . DP=31;I16=15,15,1,0,1080,39870,8,64,1769,105241,60,3600,519,11211,15,225;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.34245;MQBZ=0.182574;MQSBZ=-1.0328;BQBZ=-1.68266;NMBZ=1.92049;SCBZ=-0.262467;FS=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,24,207,24,207,207:8:0 0,15,151,15,151,151:5:0 +17 582 . C G,<*> 0 . DP=31;I16=15,15,1,0,1080,39870,8,64,1769,105241,60,3600,519,11211,15,225;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.34259;MQBZ=0.182574;MQSBZ=-1.0328;BQBZ=-1.68266;NMBZ=1.92049;SCBZ=-0.262467;FS=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,24,207,24,207,207:8:0 0,15,151,15,151,151:5:0 17 583 . T <*> 0 . DP=30;I16=16,14,0,0,1135,43913,0,0,1769,105241,0,0,539,11523,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,24,238:8:0 0,15,163:5:0 17 584 . C <*> 0 . DP=31;I16=17,14,0,0,1069,39521,0,0,1798,106082,0,0,544,11644,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,24,209:8:0 0,15,157:5:0 17 585 . A <*> 0 . DP=31;I16=17,14,0,0,1096,39866,0,0,1798,106082,0,0,549,11751,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,24,211:8:0 0,15,157:5:0 @@ -516,10 +516,10 @@ 17 590 . C <*> 0 . DP=32;I16=17,15,0,0,1103,41355,0,0,1858,109682,0,0,574,12576,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,24,194:8:0 0,18,175:6:0 17 591 . A <*> 0 . DP=31;I16=16,15,0,0,1164,44088,0,0,1798,106082,0,0,579,12695,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,209:7:0 0,18,188:6:0 17 592 . A <*> 0 . DP=31;I16=16,15,0,0,1121,42193,0,0,1798,106082,0,0,583,12795,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,215:7:0 0,18,182:6:0 -17 593 . C A,<*> 0 . DP=31;I16=16,14,0,1,1071,39925,7,49,1769,105241,29,841,561,12253,25,625;QS=2.97021,0.0297872,0;SGB=-0.556633;RPBZ=0.559412;MQBZ=-3.80789;MQSBZ=-0.0464238;BQBZ=-1.57464;NMBZ=2.13779;SCBZ=3.67454;FS=0;MQ0F=0 PL:DP:DV 0,54,255,54,255,255:18:0 0,12,184,18,187,185:7:1 0,18,174,18,174,174:6:0 +17 593 . C A,<*> 0 . DP=31;I16=16,14,0,1,1071,39925,7,49,1769,105241,29,841,561,12253,25,625;QS=2.97021,0.0297872,0;SGB=-0.556633;RPBZ=0.559355;MQBZ=-3.80789;MQSBZ=-0.0464238;BQBZ=-1.57464;NMBZ=2.13779;SCBZ=3.67454;FS=0;MQ0F=0 PL:DP:DV 0,54,255,54,255,255:18:0 0,12,184,18,187,185:7:1 0,18,174,18,174,174:6:0 17 594 . A G,<*> 0 . DP=33;I16=16,16,1,0,1161,42757,4,16,1858,109682,60,3600,572,12672,15,225;QS=2.99359,0.00641026,0;SGB=-0.556633;RPBZ=-0.998367;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68954;NMBZ=1.76408;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:DV 0,42,255,51,255,255:18:1 0,21,205,21,205,205:7:0 0,24,213,24,213,213:8:0 17 595 . A <*> 0 . DP=33;I16=17,16,0,0,1136,40412,0,0,1918,113282,0,0,589,12905,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,198:7:0 0,24,218:8:0 -17 596 . A G,<*> 0 . DP=33;I16=16,16,1,0,1061,37187,8,64,1858,109682,60,3600,590,12952,1,1;QS=2.98564,0.0143627,0;SGB=-0.556633;RPBZ=1.68132;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68357;NMBZ=1.61602;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,21,169,21,169,169:7:0 0,24,231,24,231,231:8:0 +17 596 . A G,<*> 0 . DP=33;I16=16,16,1,0,1061,37187,8,64,1858,109682,60,3600,590,12952,1,1;QS=2.98564,0.0143627,0;SGB=-0.556633;RPBZ=1.68146;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68357;NMBZ=1.61602;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,21,169,21,169,169:7:0 0,24,231,24,231,231:8:0 17 597 . C <*> 0 . DP=33;I16=17,16,0,0,1196,44890,0,0,1918,113282,0,0,592,12990,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,204:7:0 0,24,220:8:0 17 598 . T <*> 0 . DP=33;I16=16,17,0,0,1219,47333,0,0,1918,113282,0,0,597,13029,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,21,217:7:0 0,27,242:9:0 17 599 . T <*> 0 . DP=33;I16=16,17,0,0,1182,43598,0,0,1918,113282,0,0,599,13095,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,21,197:7:0 0,27,247:9:0 diff --git a/test/mpileup/mpileup.4.out b/test/mpileup/mpileup.4.out index a2a6c1272..8ae54d360 100644 --- a/test/mpileup/mpileup.4.out +++ b/test/mpileup/mpileup.4.out @@ -30,7 +30,7 @@ 17 101 . C <*> 0 . DP=18;DPR=17,0;I16=16,1,0,0,630,24730,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,182:9:0:0:9,0,0,0:9,0 0,9,108:3:0:0:2,1,0,0:3,0 0,15,132:5:0:0:5,0,0,0:5,0 17 102 . C <*> 0 . DP=18;DPR=17,0;I16=16,1,0,0,676,27812,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,188:9:0:0:9,0,0,0:9,0 0,9,121:3:0:0:2,1,0,0:3,0 0,15,139:5:0:0:5,0,0,0:5,0 17 103 . T C,<*> 0 . DP=18;DPR=16,1,0;I16=15,1,1,0,668,28542,6,36,929,54841,29,841,323,7035,6,36;QS=2.98256,0.0174419,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64924;NMBZ=2.45514;SCBZ=4;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,17,184,24,187,185:9:1:0:8,0,1,0:8,1,0 0,9,118,9,118,118:3:0:0:2,1,0,0:3,0,0 0,15,147,15,147,147:5:0:0:5,0,0,0:5,0,0 -17 104 . G C,<*> 0 . DP=18;DPR=16,1,0;I16=15,1,1,0,601,24163,3,9,929,54841,29,841,320,6884,7,49;QS=2.98726,0.0127389,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64309;NMBZ=2.45514;SCBZ=2.91548;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,173,24,176,173:9:1:0:8,0,1,0:8,1,0 0,9,101,9,101,101:3:0:0:2,1,0,0:3,0,0 0,15,133,15,133,133:5:0:0:5,0,0,0:5,0,0 +17 104 . G C,<*> 0 . DP=18;DPR=16,1,0;I16=15,1,1,0,601,24163,3,9,929,54841,29,841,320,6884,7,49;QS=2.98726,0.0127389,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64309;NMBZ=2.45514;SCBZ=4;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,173,24,176,173:9:1:0:8,0,1,0:8,1,0 0,9,101,9,101,101:3:0:0:2,1,0,0:3,0,0 0,15,133,15,133,133:5:0:0:5,0,0,0:5,0,0 17 105 . G <*> 0 . DP=19;DPR=18,0;I16=17,1,0,0,603,22351,0,0,1018,59282,0,0,325,6815,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,171:10:0:0:10,0,0,0:10,0 0,9,106:3:0:0:2,1,0,0:3,0 0,15,125:5:0:0:5,0,0,0:5,0 17 106 . G <*> 0 . DP=19;DPR=18,0;I16=17,1,0,0,636,25058,0,0,1018,59282,0,0,324,6718,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,190:10:0:0:10,0,0,0:10,0 0,9,92:3:0:0:2,1,0,0:3,0 0,15,124:5:0:0:5,0,0,0:5,0 17 107 . C <*> 0 . DP=19;DPR=18,0;I16=17,1,0,0,686,27952,0,0,1018,59282,0,0,323,6643,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,192:10:0:0:10,0,0,0:10,0 0,9,119:3:0:0:2,1,0,0:3,0 0,15,136:5:0:0:5,0,0,0:5,0 @@ -85,7 +85,7 @@ 17 156 . C <*> 0 . DP=14;DPR=14,0;I16=12,2,0,0,536,20884,0,0,809,47641,0,0,266,5934,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,163:7:0:0:7,0,0,0:7,0 0,6,84:2:0:0:1,1,0,0:2,0 0,15,150:5:0:0:4,1,0,0:5,0 17 157 . C <*> 0 . DP=14;DPR=14,0;I16=12,2,0,0,555,22081,0,0,809,47641,0,0,264,5904,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,169:7:0:0:7,0,0,0:7,0 0,6,85:2:0:0:1,1,0,0:2,0 0,15,149:5:0:0:4,1,0,0:5,0 17 158 . T <*> 0 . DP=14;DPR=14,0;I16=12,2,0,0,568,23154,0,0,809,47641,0,0,262,5886,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,170:7:0:0:7,0,0,0:7,0 0,6,84:2:0:0:1,1,0,0:2,0 0,15,159:5:0:0:4,1,0,0:5,0 -17 159 . A G,<*> 0 . DP=15;DPR=14,1,0;I16=12,2,1,0,519,19467,5,25,809,47641,60,3600,260,5880,0,0;QS=2.97076,0.0292398,0;SGB=-0.556633;RPBZ=-1.62163;MQBZ=0.267261;MQSBZ=-2.54951;BQBZ=-1.63041;NMBZ=0;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,157,21,157,157:7:0:0:7,0,0,0:7,0,0 0,6,83,6,83,83:2:0:0:1,1,0,0:2,0,0 0,10,129,15,132,129:6:1:0:4,1,1,0:5,1,0 +17 159 . A G,<*> 0 . DP=15;DPR=14,1,0;I16=12,2,1,0,519,19467,5,25,809,47641,60,3600,260,5880,0,0;QS=2.97076,0.0292398,0;SGB=-0.556633;RPBZ=-1.62019;MQBZ=0.267261;MQSBZ=-2.54951;BQBZ=-1.63041;NMBZ=0;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,157,21,157,157:7:0:0:7,0,0,0:7,0,0 0,6,83,6,83,83:2:0:0:1,1,0,0:2,0,0 0,10,129,15,132,129:6:1:0:4,1,1,0:5,1,0 17 160 . G <*> 0 . DP=15;DPR=15,0;I16=13,2,0,0,547,20633,0,0,869,51241,0,0,259,5887,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,165:7:0:0:7,0,0,0:7,0 0,6,85:2:0:0:1,1,0,0:2,0 0,18,139:6:0:0:5,1,0,0:6,0 17 161 . A <*> 0 . DP=15;DPR=15,0;I16=13,2,0,0,568,21610,0,0,869,51241,0,0,258,5908,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,157:7:0:0:7,0,0,0:7,0 0,6,83:2:0:0:1,1,0,0:2,0 0,18,162:6:0:0:5,1,0,0:6,0 17 162 . A <*> 0 . DP=15;DPR=15,0;I16=13,2,0,0,558,21206,0,0,869,51241,0,0,255,5843,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,147:7:0:0:7,0,0,0:7,0 0,6,87:2:0:0:1,1,0,0:2,0 0,18,167:6:0:0:5,1,0,0:6,0 @@ -149,10 +149,10 @@ 17 220 . G <*> 0 . DP=14;DPR=14,0;I16=11,3,0,0,495,18407,0,0,747,42123,0,0,267,6079,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,188:7:0:0:6,1,0,0:7,0 0,9,88:3:0:0:1,2,0,0:3,0 0,12,84:4:0:0:4,0,0,0:4,0 17 221 . A <*> 0 . DP=14;DPR=14,0;I16=11,3,0,0,488,17688,0,0,747,42123,0,0,267,6135,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,176:7:0:0:6,1,0,0:7,0 0,9,89:3:0:0:1,2,0,0:3,0 0,12,101:4:0:0:4,0,0,0:4,0 17 222 . A <*> 0 . DP=14;DPR=14,0;I16=11,3,0,0,479,17747,0,0,747,42123,0,0,267,6203,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,186:7:0:0:6,1,0,0:7,0 0,9,89:3:0:0:1,2,0,0:3,0 0,12,73:4:0:0:4,0,0,0:4,0 -17 223 . G T,<*> 0 . DP=13;DPR=12,1,0;I16=9,3,1,0,412,14782,8,64,627,34923,60,3600,243,5657,25,625;QS=2.96596,0.0340426,0;SGB=-0.556633;RPBZ=1.06904;MQBZ=0.547723;MQSBZ=-3.4641;BQBZ=-1.60577;NMBZ=-0.288675;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,11,166,18,169,167:7:1:0:5,1,1,0:6,1,0 0,6,53,6,53,53:2:0:0:0,2,0,0:2,0,0 0,12,81,12,81,81:4:0:0:4,0,0,0:4,0,0 +17 223 . G T,<*> 0 . DP=13;DPR=12,1,0;I16=9,3,1,0,412,14782,8,64,627,34923,60,3600,243,5657,25,625;QS=2.96596,0.0340426,0;SGB=-0.556633;RPBZ=1.07052;MQBZ=0.547723;MQSBZ=-3.4641;BQBZ=-1.60577;NMBZ=-0.288675;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,11,166,18,169,167:7:1:0:5,1,1,0:6,1,0 0,6,53,6,53,53:2:0:0:0,2,0,0:2,0,0 0,12,81,12,81,81:4:0:0:4,0,0,0:4,0,0 17 224 . G <*> 0 . DP=12;DPR=12,0;I16=9,3,0,0,379,12759,0,0,627,34923,0,0,270,6370,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,168:6:0:0:5,1,0,0:6,0 0,6,50:2:0:0:0,2,0,0:2,0 0,12,70:4:0:0:4,0,0,0:4,0 17 225 . C <*> 0 . DP=12;DPR=12,0;I16=9,3,0,0,390,13960,0,0,627,34923,0,0,272,6466,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,165:6:0:0:5,1,0,0:6,0 0,6,48:2:0:0:0,2,0,0:2,0 0,12,86:4:0:0:4,0,0,0:4,0 -17 226 . A G,C,<*> 0 . DP=13;DPR=11,1,1,0;I16=8,3,1,1,381,13669,6,18,567,31323,89,4441,248,5894,44,986;QS=2.94293,0.0392157,0.0178571,0;VDB=0.84;SGB=-2.62246;RPBZ=-0.592972;MQBZ=-0.615457;MQSBZ=-3.4641;BQBZ=-2.17723;NMBZ=2.34521;SCBZ=2.34521;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,159,12,162,159,18,159,162,159:7:1:0:5,1,0,1:6,0,1,0 0,6,53,6,53,53,6,53,53,53:2:0:0:0,2,0,0:2,0,0,0 0,5,79,9,82,80,9,82,80,80:4:1:0:3,0,1,0:3,1,0,0 +17 226 . A G,C,<*> 0 . DP=13;DPR=11,1,1,0;I16=8,3,1,1,381,13669,6,18,567,31323,89,4441,248,5894,44,986;QS=2.94293,0.0392157,0.0178571,0;VDB=0.84;SGB=-2.62246;RPBZ=-0.592157;MQBZ=-0.615457;MQSBZ=-3.4641;BQBZ=-2.17723;NMBZ=2.34521;SCBZ=2.34521;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,159,12,162,159,18,159,162,159:7:1:0:5,1,0,1:6,0,1,0 0,6,53,6,53,53,6,53,53,53:2:0:0:0,2,0,0:2,0,0,0 0,5,79,9,82,80,9,82,80,80:4:1:0:3,0,1,0:3,1,0,0 17 227 . C <*> 0 . DP=13;DPR=13,0;I16=9,4,0,0,412,14342,0,0,656,35764,0,0,292,6878,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,190:7:0:0:5,2,0,0:7,0 0,6,53:2:0:0:0,2,0,0:2,0 0,12,75:4:0:0:4,0,0,0:4,0 17 228 . C <*> 0 . DP=13;DPR=13,0;I16=9,4,0,0,417,14381,0,0,656,35764,0,0,292,6884,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,187:7:0:0:5,2,0,0:7,0 0,6,45:2:0:0:0,2,0,0:2,0 0,12,96:4:0:0:4,0,0,0:4,0 17 229 . G <*> 0 . DP=13;DPR=13,0;I16=9,4,0,0,368,11524,0,0,656,35764,0,0,292,6898,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,145:7:0:0:5,2,0,0:7,0 0,6,53:2:0:0:0,2,0,0:2,0 0,12,70:4:0:0:4,0,0,0:4,0 @@ -193,7 +193,7 @@ 17 264 . C <*> 0 . DP=22;DPR=22,0;I16=10,12,0,0,821,31325,0,0,1049,54897,0,0,386,8326,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:7,4,0,0:11,0 0,15,104:5:0:0:0,5,0,0:5,0 0,18,172:6:0:0:3,3,0,0:6,0 17 265 . A <*> 0 . DP=21;DPR=21,0;I16=9,12,0,0,800,31906,0,0,989,51297,0,0,390,8380,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:7,4,0,0:11,0 0,15,114:5:0:0:0,5,0,0:5,0 0,15,129:5:0:0:2,3,0,0:5,0 17 266 . G <*> 0 . DP=21;DPR=21,0;I16=9,12,0,0,754,28204,0,0,989,51297,0,0,394,8458,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:7,4,0,0:11,0 0,15,99:5:0:0:0,5,0,0:5,0 0,15,138:5:0:0:2,3,0,0:5,0 -17 267 . T G,<*> 0 . DP=21;DPR=20,1,0;I16=9,11,0,1,739,27465,8,64,960,50456,29,841,373,7935,25,625;QS=2.94203,0.057971,0;SGB=-0.556633;RPBZ=-0.330504;MQBZ=-1.23153;MQSBZ=-3.3021;BQBZ=-1.66282;NMBZ=2.4409;SCBZ=2.91633;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,254,33,254,254:11:0:0:7,4,0,0:11,0,0 0,6,93,12,96,96:5:1:0:0,4,0,1:4,1,0 0,15,149,15,149,149:5:0:0:2,3,0,0:5,0,0 +17 267 . T G,<*> 0 . DP=21;DPR=20,1,0;I16=9,11,0,1,739,27465,8,64,960,50456,29,841,373,7935,25,625;QS=2.94203,0.057971,0;SGB=-0.556633;RPBZ=-0.330396;MQBZ=-1.23153;MQSBZ=-3.3021;BQBZ=-1.66282;NMBZ=2.4409;SCBZ=2.91633;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,254,33,254,254:11:0:0:7,4,0,0:11,0,0 0,6,93,12,96,96:5:1:0:0,4,0,1:4,1,0 0,15,149,15,149,149:5:0:0:2,3,0,0:5,0,0 17 268 . T <*> 0 . DP=21;DPR=21,0;I16=9,12,0,0,748,27708,0,0,989,51297,0,0,402,8686,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,238:11:0:0:7,4,0,0:11,0 0,15,110:5:0:0:0,5,0,0:5,0 0,15,156:5:0:0:2,3,0,0:5,0 17 269 . C <*> 0 . DP=22;DPR=22,0;I16=9,13,0,0,767,28641,0,0,1018,52138,0,0,406,8836,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:7,5,0,0:12,0 0,15,91:5:0:0:0,5,0,0:5,0 0,15,154:5:0:0:2,3,0,0:5,0 17 270 . C <*> 0 . DP=22;DPR=22,0;I16=9,13,0,0,766,28210,0,0,1018,52138,0,0,410,8962,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:7,5,0,0:12,0 0,15,98:5:0:0:0,5,0,0:5,0 0,15,143:5:0:0:2,3,0,0:5,0 @@ -204,7 +204,7 @@ 17 275 . C <*> 0 . DP=20;DPR=20,0;I16=7,13,0,0,768,29994,0,0,898,44938,0,0,423,9519,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,15,114:5:0:0:0,5,0,0:5,0 0,12,122:4:0:0:1,3,0,0:4,0 17 276 . A <*> 0 . DP=20;DPR=20,0;I16=7,13,0,0,805,32931,0,0,898,44938,0,0,424,9538,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,253:11:0:0:6,5,0,0:11,0 0,15,122:5:0:0:0,5,0,0:5,0 0,12,124:4:0:0:1,3,0,0:4,0 17 277 . G <*> 0 . DP=20;DPR=20,0;I16=7,13,0,0,764,29732,0,0,898,44938,0,0,425,9579,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,15,114:5:0:0:0,5,0,0:5,0 0,12,121:4:0:0:1,3,0,0:4,0 -17 278 . A C,<*> 0 . DP=21;DPR=20,1,0;I16=6,14,1,0,722,26452,7,49,867,42179,60,3600,415,9521,11,121;QS=2.97935,0.020649,0;SGB=-0.556633;RPBZ=1.56989;MQBZ=1.0247;MQSBZ=-3.24037;BQBZ=-1.66667;NMBZ=-0.406816;SCBZ=-0.324037;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,22,231,30,234,231:11:1:0:5,5,1,0:10,1,0 0,18,123,18,123,123:6:0:0:0,6,0,0:6,0,0 0,12,121,12,121,121:4:0:0:1,3,0,0:4,0,0 +17 278 . A C,<*> 0 . DP=21;DPR=20,1,0;I16=6,14,1,0,722,26452,7,49,867,42179,60,3600,415,9521,11,121;QS=2.97935,0.020649,0;SGB=-0.556633;RPBZ=1.65198;MQBZ=1.0247;MQSBZ=-3.24037;BQBZ=-1.66667;NMBZ=-0.406816;SCBZ=-0.324037;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,22,231,30,234,231:11:1:0:5,5,1,0:10,1,0 0,18,123,18,123,123:6:0:0:0,6,0,0:6,0,0 0,12,121,12,121,121:4:0:0:1,3,0,0:4,0,0 17 279 . A <*> 0 . DP=22;DPR=22,0;I16=7,15,0,0,786,28694,0,0,956,46620,0,0,427,9677,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:6,6,0,0:12,0 0,18,123:6:0:0:0,6,0,0:6,0 0,12,122:4:0:0:1,3,0,0:4,0 17 280 . A <*> 0 . DP=22;DPR=22,0;I16=7,15,0,0,815,31561,0,0,956,46620,0,0,428,9684,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,253:12:0:0:6,6,0,0:12,0 0,18,130:6:0:0:0,6,0,0:6,0 0,12,129:4:0:0:1,3,0,0:4,0 17 281 . G <*> 0 . DP=22;DPR=22,0;I16=7,15,0,0,820,31416,0,0,956,46620,0,0,428,9662,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:6,6,0,0:12,0 0,18,122:6:0:0:0,6,0,0:6,0 0,12,123:4:0:0:1,3,0,0:4,0 @@ -229,7 +229,7 @@ 17 300 . A <*> 0 . DP=27;DPR=26,0;I16=11,15,0,0,1001,39455,0,0,1258,66538,0,0,469,10437,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,204:8:0:0:3,5,0,0:8,0 0,21,210:7:0:0:2,5,0,0:7,0 17 301 . G <*> 0 . DP=25;DPR=24,0;I16=10,14,0,0,928,36116,0,0,1169,62097,0,0,476,10632,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,255:10:0:0:5,5,0,0:10,0 0,21,195:7:0:0:3,4,0,0:7,0 0,21,196:7:0:0:2,5,0,0:7,0 17 302 . T <*> 0 . DP=25;DPR=24,0;I16=10,14,0,0,879,32885,0,0,1169,62097,0,0,483,10849,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,231:10:0:0:5,5,0,0:10,0 0,21,172:7:0:0:3,4,0,0:7,0 0,21,202:7:0:0:2,5,0,0:7,0 -17 302 . T TA 0 . INDEL;IDV=7;IMF=1;DP=25;DPR=6,19;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.539485,2.46052;VDB=0.260546;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.22749;BQBZ=-1.67542;NMBZ=-0.199304;SCBZ=-0.268121;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 161,0,99:11:6:6:1,4,4,2:5,6 158,0,14:7:6:0:1,0,2,4:1,6 201,21,0:7:7:0:0,0,2,5:0,7 +17 302 . T TA 0 . INDEL;IDV=7;IMF=1;DP=25;DPR=6,19;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.539485,2.46052;VDB=0.241622;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.22749;BQBZ=-1.67542;NMBZ=-0.199304;SCBZ=-0.268121;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 161,0,99:11:6:6:1,4,4,2:5,6 158,0,14:7:6:0:1,0,2,4:1,6 201,21,0:7:7:0:0,0,2,5:0,7 17 303 . G <*> 0 . DP=25;DPR=25,0;I16=10,15,0,0,968,37972,0,0,1229,65697,0,0,497,11181,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:5,6,0,0:11,0 0,21,197:7:0:0:3,4,0,0:7,0 0,21,195:7:0:0:2,5,0,0:7,0 17 304 . C <*> 0 . DP=27;DPR=27,0;I16=11,16,0,0,991,37005,0,0,1318,70138,0,0,503,11359,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:5,6,0,0:11,0 0,24,206:8:0:0:4,4,0,0:8,0 0,24,200:8:0:0:2,6,0,0:8,0 17 305 . C <*> 0 . DP=27;DPR=27,0;I16=11,16,0,0,1057,41761,0,0,1318,70138,0,0,510,11508,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:5,6,0,0:11,0 0,24,213:8:0:0:4,4,0,0:8,0 0,24,211:8:0:0:2,6,0,0:8,0 @@ -262,9 +262,9 @@ 17 332 . A <*> 0 . DP=32;DPR=32,0;I16=14,18,0,0,1156,42666,0,0,1649,90897,0,0,560,12178,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:6,6,0,0:12,0 0,27,214:9:0:0:4,5,0,0:9,0 0,33,255:11:0:0:4,7,0,0:11,0 17 333 . A <*> 0 . DP=32;DPR=32,0;I16=14,18,0,0,1141,41987,0,0,1649,90897,0,0,558,12064,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:6,6,0,0:12,0 0,27,223:9:0:0:4,5,0,0:9,0 0,33,255:11:0:0:4,7,0,0:11,0 17 334 . A <*> 0 . DP=32;DPR=32,0;I16=14,18,0,0,1162,43328,0,0,1649,90897,0,0,556,11986,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:6,6,0,0:12,0 0,27,221:9:0:0:4,5,0,0:9,0 0,33,255:11:0:0:4,7,0,0:11,0 -17 335 . A G,<*> 0 . DP=32;DPR=31,1,0;I16=13,18,1,0,1084,40336,4,16,1589,87297,60,3600,555,11943,0,0;QS=2.98919,0.0108108,0;SGB=-0.556633;RPBZ=-1.67921;MQBZ=0.622171;MQSBZ=-2.25492;BQBZ=-1.68602;NMBZ=-0.428353;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,252,33,252,252:11:0:0:5,6,0,0:11,0,0 0,27,219,27,219,219:9:0:0:4,5,0,0:9,0,0 0,25,245,33,248,245:12:1:0:4,7,1,0:11,1,0 +17 335 . A G,<*> 0 . DP=32;DPR=31,1,0;I16=13,18,1,0,1084,40336,4,16,1589,87297,60,3600,555,11943,0,0;QS=2.98919,0.0108108,0;SGB=-0.556633;RPBZ=-1.67936;MQBZ=0.622171;MQSBZ=-2.25492;BQBZ=-1.68602;NMBZ=-0.428353;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,252,33,252,252:11:0:0:5,6,0,0:11,0,0 0,27,219,27,219,219:9:0:0:4,5,0,0:9,0,0 0,25,245,33,248,245:12:1:0:4,7,1,0:11,1,0 17 336 . A <*> 0 . DP=32;DPR=32,0;I16=14,18,0,0,1094,39794,0,0,1649,90897,0,0,555,11935,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:5,6,0,0:11,0 0,27,212:9:0:0:4,5,0,0:9,0 0,36,255:12:0:0:5,7,0,0:12,0 -17 337 . C A,<*> 0 . DP=32;DPR=31,1,0;I16=14,17,0,1,1125,42481,5,25,1612,89528,37,1369,536,11590,18,324;QS=2.98113,0.0188679,0;SGB=-0.556633;RPBZ=0.812519;MQBZ=-1.03695;MQSBZ=-2.25492;BQBZ=-1.68353;NMBZ=-0.376914;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255,33,255,255:11:0:0:5,6,0,0:11,0,0 0,17,195,24,198,195:9:1:0:4,4,0,1:8,1,0 0,36,255,36,255,255:12:0:0:5,7,0,0:12,0,0 +17 337 . C A,<*> 0 . DP=32;DPR=31,1,0;I16=14,17,0,1,1125,42481,5,25,1612,89528,37,1369,536,11590,18,324;QS=2.98113,0.0188679,0;SGB=-0.556633;RPBZ=0.812593;MQBZ=-1.03695;MQSBZ=-2.25492;BQBZ=-1.68353;NMBZ=-0.376914;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255,33,255,255:11:0:0:5,6,0,0:11,0,0 0,17,195,24,198,195:9:1:0:4,4,0,1:8,1,0 0,36,255,36,255,255:12:0:0:5,7,0,0:12,0,0 17 338 . T <*> 0 . DP=30;DPR=30,0;I16=14,16,0,0,1190,47898,0,0,1560,86456,0,0,554,11878,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,255:10:0:0:5,5,0,0:10,0 0,24,226:8:0:0:4,4,0,0:8,0 0,36,255:12:0:0:5,7,0,0:12,0 17 339 . C <*> 0 . DP=31;DPR=31,0;I16=14,17,0,0,1130,43210,0,0,1589,87297,0,0,554,11874,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:5,6,0,0:11,0 0,24,185:8:0:0:4,4,0,0:8,0 0,36,255:12:0:0:5,7,0,0:12,0 17 340 . C <*> 0 . DP=31;DPR=31,0;I16=14,17,0,0,1196,47044,0,0,1589,87297,0,0,554,11852,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:5,6,0,0:11,0 0,24,221:8:0:0:4,4,0,0:8,0 0,36,255:12:0:0:5,7,0,0:12,0 @@ -286,7 +286,7 @@ 17 356 . G <*> 0 . DP=27;DPR=27,0;I16=14,13,0,0,993,37481,0,0,1465,83405,0,0,574,13174,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,228:9:0:0:4,5,0,0:9,0 0,24,201:8:0:0:5,3,0,0:8,0 0,30,255:10:0:0:5,5,0,0:10,0 17 357 . C <*> 0 . DP=28;DPR=28,0;I16=15,13,0,0,1026,39496,0,0,1525,87005,0,0,575,13209,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,255:10:0:0:5,5,0,0:10,0 0,24,205:8:0:0:5,3,0,0:8,0 0,30,252:10:0:0:5,5,0,0:10,0 17 358 . A <*> 0 . DP=28;DPR=28,0;I16=15,13,0,0,1050,40518,0,0,1525,87005,0,0,576,13216,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,254:10:0:0:5,5,0,0:10,0 0,24,197:8:0:0:5,3,0,0:8,0 0,30,255:10:0:0:5,5,0,0:10,0 -17 359 . G T,<*> 0 . DP=29;DPR=28,1,0;I16=15,13,0,1,1085,42761,10,100,1525,87005,60,3600,552,12620,25,625;QS=2.96032,0.0396825,0;SGB=-0.556633;RPBZ=-0.119567;MQBZ=0.456435;MQSBZ=-1.53333;BQBZ=-1.68246;NMBZ=3.0531;SCBZ=5.2915;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,255,30,255,255:10:0:0:5,5,0,0:10,0,0 0,13,178,21,181,180:8:1:0:5,2,0,1:7,1,0 0,33,255,33,255,255:11:0:0:5,6,0,0:11,0,0 +17 359 . G T,<*> 0 . DP=29;DPR=28,1,0;I16=15,13,0,1,1085,42761,10,100,1525,87005,60,3600,552,12620,25,625;QS=2.96032,0.0396825,0;SGB=-0.556633;RPBZ=-0.119611;MQBZ=0.456435;MQSBZ=-1.53333;BQBZ=-1.68246;NMBZ=3.0531;SCBZ=5.2915;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,255,30,255,255:10:0:0:5,5,0,0:10,0,0 0,13,178,21,181,180:8:1:0:5,2,0,1:7,1,0 0,33,255,33,255,255:11:0:0:5,6,0,0:11,0,0 17 360 . A <*> 0 . DP=29;DPR=29,0;I16=15,14,0,0,1111,43259,0,0,1585,90605,0,0,579,13297,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,252:10:0:0:5,5,0,0:10,0 0,24,220:8:0:0:5,3,0,0:8,0 0,33,255:11:0:0:5,6,0,0:11,0 17 361 . A <*> 0 . DP=29;DPR=29,0;I16=15,14,0,0,1116,43442,0,0,1585,90605,0,0,579,13273,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,252:10:0:0:5,5,0,0:10,0 0,24,219:8:0:0:5,3,0,0:8,0 0,33,255:11:0:0:5,6,0,0:11,0 17 362 . A <*> 0 . DP=29;DPR=29,0;I16=16,13,0,0,1104,42700,0,0,1585,90605,0,0,580,13272,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,218:8:0:0:5,3,0,0:8,0 0,30,255:10:0:0:5,5,0,0:10,0 @@ -296,13 +296,13 @@ 17 366 . A <*> 0 . DP=29;DPR=29,0;I16=16,13,0,0,1090,41562,0,0,1585,90605,0,0,581,13167,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,211:8:0:0:5,3,0,0:8,0 0,30,255:10:0:0:5,5,0,0:10,0 17 367 . T <*> 0 . DP=29;DPR=29,0;I16=16,13,0,0,1055,39149,0,0,1585,90605,0,0,579,13093,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,204:8:0:0:5,3,0,0:8,0 0,30,255:10:0:0:5,5,0,0:10,0 17 368 . A <*> 0 . DP=29;DPR=29,0;I16=16,13,0,0,1054,39632,0,0,1585,90605,0,0,576,12998,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,208:8:0:0:5,3,0,0:8,0 0,30,255:10:0:0:5,5,0,0:10,0 -17 369 . T G,<*> 0 . DP=28;DPR=27,1,0;I16=16,11,0,1,1037,40275,6,36,1496,86164,60,3600,548,12256,25,625;QS=2.97683,0.023166,0;SGB=-0.556633;RPBZ=0.123865;MQBZ=0.408248;MQSBZ=-1.37784;BQBZ=-1.68703;NMBZ=2.99794;SCBZ=5.19615;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,250,30,250,250:10:0:0:6,4,0,0:10,0,0 0,15,189,21,192,190:8:1:0:5,2,0,1:7,1,0 0,30,255,30,255,255:10:0:0:5,5,0,0:10,0,0 +17 369 . T G,<*> 0 . DP=28;DPR=27,1,0;I16=16,11,0,1,1037,40275,6,36,1496,86164,60,3600,548,12256,25,625;QS=2.97683,0.023166,0;SGB=-0.556633;RPBZ=0.12395;MQBZ=0.408248;MQSBZ=-1.37784;BQBZ=-1.68703;NMBZ=2.99794;SCBZ=5.19615;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,250,30,250,250:10:0:0:6,4,0,0:10,0,0 0,15,189,21,192,190:8:1:0:5,2,0,1:7,1,0 0,30,255,30,255,255:10:0:0:5,5,0,0:10,0,0 17 370 . C <*> 0 . DP=28;DPR=28,0;I16=16,12,0,0,1045,40219,0,0,1556,89764,0,0,570,12790,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,255:10:0:0:6,4,0,0:10,0 0,24,201:8:0:0:5,3,0,0:8,0 0,30,255:10:0:0:5,5,0,0:10,0 17 371 . T <*> 0 . DP=29;DPR=29,0;I16=16,13,0,0,1155,46591,0,0,1616,93364,0,0,567,12725,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,255:10:0:0:6,4,0,0:10,0 0,24,227:8:0:0:5,3,0,0:8,0 0,33,255:11:0:0:5,6,0,0:11,0 17 372 . C <*> 0 . DP=30;DPR=30,0;I16=16,14,0,0,1139,44019,0,0,1676,96964,0,0,564,12636,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,215:8:0:0:5,3,0,0:8,0 0,33,255:11:0:0:5,6,0,0:11,0 17 373 . A <*> 0 . DP=30;DPR=30,0;I16=16,14,0,0,1142,44118,0,0,1676,96964,0,0,561,12525,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,220:8:0:0:5,3,0,0:8,0 0,33,255:11:0:0:5,6,0,0:11,0 17 374 . T <*> 0 . DP=30;DPR=30,0;I16=16,14,0,0,1098,41180,0,0,1676,96964,0,0,556,12344,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,221:8:0:0:5,3,0,0:8,0 0,33,255:11:0:0:5,6,0,0:11,0 -17 375 . A T,<*> 0 . DP=31;DPR=30,1,0;I16=17,13,0,1,1138,43798,14,196,1676,96964,60,3600,547,12177,4,16;QS=2.9661,0.0338983,0;SGB=-0.556633;RPBZ=-1.45462;MQBZ=0.3849;MQSBZ=-1.26404;BQBZ=-1.68488;NMBZ=2.30253;SCBZ=-0.182574;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255,36,255,255:12:0:0:7,5,0,0:12,0,0 0,24,218,24,218,218:8:0:0:5,3,0,0:8,0,0 0,18,255,30,255,255:11:1:0:5,5,0,1:10,1,0 +17 375 . A T,<*> 0 . DP=31;DPR=30,1,0;I16=17,13,0,1,1138,43798,14,196,1676,96964,60,3600,547,12177,4,16;QS=2.9661,0.0338983,0;SGB=-0.556633;RPBZ=-1.45432;MQBZ=0.3849;MQSBZ=-1.26404;BQBZ=-1.68488;NMBZ=2.30253;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255,36,255,255:12:0:0:7,5,0,0:12,0,0 0,24,218,24,218,218:8:0:0:5,3,0,0:8,0,0 0,18,255,30,255,255:11:1:0:5,5,0,1:10,1,0 17 376 . G <*> 0 . DP=31;DPR=31,0;I16=17,14,0,0,1131,42581,0,0,1736,100564,0,0,547,12073,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:7,5,0,0:12,0 0,24,220:8:0:0:5,3,0,0:8,0 0,33,255:11:0:0:5,6,0,0:11,0 17 377 . T <*> 0 . DP=31;DPR=31,0;I16=17,14,0,0,1116,41750,0,0,1736,100564,0,0,543,11985,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:7,5,0,0:12,0 0,24,211:8:0:0:5,3,0,0:8,0 0,33,255:11:0:0:5,6,0,0:11,0 17 378 . T <*> 0 . DP=30;DPR=30,0;I16=18,12,0,0,1098,41066,0,0,1707,99723,0,0,541,11927,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255:13:0:0:8,5,0,0:13,0 0,21,186:7:0:0:5,2,0,0:7,0 0,30,255:10:0:0:5,5,0,0:10,0 @@ -311,7 +311,7 @@ 17 381 . T <*> 0 . DP=29;DPR=29,0;I16=18,11,0,0,1167,47337,0,0,1678,98882,0,0,537,11729,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:8,4,0,0:12,0 0,21,211:7:0:0:5,2,0,0:7,0 0,30,255:10:0:0:5,5,0,0:10,0 17 382 . T <*> 0 . DP=29;DPR=29,0;I16=18,11,0,0,1062,40514,0,0,1678,98882,0,0,535,11693,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:8,4,0,0:12,0 0,21,182:7:0:0:5,2,0,0:7,0 0,30,255:10:0:0:5,5,0,0:10,0 17 383 . T <*> 0 . DP=29;DPR=29,0;I16=18,11,0,0,1059,39847,0,0,1678,98882,0,0,532,11638,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:8,4,0,0:12,0 0,21,172:7:0:0:5,2,0,0:7,0 0,30,255:10:0:0:5,5,0,0:10,0 -17 384 . A C,<*> 0 . DP=31;DPR=30,1,0;I16=19,11,0,1,1077,39885,4,16,1738,102482,60,3600,504,10988,25,625;QS=2.98419,0.0158103,0;SGB=-0.556633;RPBZ=0.615415;MQBZ=0.262613;MQSBZ=-0.333409;BQBZ=-1.68746;NMBZ=3.26825;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255,39,255,255:13:0:0:8,5,0,0:13,0,0 0,15,171,21,174,171:8:1:0:6,1,0,1:7,1,0 0,30,255,30,255,255:10:0:0:5,5,0,0:10,0,0 +17 384 . A C,<*> 0 . DP=31;DPR=30,1,0;I16=19,11,0,1,1077,39885,4,16,1738,102482,60,3600,504,10988,25,625;QS=2.98419,0.0158103,0;SGB=-0.556633;RPBZ=0.615229;MQBZ=0.262613;MQSBZ=-0.333409;BQBZ=-1.68746;NMBZ=3.26825;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255,39,255,255:13:0:0:8,5,0,0:13,0,0 0,15,171,21,174,171:8:1:0:6,1,0,1:7,1,0 0,30,255,30,255,255:10:0:0:5,5,0,0:10,0,0 17 385 . C <*> 0 . DP=31;DPR=31,0;I16=19,12,0,0,1118,41180,0,0,1798,106082,0,0,527,11569,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255:13:0:0:8,5,0,0:13,0 0,24,186:8:0:0:6,2,0,0:8,0 0,30,255:10:0:0:5,5,0,0:10,0 17 386 . T <*> 0 . DP=30;DPR=30,0;I16=18,12,0,0,1158,45592,0,0,1738,102482,0,0,526,11556,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255:13:0:0:8,5,0,0:13,0 0,21,191:7:0:0:5,2,0,0:7,0 0,30,255:10:0:0:5,5,0,0:10,0 17 387 . T <*> 0 . DP=30;DPR=30,0;I16=18,12,0,0,1105,41821,0,0,1738,102482,0,0,525,11573,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255:13:0:0:8,5,0,0:13,0 0,21,187:7:0:0:5,2,0,0:7,0 0,30,255:10:0:0:5,5,0,0:10,0 @@ -339,7 +339,7 @@ 17 409 . T <*> 0 . DP=29;DPR=29,0;I16=17,12,0,0,1100,42734,0,0,1678,98882,0,0,525,11503,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,42,255:14:0:0:8,6,0,0:14,0 0,12,131:4:0:0:2,2,0,0:4,0 0,33,255:11:0:0:7,4,0,0:11,0 17 410 . T <*> 0 . DP=29;DPR=29,0;I16=17,12,0,0,1035,38325,0,0,1678,98882,0,0,524,11432,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,42,255:14:0:0:8,6,0,0:14,0 0,12,125:4:0:0:2,2,0,0:4,0 0,33,255:11:0:0:7,4,0,0:11,0 17 411 . T <*> 0 . DP=29;DPR=29,0;I16=17,12,0,0,1022,37928,0,0,1678,98882,0,0,522,11342,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,42,255:14:0:0:8,6,0,0:14,0 0,12,111:4:0:0:2,2,0,0:4,0 0,33,255:11:0:0:7,4,0,0:11,0 -17 412 . C T,<*> 0 . DP=30;DPR=29,1,0;I16=17,12,1,0,1094,42458,14,196,1678,98882,60,3600,495,10659,25,625;QS=2.97455,0.0254545,0;SGB=-0.556633;RPBZ=-0.404685;MQBZ=0.267261;MQSBZ=-0.293785;BQBZ=-1.6942;NMBZ=-0.267102;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,255,42,255,255:15:1:0:8,6,1,0:14,1,0 0,12,124,12,124,124:4:0:0:2,2,0,0:4,0,0 0,33,255,33,255,255:11:0:0:7,4,0,0:11,0,0 +17 412 . C T,<*> 0 . DP=30;DPR=29,1,0;I16=17,12,1,0,1094,42458,14,196,1678,98882,60,3600,495,10659,25,625;QS=2.97455,0.0254545,0;SGB=-0.556633;RPBZ=-0.40473;MQBZ=0.267261;MQSBZ=-0.293785;BQBZ=-1.6942;NMBZ=-0.267102;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,255,42,255,255:15:1:0:8,6,1,0:14,1,0 0,12,124,12,124,124:4:0:0:2,2,0,0:4,0,0 0,33,255,33,255,255:11:0:0:7,4,0,0:11,0,0 17 413 . A <*> 0 . DP=31;DPR=31,0;I16=18,13,0,0,1189,45985,0,0,1798,106082,0,0,520,11258,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:9,8,0,0:17,0 0,9,102:3:0:0:2,1,0,0:3,0 0,33,255:11:0:0:7,4,0,0:11,0 17 414 . T <*> 0 . DP=30;DPR=30,0;I16=18,12,0,0,1151,44355,0,0,1738,102482,0,0,523,11265,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:9,7,0,0:16,0 0,9,109:3:0:0:2,1,0,0:3,0 0,33,255:11:0:0:7,4,0,0:11,0 17 415 . G <*> 0 . DP=30;DPR=30,0;I16=18,12,0,0,1131,43175,0,0,1738,102482,0,0,526,11306,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:9,7,0,0:16,0 0,9,110:3:0:0:2,1,0,0:3,0 0,33,255:11:0:0:7,4,0,0:11,0 @@ -364,7 +364,7 @@ 17 434 . T <*> 0 . DP=29;DPR=29,0;I16=15,14,0,0,1036,37654,0,0,1647,96123,0,0,561,12567,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:8,8,0,0:16,0 0,9,98:3:0:0:2,1,0,0:3,0 0,30,243:10:0:0:5,5,0,0:10,0 17 435 . A <*> 0 . DP=29;DPR=29,0;I16=15,14,0,0,1035,38091,0,0,1647,96123,0,0,562,12596,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:8,8,0,0:16,0 0,9,103:3:0:0:2,1,0,0:3,0 0,30,237:10:0:0:5,5,0,0:10,0 17 436 . T <*> 0 . DP=28;DPR=28,0;I16=14,14,0,0,998,36220,0,0,1587,92523,0,0,564,12654,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:8,8,0,0:16,0 0,9,110:3:0:0:2,1,0,0:3,0 0,27,223:9:0:0:4,5,0,0:9,0 -17 437 . T G,<*> 0 . DP=28;DPR=27,1,0;I16=13,14,1,0,990,36832,6,36,1558,91682,29,841,549,12435,16,256;QS=2.9781,0.0218978,0;SGB=-0.556633;RPBZ=-1.36195;MQBZ=-2.88675;MQSBZ=0.6;BQBZ=-1.67909;NMBZ=-0.19245;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255,48,255,255:16:0:0:8,8,0,0:16,0,0 0,9,109,9,109,109:3:0:0:2,1,0,0:3,0,0 0,17,200,24,203,201:9:1:0:3,5,1,0:8,1,0 +17 437 . T G,<*> 0 . DP=28;DPR=27,1,0;I16=13,14,1,0,990,36832,6,36,1558,91682,29,841,549,12435,16,256;QS=2.9781,0.0218978,0;SGB=-0.556633;RPBZ=-1.36214;MQBZ=-2.88675;MQSBZ=0.6;BQBZ=-1.67909;NMBZ=-0.19245;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255,48,255,255:16:0:0:8,8,0,0:16,0,0 0,9,109,9,109,109:3:0:0:2,1,0,0:3,0,0 0,17,200,24,203,201:9:1:0:3,5,1,0:8,1,0 17 438 . A <*> 0 . DP=28;DPR=28,0;I16=14,14,0,0,984,35784,0,0,1587,92523,0,0,565,12707,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:8,8,0,0:16,0 0,9,107:3:0:0:2,1,0,0:3,0 0,27,220:9:0:0:4,5,0,0:9,0 17 439 . C <*> 0 . DP=28;DPR=28,0;I16=14,14,0,0,1055,40273,0,0,1587,92523,0,0,563,12649,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:8,8,0,0:16,0 0,9,107:3:0:0:2,1,0,0:3,0 0,27,224:9:0:0:4,5,0,0:9,0 17 440 . A <*> 0 . DP=28;DPR=28,0;I16=14,14,0,0,1095,43251,0,0,1587,92523,0,0,561,12615,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:8,8,0,0:16,0 0,9,115:3:0:0:2,1,0,0:3,0 0,27,247:9:0:0:4,5,0,0:9,0 @@ -392,7 +392,7 @@ 17 462 . G <*> 0 . DP=32;DPR=31,0;I16=18,13,0,0,1169,46001,0,0,1775,103851,0,0,577,12669,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:10,7,0,0:17,0 0,12,131:4:0:0:3,1,0,0:4,0 0,30,241:10:0:0:5,5,0,0:10,0 17 463 . G <*> 0 . DP=32;DPR=31,0;I16=18,13,0,0,1095,41573,0,0,1775,103851,0,0,583,12729,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:10,7,0,0:17,0 0,12,126:4:0:0:3,1,0,0:4,0 0,30,221:10:0:0:5,5,0,0:10,0 17 464 . A <*> 0 . DP=32;DPR=31,0;I16=18,13,0,0,1100,41724,0,0,1775,103851,0,0,589,12821,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:10,7,0,0:17,0 0,12,148:4:0:0:3,1,0,0:4,0 0,30,217:10:0:0:5,5,0,0:10,0 -17 465 . C T,<*> 0 . DP=33;DPR=31,1,0;I16=19,12,0,1,1173,45601,4,16,1775,103851,60,3600,589,12909,6,36;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.67936;MQBZ=0.321288;MQSBZ=0.341466;BQBZ=-1.68493;NMBZ=3.21288;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255,51,255,255:17:0:0:10,7,0,0:17,0,0 0,15,158,15,158,158:5:0:0:4,1,0,0:5,0,0 0,20,224,27,227,224:10:1:0:5,4,0,1:9,1,0 +17 465 . C T,<*> 0 . DP=33;DPR=31,1,0;I16=19,12,0,1,1173,45601,4,16,1775,103851,60,3600,589,12909,6,36;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.67982;MQBZ=0.321288;MQSBZ=0.341466;BQBZ=-1.68493;NMBZ=3.21288;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255,51,255,255:17:0:0:10,7,0,0:17,0,0 0,15,158,15,158,158:5:0:0:4,1,0,0:5,0,0 0,20,224,27,227,224:10:1:0:5,4,0,1:9,1,0 17 466 . A <*> 0 . DP=34;DPR=33,0;I16=20,13,0,0,1268,49686,0,0,1895,111051,0,0,602,13102,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:11,7,0,0:18,0 0,15,173:5:0:0:4,1,0,0:5,0 0,30,255:10:0:0:5,5,0,0:10,0 17 467 . A <*> 0 . DP=34;DPR=33,0;I16=20,13,0,0,1246,48610,0,0,1895,111051,0,0,608,13194,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:11,7,0,0:18,0 0,15,177:5:0:0:4,1,0,0:5,0 0,30,251:10:0:0:5,5,0,0:10,0 17 468 . A <*> 0 . DP=35;DPR=34,0;I16=21,13,0,0,1253,48095,0,0,1955,114651,0,0,613,13273,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:12,7,0,0:19,0 0,15,174:5:0:0:4,1,0,0:5,0 0,30,251:10:0:0:5,5,0,0:10,0 @@ -415,7 +415,7 @@ 17 485 . G <*> 0 . DP=35;DPR=35,0;I16=23,12,0,0,1329,51411,0,0,2015,118251,0,0,669,14931,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:12,6,0,0:18,0 0,18,160:6:0:0:5,1,0,0:6,0 0,33,255:11:0:0:6,5,0,0:11,0 17 486 . A <*> 0 . DP=34;DPR=34,0;I16=22,12,0,0,1313,51667,0,0,1955,114651,0,0,671,14989,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:11,6,0,0:17,0 0,18,173:6:0:0:5,1,0,0:6,0 0,33,255:11:0:0:6,5,0,0:11,0 17 487 . G <*> 0 . DP=34;DPR=34,0;I16=22,12,0,0,1300,50304,0,0,1955,114651,0,0,672,15030,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:11,6,0,0:17,0 0,18,169:6:0:0:5,1,0,0:6,0 0,33,255:11:0:0:6,5,0,0:11,0 -17 488 . A G,<*> 0 . DP=35;DPR=34,1,0;I16=22,12,1,0,1278,48412,4,16,1986,117410,29,841,646,14380,25,625;QS=2.98947,0.0105263,0;SGB=-0.556633;RPBZ=0.544734;MQBZ=-3.36505;MQSBZ=0.10737;BQBZ=-1.69552;NMBZ=-0.171499;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255,54,255,255:18:0:0:12,6,0,0:18,0,0 0,18,177,18,177,177:6:0:0:5,1,0,0:6,0,0 0,23,255,30,255,255:11:1:0:5,5,1,0:10,1,0 +17 488 . A G,<*> 0 . DP=35;DPR=34,1,0;I16=22,12,1,0,1278,48412,4,16,1986,117410,29,841,646,14380,25,625;QS=2.98947,0.0105263,0;SGB=-0.556633;RPBZ=0.594463;MQBZ=-3.36505;MQSBZ=0.10737;BQBZ=-1.69552;NMBZ=-0.171499;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255,54,255,255:18:0:0:12,6,0,0:18,0,0 0,18,177,18,177,177:6:0:0:5,1,0,0:6,0,0 0,23,255,30,255,255:11:1:0:5,5,1,0:10,1,0 17 489 . A <*> 0 . DP=35;DPR=35,0;I16=23,12,0,0,1264,46916,0,0,2015,118251,0,0,671,15015,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:12,6,0,0:18,0 0,18,175:6:0:0:5,1,0,0:6,0 0,33,255:11:0:0:6,5,0,0:11,0 17 490 . A <*> 0 . DP=36;DPR=36,0;I16=24,12,0,0,1332,50280,0,0,2075,121851,0,0,671,15061,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:12,6,0,0:18,0 0,21,188:7:0:0:6,1,0,0:7,0 0,33,255:11:0:0:6,5,0,0:11,0 17 491 . T <*> 0 . DP=36;DPR=36,0;I16=24,12,0,0,1284,46802,0,0,2075,121851,0,0,671,15093,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:12,6,0,0:18,0 0,21,178:7:0:0:6,1,0,0:7,0 0,33,255:11:0:0:6,5,0,0:11,0 @@ -439,9 +439,9 @@ 17 509 . C <*> 0 . DP=34;DPR=34,0;I16=24,10,0,0,1272,48272,0,0,1986,117410,0,0,640,14430,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:13,5,0,0:18,0 0,21,186:7:0:0:6,1,0,0:7,0 0,27,241:9:0:0:5,4,0,0:9,0 17 510 . A <*> 0 . DP=34;DPR=34,0;I16=23,11,0,0,1211,44827,0,0,1986,117410,0,0,638,14398,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:13,6,0,0:19,0 0,21,187:7:0:0:6,1,0,0:7,0 0,24,221:8:0:0:4,4,0,0:8,0 17 511 . A <*> 0 . DP=34;DPR=34,0;I16=23,11,0,0,1238,46516,0,0,1986,117410,0,0,637,14395,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:13,6,0,0:19,0 0,21,195:7:0:0:6,1,0,0:7,0 0,24,233:8:0:0:4,4,0,0:8,0 -17 512 . A C,<*> 0 . DP=33;DPR=32,1,0;I16=22,10,0,1,1133,41513,13,169,1866,110210,60,3600,628,14340,9,81;QS=2.97766,0.0223368,0;SGB=-0.556633;RPBZ=-1.47091;MQBZ=0.253876;MQSBZ=-0.461593;BQBZ=-1.68442;NMBZ=2.68627;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255,51,255,255:18:1:0:12,5,0,1:17,1,0 0,21,183,21,183,183:7:0:0:6,1,0,0:7,0,0 0,24,231,24,231,231:8:0:0:4,4,0,0:8,0,0 -17 513 . A T,<*> 0 . DP=32;DPR=31,1,0;I16=21,10,1,0,1125,42283,12,144,1806,106610,60,3600,623,14249,15,225;QS=2.97966,0.020339,0;SGB=-0.556633;RPBZ=-1.24598;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.57376;NMBZ=2.63913;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,37,255,48,255,255:17:1:0:11,5,1,0:16,1,0 0,21,177,21,177,177:7:0:0:6,1,0,0:7,0,0 0,24,233,24,233,233:8:0:0:4,4,0,0:8,0,0 -17 514 . A T,<*> 0 . DP=32;DPR=31,1,0;I16=22,9,0,1,1086,40204,16,256,1806,106610,60,3600,627,14381,11,121;QS=2.97127,0.0287253,0;SGB=-0.556633;RPBZ=-1.46267;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.46657;NMBZ=2.63913;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,34,255,48,255,255:17:1:0:12,4,0,1:16,1,0 0,21,172,21,172,172:7:0:0:6,1,0,0:7,0,0 0,24,235,24,235,235:8:0:0:4,4,0,0:8,0,0 +17 512 . A C,<*> 0 . DP=33;DPR=32,1,0;I16=22,10,0,1,1133,41513,13,169,1866,110210,60,3600,628,14340,9,81;QS=2.97766,0.0223368,0;SGB=-0.556633;RPBZ=-1.47079;MQBZ=0.253876;MQSBZ=-0.461593;BQBZ=-1.68442;NMBZ=2.68627;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255,51,255,255:18:1:0:12,5,0,1:17,1,0 0,21,183,21,183,183:7:0:0:6,1,0,0:7,0,0 0,24,231,24,231,231:8:0:0:4,4,0,0:8,0,0 +17 513 . A T,<*> 0 . DP=32;DPR=31,1,0;I16=21,10,1,0,1125,42283,12,144,1806,106610,60,3600,623,14249,15,225;QS=2.97966,0.020339,0;SGB=-0.556633;RPBZ=-1.24609;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.57376;NMBZ=2.63913;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,37,255,48,255,255:17:1:0:11,5,1,0:16,1,0 0,21,177,21,177,177:7:0:0:6,1,0,0:7,0,0 0,24,233,24,233,233:8:0:0:4,4,0,0:8,0,0 +17 514 . A T,<*> 0 . DP=32;DPR=31,1,0;I16=22,9,0,1,1086,40204,16,256,1806,106610,60,3600,627,14381,11,121;QS=2.97127,0.0287253,0;SGB=-0.556633;RPBZ=-1.4628;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.46657;NMBZ=2.63913;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,34,255,48,255,255:17:1:0:12,4,0,1:16,1,0 0,21,172,21,172,172:7:0:0:6,1,0,0:7,0,0 0,24,235,24,235,235:8:0:0:4,4,0,0:8,0,0 17 515 . C <*> 0 . DP=32;DPR=32,0;I16=22,10,0,0,1050,37704,0,0,1866,110210,0,0,638,14554,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:12,5,0,0:17,0 0,21,169:7:0:0:6,1,0,0:7,0 0,24,211:8:0:0:4,4,0,0:8,0 17 516 . C <*> 0 . DP=32;DPR=32,0;I16=22,10,0,0,1109,40651,0,0,1866,110210,0,0,637,14579,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:12,5,0,0:17,0 0,21,187:7:0:0:6,1,0,0:7,0 0,24,215:8:0:0:4,4,0,0:8,0 17 517 . T <*> 0 . DP=33;DPR=33,0;I16=23,10,0,0,1269,49995,0,0,1926,113810,0,0,636,14626,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:13,5,0,0:18,0 0,21,201:7:0:0:6,1,0,0:7,0 0,24,242:8:0:0:4,4,0,0:8,0 @@ -450,7 +450,7 @@ 17 520 . T <*> 0 . DP=36;DPR=36,0;I16=25,11,0,0,1243,45051,0,0,2106,124610,0,0,638,14818,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,63,255:21:0:0:15,6,0,0:21,0 0,21,180:7:0:0:6,1,0,0:7,0 0,24,223:8:0:0:4,4,0,0:8,0 17 521 . C <*> 0 . DP=34;DPR=34,0;I16=25,9,0,0,1281,49527,0,0,1986,117410,0,0,641,14875,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,60,255:20:0:0:15,5,0,0:20,0 0,21,191:7:0:0:6,1,0,0:7,0 0,21,204:7:0:0:4,3,0,0:7,0 17 522 . A <*> 0 . DP=32;DPR=32,0;I16=24,8,0,0,1158,43228,0,0,1897,112969,0,0,646,14960,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,60,255:20:0:0:15,5,0,0:20,0 0,21,185:7:0:0:6,1,0,0:7,0 0,15,170:5:0:0:3,2,0,0:5,0 -17 523 . T G,<*> 0 . DP=32;DPR=31,1,0;I16=23,8,1,0,1184,45708,15,225,1837,109369,60,3600,626,14446,25,625;QS=2.9794,0.0206044,0;SGB=-0.556633;RPBZ=1.13753;MQBZ=0.179605;MQSBZ=-1.73205;BQBZ=-1.68805;NMBZ=2.89159;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,44,255,57,255,255:20:1:0:14,5,1,0:19,1,0 0,21,191,21,191,191:7:0:0:6,1,0,0:7,0,0 0,15,166,15,166,166:5:0:0:3,2,0,0:5,0,0 +17 523 . T G,<*> 0 . DP=32;DPR=31,1,0;I16=23,8,1,0,1184,45708,15,225,1837,109369,60,3600,626,14446,25,625;QS=2.9794,0.0206044,0;SGB=-0.556633;RPBZ=1.13742;MQBZ=0.179605;MQSBZ=-1.73205;BQBZ=-1.68805;NMBZ=2.89159;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,44,255,57,255,255:20:1:0:14,5,1,0:19,1,0 0,21,191,21,191,191:7:0:0:6,1,0,0:7,0,0 0,15,166,15,166,166:5:0:0:3,2,0,0:5,0,0 17 524 . T <*> 0 . DP=32;DPR=32,0;I16=24,8,0,0,1096,39618,0,0,1897,112969,0,0,654,15108,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,60,255:20:0:0:15,5,0,0:20,0 0,21,194:7:0:0:6,1,0,0:7,0 0,15,150:5:0:0:3,2,0,0:5,0 17 525 . G <*> 0 . DP=32;DPR=32,0;I16=24,8,0,0,1188,45718,0,0,1897,112969,0,0,656,15120,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,60,255:20:0:0:15,5,0,0:20,0 0,21,188:7:0:0:6,1,0,0:7,0 0,15,133:5:0:0:3,2,0,0:5,0 17 526 . C <*> 0 . DP=32;DPR=32,0;I16=24,8,0,0,1154,44014,0,0,1897,112969,0,0,658,15156,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,60,255:20:0:0:15,5,0,0:20,0 0,21,185:7:0:0:6,1,0,0:7,0 0,15,137:5:0:0:3,2,0,0:5,0 @@ -462,7 +462,7 @@ 17 532 . T <*> 0 . DP=32;DPR=32,0;I16=25,7,0,0,1161,43607,0,0,1897,112969,0,0,649,14477,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:15,4,0,0:19,0 0,21,181:7:0:0:6,1,0,0:7,0 0,18,192:6:0:0:4,2,0,0:6,0 17 533 . C <*> 0 . DP=32;DPR=32,0;I16=25,7,0,0,1154,44084,0,0,1897,112969,0,0,644,14274,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:15,4,0,0:19,0 0,21,178:7:0:0:6,1,0,0:7,0 0,18,180:6:0:0:4,2,0,0:6,0 17 534 . T <*> 0 . DP=31;DPR=31,0;I16=24,7,0,0,1222,49526,0,0,1837,109369,0,0,640,14104,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:14,4,0,0:18,0 0,21,205:7:0:0:6,1,0,0:7,0 0,18,205:6:0:0:4,2,0,0:6,0 -17 535 . A G,<*> 0 . DP=31;DPR=30,1,0;I16=24,6,0,1,1080,39870,8,64,1777,105769,60,3600,611,13341,25,625;QS=2.98623,0.0137694,0;SGB=-0.556633;RPBZ=-0.894608;MQBZ=0.182574;MQSBZ=-1.85164;BQBZ=-1.6854;NMBZ=2.94255;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,41,255,51,255,255:18:1:0:14,3,0,1:17,1,0 0,21,194,21,194,194:7:0:0:6,1,0,0:7,0,0 0,18,189,18,189,189:6:0:0:4,2,0,0:6,0,0 +17 535 . A G,<*> 0 . DP=31;DPR=30,1,0;I16=24,6,0,1,1080,39870,8,64,1777,105769,60,3600,611,13341,25,625;QS=2.98623,0.0137694,0;SGB=-0.556633;RPBZ=-0.894788;MQBZ=0.182574;MQSBZ=-1.85164;BQBZ=-1.6854;NMBZ=2.94255;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,41,255,51,255,255:18:1:0:14,3,0,1:17,1,0 0,21,194,21,194,194:7:0:0:6,1,0,0:7,0,0 0,18,189,18,189,189:6:0:0:4,2,0,0:6,0,0 17 536 . C <*> 0 . DP=31;DPR=31,0;I16=24,7,0,0,1095,40551,0,0,1837,109369,0,0,631,13809,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:14,4,0,0:18,0 0,21,184:7:0:0:6,1,0,0:7,0 0,18,157:6:0:0:4,2,0,0:6,0 17 537 . C <*> 0 . DP=31;DPR=31,0;I16=24,7,0,0,1049,38677,0,0,1837,109369,0,0,626,13682,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:14,4,0,0:18,0 0,21,172:7:0:0:6,1,0,0:7,0 0,18,183:6:0:0:4,2,0,0:6,0 17 538 . A <*> 0 . DP=31;DPR=31,0;I16=24,7,0,0,1138,42478,0,0,1837,109369,0,0,620,13536,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:14,4,0,0:18,0 0,21,189:7:0:0:6,1,0,0:7,0 0,18,181:6:0:0:4,2,0,0:6,0 @@ -509,7 +509,7 @@ 17 579 . G <*> 0 . DP=30;DPR=30,0;I16=16,14,0,0,1038,38820,0,0,1769,105241,0,0,523,11335,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:8,9,0,0:17,0 0,24,224:8:0:0:4,4,0,0:8,0 0,15,144:5:0:0:4,1,0,0:5,0 17 580 . A C,<*> 0 . DP=30;DPR=29,1,0;I16=15,14,1,0,1060,39178,16,256,1709,101641,60,3600,510,11078,17,289;QS=2.97338,0.0266223,0;SGB=-0.556633;RPBZ=1.32953;MQBZ=0.185695;MQSBZ=-1.06904;BQBZ=-1.69093;NMBZ=1.86885;SCBZ=-0.267102;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,34,255,48,255,255:17:1:0:7,9,1,0:16,1,0 0,24,221,24,221,221:8:0:0:4,4,0,0:8,0,0 0,15,155,15,155,155:5:0:0:4,1,0,0:5,0,0 17 581 . A <*> 0 . DP=31;DPR=31,0;I16=16,15,0,0,1083,39215,0,0,1829,108841,0,0,530,11384,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:8,10,0,0:18,0 0,24,223:8:0:0:4,4,0,0:8,0 0,15,153:5:0:0:4,1,0,0:5,0 -17 582 . C G,<*> 0 . DP=31;DPR=30,1,0;I16=15,15,1,0,1080,39870,8,64,1769,105241,60,3600,519,11211,15,225;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.34245;MQBZ=0.182574;MQSBZ=-1.0328;BQBZ=-1.68266;NMBZ=1.92049;SCBZ=-0.262467;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,41,255,51,255,255:18:1:0:7,10,1,0:17,1,0 0,24,207,24,207,207:8:0:0:4,4,0,0:8,0,0 0,15,151,15,151,151:5:0:0:4,1,0,0:5,0,0 +17 582 . C G,<*> 0 . DP=31;DPR=30,1,0;I16=15,15,1,0,1080,39870,8,64,1769,105241,60,3600,519,11211,15,225;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.34259;MQBZ=0.182574;MQSBZ=-1.0328;BQBZ=-1.68266;NMBZ=1.92049;SCBZ=-0.262467;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,41,255,51,255,255:18:1:0:7,10,1,0:17,1,0 0,24,207,24,207,207:8:0:0:4,4,0,0:8,0,0 0,15,151,15,151,151:5:0:0:4,1,0,0:5,0,0 17 583 . T <*> 0 . DP=30;DPR=30,0;I16=16,14,0,0,1135,43913,0,0,1769,105241,0,0,539,11523,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:8,9,0,0:17,0 0,24,238:8:0:0:4,4,0,0:8,0 0,15,163:5:0:0:4,1,0,0:5,0 17 584 . C <*> 0 . DP=31;DPR=31,0;I16=17,14,0,0,1069,39521,0,0,1798,106082,0,0,544,11644,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:9,9,0,0:18,0 0,24,209:8:0:0:4,4,0,0:8,0 0,15,157:5:0:0:4,1,0,0:5,0 17 585 . A <*> 0 . DP=31;DPR=31,0;I16=17,14,0,0,1096,39866,0,0,1798,106082,0,0,549,11751,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:9,9,0,0:18,0 0,24,211:8:0:0:4,4,0,0:8,0 0,15,157:5:0:0:4,1,0,0:5,0 @@ -520,10 +520,10 @@ 17 590 . C <*> 0 . DP=32;DPR=32,0;I16=17,15,0,0,1103,41355,0,0,1858,109682,0,0,574,12576,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:9,9,0,0:18,0 0,24,194:8:0:0:4,4,0,0:8,0 0,18,175:6:0:0:4,2,0,0:6,0 17 591 . A <*> 0 . DP=31;DPR=31,0;I16=16,15,0,0,1164,44088,0,0,1798,106082,0,0,579,12695,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:9,9,0,0:18,0 0,21,209:7:0:0:3,4,0,0:7,0 0,18,188:6:0:0:4,2,0,0:6,0 17 592 . A <*> 0 . DP=31;DPR=31,0;I16=16,15,0,0,1121,42193,0,0,1798,106082,0,0,583,12795,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:9,9,0,0:18,0 0,21,215:7:0:0:3,4,0,0:7,0 0,18,182:6:0:0:4,2,0,0:6,0 -17 593 . C A,<*> 0 . DP=31;DPR=30,1,0;I16=16,14,0,1,1071,39925,7,49,1769,105241,29,841,561,12253,25,625;QS=2.97021,0.0297872,0;SGB=-0.556633;RPBZ=0.559412;MQBZ=-3.80789;MQSBZ=-0.0464238;BQBZ=-1.57464;NMBZ=2.13779;SCBZ=3.67454;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255,54,255,255:18:0:0:9,9,0,0:18,0,0 0,12,184,18,187,185:7:1:0:3,3,0,1:6,1,0 0,18,174,18,174,174:6:0:0:4,2,0,0:6,0,0 +17 593 . C A,<*> 0 . DP=31;DPR=30,1,0;I16=16,14,0,1,1071,39925,7,49,1769,105241,29,841,561,12253,25,625;QS=2.97021,0.0297872,0;SGB=-0.556633;RPBZ=0.559355;MQBZ=-3.80789;MQSBZ=-0.0464238;BQBZ=-1.57464;NMBZ=2.13779;SCBZ=3.67454;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255,54,255,255:18:0:0:9,9,0,0:18,0,0 0,12,184,18,187,185:7:1:0:3,3,0,1:6,1,0 0,18,174,18,174,174:6:0:0:4,2,0,0:6,0,0 17 594 . A G,<*> 0 . DP=33;DPR=32,1,0;I16=16,16,1,0,1161,42757,4,16,1858,109682,60,3600,572,12672,15,225;QS=2.99359,0.00641026,0;SGB=-0.556633;RPBZ=-0.998367;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68954;NMBZ=1.76408;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,42,255,51,255,255:18:1:0:8,9,1,0:17,1,0 0,21,205,21,205,205:7:0:0:3,4,0,0:7,0,0 0,24,213,24,213,213:8:0:0:5,3,0,0:8,0,0 17 595 . A <*> 0 . DP=33;DPR=33,0;I16=17,16,0,0,1136,40412,0,0,1918,113282,0,0,589,12905,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:9,9,0,0:18,0 0,21,198:7:0:0:3,4,0,0:7,0 0,24,218:8:0:0:5,3,0,0:8,0 -17 596 . A G,<*> 0 . DP=33;DPR=32,1,0;I16=16,16,1,0,1061,37187,8,64,1858,109682,60,3600,590,12952,1,1;QS=2.98564,0.0143627,0;SGB=-0.556633;RPBZ=1.68132;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68357;NMBZ=1.61602;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,41,255,51,255,255:18:1:0:8,9,1,0:17,1,0 0,21,169,21,169,169:7:0:0:3,4,0,0:7,0,0 0,24,231,24,231,231:8:0:0:5,3,0,0:8,0,0 +17 596 . A G,<*> 0 . DP=33;DPR=32,1,0;I16=16,16,1,0,1061,37187,8,64,1858,109682,60,3600,590,12952,1,1;QS=2.98564,0.0143627,0;SGB=-0.556633;RPBZ=1.68146;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68357;NMBZ=1.61602;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,41,255,51,255,255:18:1:0:8,9,1,0:17,1,0 0,21,169,21,169,169:7:0:0:3,4,0,0:7,0,0 0,24,231,24,231,231:8:0:0:5,3,0,0:8,0,0 17 597 . C <*> 0 . DP=33;DPR=33,0;I16=17,16,0,0,1196,44890,0,0,1918,113282,0,0,592,12990,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:9,9,0,0:18,0 0,21,204:7:0:0:3,4,0,0:7,0 0,24,220:8:0:0:5,3,0,0:8,0 17 598 . T <*> 0 . DP=33;DPR=33,0;I16=16,17,0,0,1219,47333,0,0,1918,113282,0,0,597,13029,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:8,9,0,0:17,0 0,21,217:7:0:0:3,4,0,0:7,0 0,27,242:9:0:0:5,4,0,0:9,0 17 599 . T <*> 0 . DP=33;DPR=33,0;I16=16,17,0,0,1182,43598,0,0,1918,113282,0,0,599,13095,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:8,9,0,0:17,0 0,21,197:7:0:0:3,4,0,0:7,0 0,27,247:9:0:0:5,4,0,0:9,0 diff --git a/test/mpileup/mpileup.5.out b/test/mpileup/mpileup.5.out index b25f199e5..a3cc62224 100644 --- a/test/mpileup/mpileup.5.out +++ b/test/mpileup/mpileup.5.out @@ -32,7 +32,7 @@ 17 101 . C <*> 0 . DP=18;ADF=16,0;ADR=1,0;AD=17,0;I16=16,1,0,0,630,24730,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,182:9:0:9,0:0,0:9,0 0,9,108:3:0:2,0:1,0:3,0 0,15,132:5:0:5,0:0,0:5,0 17 102 . C <*> 0 . DP=18;ADF=16,0;ADR=1,0;AD=17,0;I16=16,1,0,0,676,27812,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,188:9:0:9,0:0,0:9,0 0,9,121:3:0:2,0:1,0:3,0 0,15,139:5:0:5,0:0,0:5,0 17 103 . T C,<*> 0 . DP=18;ADF=15,1,0;ADR=1,0,0;AD=16,1,0;I16=15,1,1,0,668,28542,6,36,929,54841,29,841,323,7035,6,36;QS=2.98256,0.0174419,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64924;NMBZ=2.45514;SCBZ=4;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,17,184,24,187,185:9:0:8,1,0:0,0,0:8,1,0 0,9,118,9,118,118:3:0:2,0,0:1,0,0:3,0,0 0,15,147,15,147,147:5:0:5,0,0:0,0,0:5,0,0 -17 104 . G C,<*> 0 . DP=18;ADF=15,1,0;ADR=1,0,0;AD=16,1,0;I16=15,1,1,0,601,24163,3,9,929,54841,29,841,320,6884,7,49;QS=2.98726,0.0127389,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64309;NMBZ=2.45514;SCBZ=2.91548;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,173,24,176,173:9:0:8,1,0:0,0,0:8,1,0 0,9,101,9,101,101:3:0:2,0,0:1,0,0:3,0,0 0,15,133,15,133,133:5:0:5,0,0:0,0,0:5,0,0 +17 104 . G C,<*> 0 . DP=18;ADF=15,1,0;ADR=1,0,0;AD=16,1,0;I16=15,1,1,0,601,24163,3,9,929,54841,29,841,320,6884,7,49;QS=2.98726,0.0127389,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64309;NMBZ=2.45514;SCBZ=4;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,173,24,176,173:9:0:8,1,0:0,0,0:8,1,0 0,9,101,9,101,101:3:0:2,0,0:1,0,0:3,0,0 0,15,133,15,133,133:5:0:5,0,0:0,0,0:5,0,0 17 105 . G <*> 0 . DP=19;ADF=17,0;ADR=1,0;AD=18,0;I16=17,1,0,0,603,22351,0,0,1018,59282,0,0,325,6815,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,171:10:0:10,0:0,0:10,0 0,9,106:3:0:2,0:1,0:3,0 0,15,125:5:0:5,0:0,0:5,0 17 106 . G <*> 0 . DP=19;ADF=17,0;ADR=1,0;AD=18,0;I16=17,1,0,0,636,25058,0,0,1018,59282,0,0,324,6718,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,190:10:0:10,0:0,0:10,0 0,9,92:3:0:2,0:1,0:3,0 0,15,124:5:0:5,0:0,0:5,0 17 107 . C <*> 0 . DP=19;ADF=17,0;ADR=1,0;AD=18,0;I16=17,1,0,0,686,27952,0,0,1018,59282,0,0,323,6643,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,192:10:0:10,0:0,0:10,0 0,9,119:3:0:2,0:1,0:3,0 0,15,136:5:0:5,0:0,0:5,0 @@ -87,7 +87,7 @@ 17 156 . C <*> 0 . DP=14;ADF=12,0;ADR=2,0;AD=14,0;I16=12,2,0,0,536,20884,0,0,809,47641,0,0,266,5934,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,163:7:0:7,0:0,0:7,0 0,6,84:2:0:1,0:1,0:2,0 0,15,150:5:0:4,0:1,0:5,0 17 157 . C <*> 0 . DP=14;ADF=12,0;ADR=2,0;AD=14,0;I16=12,2,0,0,555,22081,0,0,809,47641,0,0,264,5904,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,169:7:0:7,0:0,0:7,0 0,6,85:2:0:1,0:1,0:2,0 0,15,149:5:0:4,0:1,0:5,0 17 158 . T <*> 0 . DP=14;ADF=12,0;ADR=2,0;AD=14,0;I16=12,2,0,0,568,23154,0,0,809,47641,0,0,262,5886,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,170:7:0:7,0:0,0:7,0 0,6,84:2:0:1,0:1,0:2,0 0,15,159:5:0:4,0:1,0:5,0 -17 159 . A G,<*> 0 . DP=15;ADF=12,1,0;ADR=2,0,0;AD=14,1,0;I16=12,2,1,0,519,19467,5,25,809,47641,60,3600,260,5880,0,0;QS=2.97076,0.0292398,0;SGB=-0.556633;RPBZ=-1.62163;MQBZ=0.267261;MQSBZ=-2.54951;BQBZ=-1.63041;NMBZ=0;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,157,21,157,157:7:0:7,0,0:0,0,0:7,0,0 0,6,83,6,83,83:2:0:1,0,0:1,0,0:2,0,0 0,10,129,15,132,129:6:0:4,1,0:1,0,0:5,1,0 +17 159 . A G,<*> 0 . DP=15;ADF=12,1,0;ADR=2,0,0;AD=14,1,0;I16=12,2,1,0,519,19467,5,25,809,47641,60,3600,260,5880,0,0;QS=2.97076,0.0292398,0;SGB=-0.556633;RPBZ=-1.62019;MQBZ=0.267261;MQSBZ=-2.54951;BQBZ=-1.63041;NMBZ=0;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,157,21,157,157:7:0:7,0,0:0,0,0:7,0,0 0,6,83,6,83,83:2:0:1,0,0:1,0,0:2,0,0 0,10,129,15,132,129:6:0:4,1,0:1,0,0:5,1,0 17 160 . G <*> 0 . DP=15;ADF=13,0;ADR=2,0;AD=15,0;I16=13,2,0,0,547,20633,0,0,869,51241,0,0,259,5887,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,165:7:0:7,0:0,0:7,0 0,6,85:2:0:1,0:1,0:2,0 0,18,139:6:0:5,0:1,0:6,0 17 161 . A <*> 0 . DP=15;ADF=13,0;ADR=2,0;AD=15,0;I16=13,2,0,0,568,21610,0,0,869,51241,0,0,258,5908,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,157:7:0:7,0:0,0:7,0 0,6,83:2:0:1,0:1,0:2,0 0,18,162:6:0:5,0:1,0:6,0 17 162 . A <*> 0 . DP=15;ADF=13,0;ADR=2,0;AD=15,0;I16=13,2,0,0,558,21206,0,0,869,51241,0,0,255,5843,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,147:7:0:7,0:0,0:7,0 0,6,87:2:0:1,0:1,0:2,0 0,18,167:6:0:5,0:1,0:6,0 @@ -151,10 +151,10 @@ 17 220 . G <*> 0 . DP=14;ADF=11,0;ADR=3,0;AD=14,0;I16=11,3,0,0,495,18407,0,0,747,42123,0,0,267,6079,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,188:7:0:6,0:1,0:7,0 0,9,88:3:0:1,0:2,0:3,0 0,12,84:4:0:4,0:0,0:4,0 17 221 . A <*> 0 . DP=14;ADF=11,0;ADR=3,0;AD=14,0;I16=11,3,0,0,488,17688,0,0,747,42123,0,0,267,6135,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,176:7:0:6,0:1,0:7,0 0,9,89:3:0:1,0:2,0:3,0 0,12,101:4:0:4,0:0,0:4,0 17 222 . A <*> 0 . DP=14;ADF=11,0;ADR=3,0;AD=14,0;I16=11,3,0,0,479,17747,0,0,747,42123,0,0,267,6203,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,186:7:0:6,0:1,0:7,0 0,9,89:3:0:1,0:2,0:3,0 0,12,73:4:0:4,0:0,0:4,0 -17 223 . G T,<*> 0 . DP=13;ADF=9,1,0;ADR=3,0,0;AD=12,1,0;I16=9,3,1,0,412,14782,8,64,627,34923,60,3600,243,5657,25,625;QS=2.96596,0.0340426,0;SGB=-0.556633;RPBZ=1.06904;MQBZ=0.547723;MQSBZ=-3.4641;BQBZ=-1.60577;NMBZ=-0.288675;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,11,166,18,169,167:7:0:5,1,0:1,0,0:6,1,0 0,6,53,6,53,53:2:0:0,0,0:2,0,0:2,0,0 0,12,81,12,81,81:4:0:4,0,0:0,0,0:4,0,0 +17 223 . G T,<*> 0 . DP=13;ADF=9,1,0;ADR=3,0,0;AD=12,1,0;I16=9,3,1,0,412,14782,8,64,627,34923,60,3600,243,5657,25,625;QS=2.96596,0.0340426,0;SGB=-0.556633;RPBZ=1.07052;MQBZ=0.547723;MQSBZ=-3.4641;BQBZ=-1.60577;NMBZ=-0.288675;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,11,166,18,169,167:7:0:5,1,0:1,0,0:6,1,0 0,6,53,6,53,53:2:0:0,0,0:2,0,0:2,0,0 0,12,81,12,81,81:4:0:4,0,0:0,0,0:4,0,0 17 224 . G <*> 0 . DP=12;ADF=9,0;ADR=3,0;AD=12,0;I16=9,3,0,0,379,12759,0,0,627,34923,0,0,270,6370,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,168:6:0:5,0:1,0:6,0 0,6,50:2:0:0,0:2,0:2,0 0,12,70:4:0:4,0:0,0:4,0 17 225 . C <*> 0 . DP=12;ADF=9,0;ADR=3,0;AD=12,0;I16=9,3,0,0,390,13960,0,0,627,34923,0,0,272,6466,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,165:6:0:5,0:1,0:6,0 0,6,48:2:0:0,0:2,0:2,0 0,12,86:4:0:4,0:0,0:4,0 -17 226 . A G,C,<*> 0 . DP=13;ADF=8,1,0,0;ADR=3,0,1,0;AD=11,1,1,0;I16=8,3,1,1,381,13669,6,18,567,31323,89,4441,248,5894,44,986;QS=2.94293,0.0392157,0.0178571,0;VDB=0.84;SGB=-2.62246;RPBZ=-0.592972;MQBZ=-0.615457;MQSBZ=-3.4641;BQBZ=-2.17723;NMBZ=2.34521;SCBZ=2.34521;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,159,12,162,159,18,159,162,159:7:0:5,0,0,0:1,0,1,0:6,0,1,0 0,6,53,6,53,53,6,53,53,53:2:0:0,0,0,0:2,0,0,0:2,0,0,0 0,5,79,9,82,80,9,82,80,80:4:0:3,1,0,0:0,0,0,0:3,1,0,0 +17 226 . A G,C,<*> 0 . DP=13;ADF=8,1,0,0;ADR=3,0,1,0;AD=11,1,1,0;I16=8,3,1,1,381,13669,6,18,567,31323,89,4441,248,5894,44,986;QS=2.94293,0.0392157,0.0178571,0;VDB=0.84;SGB=-2.62246;RPBZ=-0.592157;MQBZ=-0.615457;MQSBZ=-3.4641;BQBZ=-2.17723;NMBZ=2.34521;SCBZ=2.34521;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,159,12,162,159,18,159,162,159:7:0:5,0,0,0:1,0,1,0:6,0,1,0 0,6,53,6,53,53,6,53,53,53:2:0:0,0,0,0:2,0,0,0:2,0,0,0 0,5,79,9,82,80,9,82,80,80:4:0:3,1,0,0:0,0,0,0:3,1,0,0 17 227 . C <*> 0 . DP=13;ADF=9,0;ADR=4,0;AD=13,0;I16=9,4,0,0,412,14342,0,0,656,35764,0,0,292,6878,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,190:7:0:5,0:2,0:7,0 0,6,53:2:0:0,0:2,0:2,0 0,12,75:4:0:4,0:0,0:4,0 17 228 . C <*> 0 . DP=13;ADF=9,0;ADR=4,0;AD=13,0;I16=9,4,0,0,417,14381,0,0,656,35764,0,0,292,6884,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,187:7:0:5,0:2,0:7,0 0,6,45:2:0:0,0:2,0:2,0 0,12,96:4:0:4,0:0,0:4,0 17 229 . G <*> 0 . DP=13;ADF=9,0;ADR=4,0;AD=13,0;I16=9,4,0,0,368,11524,0,0,656,35764,0,0,292,6898,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,145:7:0:5,0:2,0:7,0 0,6,53:2:0:0,0:2,0:2,0 0,12,70:4:0:4,0:0,0:4,0 @@ -195,7 +195,7 @@ 17 264 . C <*> 0 . DP=22;ADF=10,0;ADR=12,0;AD=22,0;I16=10,12,0,0,821,31325,0,0,1049,54897,0,0,386,8326,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:7,0:4,0:11,0 0,15,104:5:0:0,0:5,0:5,0 0,18,172:6:0:3,0:3,0:6,0 17 265 . A <*> 0 . DP=21;ADF=9,0;ADR=12,0;AD=21,0;I16=9,12,0,0,800,31906,0,0,989,51297,0,0,390,8380,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:7,0:4,0:11,0 0,15,114:5:0:0,0:5,0:5,0 0,15,129:5:0:2,0:3,0:5,0 17 266 . G <*> 0 . DP=21;ADF=9,0;ADR=12,0;AD=21,0;I16=9,12,0,0,754,28204,0,0,989,51297,0,0,394,8458,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:7,0:4,0:11,0 0,15,99:5:0:0,0:5,0:5,0 0,15,138:5:0:2,0:3,0:5,0 -17 267 . T G,<*> 0 . DP=21;ADF=9,0,0;ADR=11,1,0;AD=20,1,0;I16=9,11,0,1,739,27465,8,64,960,50456,29,841,373,7935,25,625;QS=2.94203,0.057971,0;SGB=-0.556633;RPBZ=-0.330504;MQBZ=-1.23153;MQSBZ=-3.3021;BQBZ=-1.66282;NMBZ=2.4409;SCBZ=2.91633;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,254,33,254,254:11:0:7,0,0:4,0,0:11,0,0 0,6,93,12,96,96:5:0:0,0,0:4,1,0:4,1,0 0,15,149,15,149,149:5:0:2,0,0:3,0,0:5,0,0 +17 267 . T G,<*> 0 . DP=21;ADF=9,0,0;ADR=11,1,0;AD=20,1,0;I16=9,11,0,1,739,27465,8,64,960,50456,29,841,373,7935,25,625;QS=2.94203,0.057971,0;SGB=-0.556633;RPBZ=-0.330396;MQBZ=-1.23153;MQSBZ=-3.3021;BQBZ=-1.66282;NMBZ=2.4409;SCBZ=2.91633;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,254,33,254,254:11:0:7,0,0:4,0,0:11,0,0 0,6,93,12,96,96:5:0:0,0,0:4,1,0:4,1,0 0,15,149,15,149,149:5:0:2,0,0:3,0,0:5,0,0 17 268 . T <*> 0 . DP=21;ADF=9,0;ADR=12,0;AD=21,0;I16=9,12,0,0,748,27708,0,0,989,51297,0,0,402,8686,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,238:11:0:7,0:4,0:11,0 0,15,110:5:0:0,0:5,0:5,0 0,15,156:5:0:2,0:3,0:5,0 17 269 . C <*> 0 . DP=22;ADF=9,0;ADR=13,0;AD=22,0;I16=9,13,0,0,767,28641,0,0,1018,52138,0,0,406,8836,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:7,0:5,0:12,0 0,15,91:5:0:0,0:5,0:5,0 0,15,154:5:0:2,0:3,0:5,0 17 270 . C <*> 0 . DP=22;ADF=9,0;ADR=13,0;AD=22,0;I16=9,13,0,0,766,28210,0,0,1018,52138,0,0,410,8962,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:7,0:5,0:12,0 0,15,98:5:0:0,0:5,0:5,0 0,15,143:5:0:2,0:3,0:5,0 @@ -206,7 +206,7 @@ 17 275 . C <*> 0 . DP=20;ADF=7,0;ADR=13,0;AD=20,0;I16=7,13,0,0,768,29994,0,0,898,44938,0,0,423,9519,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,15,114:5:0:0,0:5,0:5,0 0,12,122:4:0:1,0:3,0:4,0 17 276 . A <*> 0 . DP=20;ADF=7,0;ADR=13,0;AD=20,0;I16=7,13,0,0,805,32931,0,0,898,44938,0,0,424,9538,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,253:11:0:6,0:5,0:11,0 0,15,122:5:0:0,0:5,0:5,0 0,12,124:4:0:1,0:3,0:4,0 17 277 . G <*> 0 . DP=20;ADF=7,0;ADR=13,0;AD=20,0;I16=7,13,0,0,764,29732,0,0,898,44938,0,0,425,9579,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,15,114:5:0:0,0:5,0:5,0 0,12,121:4:0:1,0:3,0:4,0 -17 278 . A C,<*> 0 . DP=21;ADF=6,1,0;ADR=14,0,0;AD=20,1,0;I16=6,14,1,0,722,26452,7,49,867,42179,60,3600,415,9521,11,121;QS=2.97935,0.020649,0;SGB=-0.556633;RPBZ=1.56989;MQBZ=1.0247;MQSBZ=-3.24037;BQBZ=-1.66667;NMBZ=-0.406816;SCBZ=-0.324037;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,22,231,30,234,231:11:0:5,1,0:5,0,0:10,1,0 0,18,123,18,123,123:6:0:0,0,0:6,0,0:6,0,0 0,12,121,12,121,121:4:0:1,0,0:3,0,0:4,0,0 +17 278 . A C,<*> 0 . DP=21;ADF=6,1,0;ADR=14,0,0;AD=20,1,0;I16=6,14,1,0,722,26452,7,49,867,42179,60,3600,415,9521,11,121;QS=2.97935,0.020649,0;SGB=-0.556633;RPBZ=1.65198;MQBZ=1.0247;MQSBZ=-3.24037;BQBZ=-1.66667;NMBZ=-0.406816;SCBZ=-0.324037;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,22,231,30,234,231:11:0:5,1,0:5,0,0:10,1,0 0,18,123,18,123,123:6:0:0,0,0:6,0,0:6,0,0 0,12,121,12,121,121:4:0:1,0,0:3,0,0:4,0,0 17 279 . A <*> 0 . DP=22;ADF=7,0;ADR=15,0;AD=22,0;I16=7,15,0,0,786,28694,0,0,956,46620,0,0,427,9677,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:6,0:6,0:12,0 0,18,123:6:0:0,0:6,0:6,0 0,12,122:4:0:1,0:3,0:4,0 17 280 . A <*> 0 . DP=22;ADF=7,0;ADR=15,0;AD=22,0;I16=7,15,0,0,815,31561,0,0,956,46620,0,0,428,9684,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,253:12:0:6,0:6,0:12,0 0,18,130:6:0:0,0:6,0:6,0 0,12,129:4:0:1,0:3,0:4,0 17 281 . G <*> 0 . DP=22;ADF=7,0;ADR=15,0;AD=22,0;I16=7,15,0,0,820,31416,0,0,956,46620,0,0,428,9662,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:6,0:6,0:12,0 0,18,122:6:0:0,0:6,0:6,0 0,12,123:4:0:1,0:3,0:4,0 @@ -231,7 +231,7 @@ 17 300 . A <*> 0 . DP=27;ADF=11,0;ADR=15,0;AD=26,0;I16=11,15,0,0,1001,39455,0,0,1258,66538,0,0,469,10437,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,204:8:0:3,0:5,0:8,0 0,21,210:7:0:2,0:5,0:7,0 17 301 . G <*> 0 . DP=25;ADF=10,0;ADR=14,0;AD=24,0;I16=10,14,0,0,928,36116,0,0,1169,62097,0,0,476,10632,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,255:10:0:5,0:5,0:10,0 0,21,195:7:0:3,0:4,0:7,0 0,21,196:7:0:2,0:5,0:7,0 17 302 . T <*> 0 . DP=25;ADF=10,0;ADR=14,0;AD=24,0;I16=10,14,0,0,879,32885,0,0,1169,62097,0,0,483,10849,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,231:10:0:5,0:5,0:10,0 0,21,172:7:0:3,0:4,0:7,0 0,21,202:7:0:2,0:5,0:7,0 -17 302 . T TA 0 . INDEL;IDV=7;IMF=1;DP=25;ADF=2,8;ADR=4,11;AD=6,19;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.539485,2.46052;VDB=0.260546;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.22749;BQBZ=-1.67542;NMBZ=-0.199304;SCBZ=-0.268121;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 161,0,99:11:6:1,4:4,2:5,6 158,0,14:7:0:1,2:0,4:1,6 201,21,0:7:0:0,2:0,5:0,7 +17 302 . T TA 0 . INDEL;IDV=7;IMF=1;DP=25;ADF=2,8;ADR=4,11;AD=6,19;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.539485,2.46052;VDB=0.241622;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.22749;BQBZ=-1.67542;NMBZ=-0.199304;SCBZ=-0.268121;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 161,0,99:11:6:1,4:4,2:5,6 158,0,14:7:0:1,2:0,4:1,6 201,21,0:7:0:0,2:0,5:0,7 17 303 . G <*> 0 . DP=25;ADF=10,0;ADR=15,0;AD=25,0;I16=10,15,0,0,968,37972,0,0,1229,65697,0,0,497,11181,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:5,0:6,0:11,0 0,21,197:7:0:3,0:4,0:7,0 0,21,195:7:0:2,0:5,0:7,0 17 304 . C <*> 0 . DP=27;ADF=11,0;ADR=16,0;AD=27,0;I16=11,16,0,0,991,37005,0,0,1318,70138,0,0,503,11359,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:5,0:6,0:11,0 0,24,206:8:0:4,0:4,0:8,0 0,24,200:8:0:2,0:6,0:8,0 17 305 . C <*> 0 . DP=27;ADF=11,0;ADR=16,0;AD=27,0;I16=11,16,0,0,1057,41761,0,0,1318,70138,0,0,510,11508,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:5,0:6,0:11,0 0,24,213:8:0:4,0:4,0:8,0 0,24,211:8:0:2,0:6,0:8,0 @@ -264,9 +264,9 @@ 17 332 . A <*> 0 . DP=32;ADF=14,0;ADR=18,0;AD=32,0;I16=14,18,0,0,1156,42666,0,0,1649,90897,0,0,560,12178,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:6,0:6,0:12,0 0,27,214:9:0:4,0:5,0:9,0 0,33,255:11:0:4,0:7,0:11,0 17 333 . A <*> 0 . DP=32;ADF=14,0;ADR=18,0;AD=32,0;I16=14,18,0,0,1141,41987,0,0,1649,90897,0,0,558,12064,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:6,0:6,0:12,0 0,27,223:9:0:4,0:5,0:9,0 0,33,255:11:0:4,0:7,0:11,0 17 334 . A <*> 0 . DP=32;ADF=14,0;ADR=18,0;AD=32,0;I16=14,18,0,0,1162,43328,0,0,1649,90897,0,0,556,11986,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:6,0:6,0:12,0 0,27,221:9:0:4,0:5,0:9,0 0,33,255:11:0:4,0:7,0:11,0 -17 335 . A G,<*> 0 . DP=32;ADF=13,1,0;ADR=18,0,0;AD=31,1,0;I16=13,18,1,0,1084,40336,4,16,1589,87297,60,3600,555,11943,0,0;QS=2.98919,0.0108108,0;SGB=-0.556633;RPBZ=-1.67921;MQBZ=0.622171;MQSBZ=-2.25492;BQBZ=-1.68602;NMBZ=-0.428353;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,252,33,252,252:11:0:5,0,0:6,0,0:11,0,0 0,27,219,27,219,219:9:0:4,0,0:5,0,0:9,0,0 0,25,245,33,248,245:12:0:4,1,0:7,0,0:11,1,0 +17 335 . A G,<*> 0 . DP=32;ADF=13,1,0;ADR=18,0,0;AD=31,1,0;I16=13,18,1,0,1084,40336,4,16,1589,87297,60,3600,555,11943,0,0;QS=2.98919,0.0108108,0;SGB=-0.556633;RPBZ=-1.67936;MQBZ=0.622171;MQSBZ=-2.25492;BQBZ=-1.68602;NMBZ=-0.428353;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,252,33,252,252:11:0:5,0,0:6,0,0:11,0,0 0,27,219,27,219,219:9:0:4,0,0:5,0,0:9,0,0 0,25,245,33,248,245:12:0:4,1,0:7,0,0:11,1,0 17 336 . A <*> 0 . DP=32;ADF=14,0;ADR=18,0;AD=32,0;I16=14,18,0,0,1094,39794,0,0,1649,90897,0,0,555,11935,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:5,0:6,0:11,0 0,27,212:9:0:4,0:5,0:9,0 0,36,255:12:0:5,0:7,0:12,0 -17 337 . C A,<*> 0 . DP=32;ADF=14,0,0;ADR=17,1,0;AD=31,1,0;I16=14,17,0,1,1125,42481,5,25,1612,89528,37,1369,536,11590,18,324;QS=2.98113,0.0188679,0;SGB=-0.556633;RPBZ=0.812519;MQBZ=-1.03695;MQSBZ=-2.25492;BQBZ=-1.68353;NMBZ=-0.376914;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255,33,255,255:11:0:5,0,0:6,0,0:11,0,0 0,17,195,24,198,195:9:0:4,0,0:4,1,0:8,1,0 0,36,255,36,255,255:12:0:5,0,0:7,0,0:12,0,0 +17 337 . C A,<*> 0 . DP=32;ADF=14,0,0;ADR=17,1,0;AD=31,1,0;I16=14,17,0,1,1125,42481,5,25,1612,89528,37,1369,536,11590,18,324;QS=2.98113,0.0188679,0;SGB=-0.556633;RPBZ=0.812593;MQBZ=-1.03695;MQSBZ=-2.25492;BQBZ=-1.68353;NMBZ=-0.376914;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255,33,255,255:11:0:5,0,0:6,0,0:11,0,0 0,17,195,24,198,195:9:0:4,0,0:4,1,0:8,1,0 0,36,255,36,255,255:12:0:5,0,0:7,0,0:12,0,0 17 338 . T <*> 0 . DP=30;ADF=14,0;ADR=16,0;AD=30,0;I16=14,16,0,0,1190,47898,0,0,1560,86456,0,0,554,11878,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,255:10:0:5,0:5,0:10,0 0,24,226:8:0:4,0:4,0:8,0 0,36,255:12:0:5,0:7,0:12,0 17 339 . C <*> 0 . DP=31;ADF=14,0;ADR=17,0;AD=31,0;I16=14,17,0,0,1130,43210,0,0,1589,87297,0,0,554,11874,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:5,0:6,0:11,0 0,24,185:8:0:4,0:4,0:8,0 0,36,255:12:0:5,0:7,0:12,0 17 340 . C <*> 0 . DP=31;ADF=14,0;ADR=17,0;AD=31,0;I16=14,17,0,0,1196,47044,0,0,1589,87297,0,0,554,11852,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:5,0:6,0:11,0 0,24,221:8:0:4,0:4,0:8,0 0,36,255:12:0:5,0:7,0:12,0 @@ -288,7 +288,7 @@ 17 356 . G <*> 0 . DP=27;ADF=14,0;ADR=13,0;AD=27,0;I16=14,13,0,0,993,37481,0,0,1465,83405,0,0,574,13174,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,228:9:0:4,0:5,0:9,0 0,24,201:8:0:5,0:3,0:8,0 0,30,255:10:0:5,0:5,0:10,0 17 357 . C <*> 0 . DP=28;ADF=15,0;ADR=13,0;AD=28,0;I16=15,13,0,0,1026,39496,0,0,1525,87005,0,0,575,13209,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,255:10:0:5,0:5,0:10,0 0,24,205:8:0:5,0:3,0:8,0 0,30,252:10:0:5,0:5,0:10,0 17 358 . A <*> 0 . DP=28;ADF=15,0;ADR=13,0;AD=28,0;I16=15,13,0,0,1050,40518,0,0,1525,87005,0,0,576,13216,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,254:10:0:5,0:5,0:10,0 0,24,197:8:0:5,0:3,0:8,0 0,30,255:10:0:5,0:5,0:10,0 -17 359 . G T,<*> 0 . DP=29;ADF=15,0,0;ADR=13,1,0;AD=28,1,0;I16=15,13,0,1,1085,42761,10,100,1525,87005,60,3600,552,12620,25,625;QS=2.96032,0.0396825,0;SGB=-0.556633;RPBZ=-0.119567;MQBZ=0.456435;MQSBZ=-1.53333;BQBZ=-1.68246;NMBZ=3.0531;SCBZ=5.2915;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,255,30,255,255:10:0:5,0,0:5,0,0:10,0,0 0,13,178,21,181,180:8:0:5,0,0:2,1,0:7,1,0 0,33,255,33,255,255:11:0:5,0,0:6,0,0:11,0,0 +17 359 . G T,<*> 0 . DP=29;ADF=15,0,0;ADR=13,1,0;AD=28,1,0;I16=15,13,0,1,1085,42761,10,100,1525,87005,60,3600,552,12620,25,625;QS=2.96032,0.0396825,0;SGB=-0.556633;RPBZ=-0.119611;MQBZ=0.456435;MQSBZ=-1.53333;BQBZ=-1.68246;NMBZ=3.0531;SCBZ=5.2915;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,255,30,255,255:10:0:5,0,0:5,0,0:10,0,0 0,13,178,21,181,180:8:0:5,0,0:2,1,0:7,1,0 0,33,255,33,255,255:11:0:5,0,0:6,0,0:11,0,0 17 360 . A <*> 0 . DP=29;ADF=15,0;ADR=14,0;AD=29,0;I16=15,14,0,0,1111,43259,0,0,1585,90605,0,0,579,13297,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,252:10:0:5,0:5,0:10,0 0,24,220:8:0:5,0:3,0:8,0 0,33,255:11:0:5,0:6,0:11,0 17 361 . A <*> 0 . DP=29;ADF=15,0;ADR=14,0;AD=29,0;I16=15,14,0,0,1116,43442,0,0,1585,90605,0,0,579,13273,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,252:10:0:5,0:5,0:10,0 0,24,219:8:0:5,0:3,0:8,0 0,33,255:11:0:5,0:6,0:11,0 17 362 . A <*> 0 . DP=29;ADF=16,0;ADR=13,0;AD=29,0;I16=16,13,0,0,1104,42700,0,0,1585,90605,0,0,580,13272,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,218:8:0:5,0:3,0:8,0 0,30,255:10:0:5,0:5,0:10,0 @@ -298,13 +298,13 @@ 17 366 . A <*> 0 . DP=29;ADF=16,0;ADR=13,0;AD=29,0;I16=16,13,0,0,1090,41562,0,0,1585,90605,0,0,581,13167,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,211:8:0:5,0:3,0:8,0 0,30,255:10:0:5,0:5,0:10,0 17 367 . T <*> 0 . DP=29;ADF=16,0;ADR=13,0;AD=29,0;I16=16,13,0,0,1055,39149,0,0,1585,90605,0,0,579,13093,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,204:8:0:5,0:3,0:8,0 0,30,255:10:0:5,0:5,0:10,0 17 368 . A <*> 0 . DP=29;ADF=16,0;ADR=13,0;AD=29,0;I16=16,13,0,0,1054,39632,0,0,1585,90605,0,0,576,12998,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,208:8:0:5,0:3,0:8,0 0,30,255:10:0:5,0:5,0:10,0 -17 369 . T G,<*> 0 . DP=28;ADF=16,0,0;ADR=11,1,0;AD=27,1,0;I16=16,11,0,1,1037,40275,6,36,1496,86164,60,3600,548,12256,25,625;QS=2.97683,0.023166,0;SGB=-0.556633;RPBZ=0.123865;MQBZ=0.408248;MQSBZ=-1.37784;BQBZ=-1.68703;NMBZ=2.99794;SCBZ=5.19615;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,250,30,250,250:10:0:6,0,0:4,0,0:10,0,0 0,15,189,21,192,190:8:0:5,0,0:2,1,0:7,1,0 0,30,255,30,255,255:10:0:5,0,0:5,0,0:10,0,0 +17 369 . T G,<*> 0 . DP=28;ADF=16,0,0;ADR=11,1,0;AD=27,1,0;I16=16,11,0,1,1037,40275,6,36,1496,86164,60,3600,548,12256,25,625;QS=2.97683,0.023166,0;SGB=-0.556633;RPBZ=0.12395;MQBZ=0.408248;MQSBZ=-1.37784;BQBZ=-1.68703;NMBZ=2.99794;SCBZ=5.19615;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,250,30,250,250:10:0:6,0,0:4,0,0:10,0,0 0,15,189,21,192,190:8:0:5,0,0:2,1,0:7,1,0 0,30,255,30,255,255:10:0:5,0,0:5,0,0:10,0,0 17 370 . C <*> 0 . DP=28;ADF=16,0;ADR=12,0;AD=28,0;I16=16,12,0,0,1045,40219,0,0,1556,89764,0,0,570,12790,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,255:10:0:6,0:4,0:10,0 0,24,201:8:0:5,0:3,0:8,0 0,30,255:10:0:5,0:5,0:10,0 17 371 . T <*> 0 . DP=29;ADF=16,0;ADR=13,0;AD=29,0;I16=16,13,0,0,1155,46591,0,0,1616,93364,0,0,567,12725,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,255:10:0:6,0:4,0:10,0 0,24,227:8:0:5,0:3,0:8,0 0,33,255:11:0:5,0:6,0:11,0 17 372 . C <*> 0 . DP=30;ADF=16,0;ADR=14,0;AD=30,0;I16=16,14,0,0,1139,44019,0,0,1676,96964,0,0,564,12636,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,215:8:0:5,0:3,0:8,0 0,33,255:11:0:5,0:6,0:11,0 17 373 . A <*> 0 . DP=30;ADF=16,0;ADR=14,0;AD=30,0;I16=16,14,0,0,1142,44118,0,0,1676,96964,0,0,561,12525,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,220:8:0:5,0:3,0:8,0 0,33,255:11:0:5,0:6,0:11,0 17 374 . T <*> 0 . DP=30;ADF=16,0;ADR=14,0;AD=30,0;I16=16,14,0,0,1098,41180,0,0,1676,96964,0,0,556,12344,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,221:8:0:5,0:3,0:8,0 0,33,255:11:0:5,0:6,0:11,0 -17 375 . A T,<*> 0 . DP=31;ADF=17,0,0;ADR=13,1,0;AD=30,1,0;I16=17,13,0,1,1138,43798,14,196,1676,96964,60,3600,547,12177,4,16;QS=2.9661,0.0338983,0;SGB=-0.556633;RPBZ=-1.45462;MQBZ=0.3849;MQSBZ=-1.26404;BQBZ=-1.68488;NMBZ=2.30253;SCBZ=-0.182574;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255,36,255,255:12:0:7,0,0:5,0,0:12,0,0 0,24,218,24,218,218:8:0:5,0,0:3,0,0:8,0,0 0,18,255,30,255,255:11:0:5,0,0:5,1,0:10,1,0 +17 375 . A T,<*> 0 . DP=31;ADF=17,0,0;ADR=13,1,0;AD=30,1,0;I16=17,13,0,1,1138,43798,14,196,1676,96964,60,3600,547,12177,4,16;QS=2.9661,0.0338983,0;SGB=-0.556633;RPBZ=-1.45432;MQBZ=0.3849;MQSBZ=-1.26404;BQBZ=-1.68488;NMBZ=2.30253;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255,36,255,255:12:0:7,0,0:5,0,0:12,0,0 0,24,218,24,218,218:8:0:5,0,0:3,0,0:8,0,0 0,18,255,30,255,255:11:0:5,0,0:5,1,0:10,1,0 17 376 . G <*> 0 . DP=31;ADF=17,0;ADR=14,0;AD=31,0;I16=17,14,0,0,1131,42581,0,0,1736,100564,0,0,547,12073,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:7,0:5,0:12,0 0,24,220:8:0:5,0:3,0:8,0 0,33,255:11:0:5,0:6,0:11,0 17 377 . T <*> 0 . DP=31;ADF=17,0;ADR=14,0;AD=31,0;I16=17,14,0,0,1116,41750,0,0,1736,100564,0,0,543,11985,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:7,0:5,0:12,0 0,24,211:8:0:5,0:3,0:8,0 0,33,255:11:0:5,0:6,0:11,0 17 378 . T <*> 0 . DP=30;ADF=18,0;ADR=12,0;AD=30,0;I16=18,12,0,0,1098,41066,0,0,1707,99723,0,0,541,11927,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255:13:0:8,0:5,0:13,0 0,21,186:7:0:5,0:2,0:7,0 0,30,255:10:0:5,0:5,0:10,0 @@ -313,7 +313,7 @@ 17 381 . T <*> 0 . DP=29;ADF=18,0;ADR=11,0;AD=29,0;I16=18,11,0,0,1167,47337,0,0,1678,98882,0,0,537,11729,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:8,0:4,0:12,0 0,21,211:7:0:5,0:2,0:7,0 0,30,255:10:0:5,0:5,0:10,0 17 382 . T <*> 0 . DP=29;ADF=18,0;ADR=11,0;AD=29,0;I16=18,11,0,0,1062,40514,0,0,1678,98882,0,0,535,11693,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:8,0:4,0:12,0 0,21,182:7:0:5,0:2,0:7,0 0,30,255:10:0:5,0:5,0:10,0 17 383 . T <*> 0 . DP=29;ADF=18,0;ADR=11,0;AD=29,0;I16=18,11,0,0,1059,39847,0,0,1678,98882,0,0,532,11638,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:8,0:4,0:12,0 0,21,172:7:0:5,0:2,0:7,0 0,30,255:10:0:5,0:5,0:10,0 -17 384 . A C,<*> 0 . DP=31;ADF=19,0,0;ADR=11,1,0;AD=30,1,0;I16=19,11,0,1,1077,39885,4,16,1738,102482,60,3600,504,10988,25,625;QS=2.98419,0.0158103,0;SGB=-0.556633;RPBZ=0.615415;MQBZ=0.262613;MQSBZ=-0.333409;BQBZ=-1.68746;NMBZ=3.26825;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255,39,255,255:13:0:8,0,0:5,0,0:13,0,0 0,15,171,21,174,171:8:0:6,0,0:1,1,0:7,1,0 0,30,255,30,255,255:10:0:5,0,0:5,0,0:10,0,0 +17 384 . A C,<*> 0 . DP=31;ADF=19,0,0;ADR=11,1,0;AD=30,1,0;I16=19,11,0,1,1077,39885,4,16,1738,102482,60,3600,504,10988,25,625;QS=2.98419,0.0158103,0;SGB=-0.556633;RPBZ=0.615229;MQBZ=0.262613;MQSBZ=-0.333409;BQBZ=-1.68746;NMBZ=3.26825;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255,39,255,255:13:0:8,0,0:5,0,0:13,0,0 0,15,171,21,174,171:8:0:6,0,0:1,1,0:7,1,0 0,30,255,30,255,255:10:0:5,0,0:5,0,0:10,0,0 17 385 . C <*> 0 . DP=31;ADF=19,0;ADR=12,0;AD=31,0;I16=19,12,0,0,1118,41180,0,0,1798,106082,0,0,527,11569,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255:13:0:8,0:5,0:13,0 0,24,186:8:0:6,0:2,0:8,0 0,30,255:10:0:5,0:5,0:10,0 17 386 . T <*> 0 . DP=30;ADF=18,0;ADR=12,0;AD=30,0;I16=18,12,0,0,1158,45592,0,0,1738,102482,0,0,526,11556,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255:13:0:8,0:5,0:13,0 0,21,191:7:0:5,0:2,0:7,0 0,30,255:10:0:5,0:5,0:10,0 17 387 . T <*> 0 . DP=30;ADF=18,0;ADR=12,0;AD=30,0;I16=18,12,0,0,1105,41821,0,0,1738,102482,0,0,525,11573,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255:13:0:8,0:5,0:13,0 0,21,187:7:0:5,0:2,0:7,0 0,30,255:10:0:5,0:5,0:10,0 @@ -341,7 +341,7 @@ 17 409 . T <*> 0 . DP=29;ADF=17,0;ADR=12,0;AD=29,0;I16=17,12,0,0,1100,42734,0,0,1678,98882,0,0,525,11503,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,42,255:14:0:8,0:6,0:14,0 0,12,131:4:0:2,0:2,0:4,0 0,33,255:11:0:7,0:4,0:11,0 17 410 . T <*> 0 . DP=29;ADF=17,0;ADR=12,0;AD=29,0;I16=17,12,0,0,1035,38325,0,0,1678,98882,0,0,524,11432,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,42,255:14:0:8,0:6,0:14,0 0,12,125:4:0:2,0:2,0:4,0 0,33,255:11:0:7,0:4,0:11,0 17 411 . T <*> 0 . DP=29;ADF=17,0;ADR=12,0;AD=29,0;I16=17,12,0,0,1022,37928,0,0,1678,98882,0,0,522,11342,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,42,255:14:0:8,0:6,0:14,0 0,12,111:4:0:2,0:2,0:4,0 0,33,255:11:0:7,0:4,0:11,0 -17 412 . C T,<*> 0 . DP=30;ADF=17,1,0;ADR=12,0,0;AD=29,1,0;I16=17,12,1,0,1094,42458,14,196,1678,98882,60,3600,495,10659,25,625;QS=2.97455,0.0254545,0;SGB=-0.556633;RPBZ=-0.404685;MQBZ=0.267261;MQSBZ=-0.293785;BQBZ=-1.6942;NMBZ=-0.267102;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,255,42,255,255:15:0:8,1,0:6,0,0:14,1,0 0,12,124,12,124,124:4:0:2,0,0:2,0,0:4,0,0 0,33,255,33,255,255:11:0:7,0,0:4,0,0:11,0,0 +17 412 . C T,<*> 0 . DP=30;ADF=17,1,0;ADR=12,0,0;AD=29,1,0;I16=17,12,1,0,1094,42458,14,196,1678,98882,60,3600,495,10659,25,625;QS=2.97455,0.0254545,0;SGB=-0.556633;RPBZ=-0.40473;MQBZ=0.267261;MQSBZ=-0.293785;BQBZ=-1.6942;NMBZ=-0.267102;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,255,42,255,255:15:0:8,1,0:6,0,0:14,1,0 0,12,124,12,124,124:4:0:2,0,0:2,0,0:4,0,0 0,33,255,33,255,255:11:0:7,0,0:4,0,0:11,0,0 17 413 . A <*> 0 . DP=31;ADF=18,0;ADR=13,0;AD=31,0;I16=18,13,0,0,1189,45985,0,0,1798,106082,0,0,520,11258,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:9,0:8,0:17,0 0,9,102:3:0:2,0:1,0:3,0 0,33,255:11:0:7,0:4,0:11,0 17 414 . T <*> 0 . DP=30;ADF=18,0;ADR=12,0;AD=30,0;I16=18,12,0,0,1151,44355,0,0,1738,102482,0,0,523,11265,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:9,0:7,0:16,0 0,9,109:3:0:2,0:1,0:3,0 0,33,255:11:0:7,0:4,0:11,0 17 415 . G <*> 0 . DP=30;ADF=18,0;ADR=12,0;AD=30,0;I16=18,12,0,0,1131,43175,0,0,1738,102482,0,0,526,11306,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:9,0:7,0:16,0 0,9,110:3:0:2,0:1,0:3,0 0,33,255:11:0:7,0:4,0:11,0 @@ -366,7 +366,7 @@ 17 434 . T <*> 0 . DP=29;ADF=15,0;ADR=14,0;AD=29,0;I16=15,14,0,0,1036,37654,0,0,1647,96123,0,0,561,12567,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:8,0:8,0:16,0 0,9,98:3:0:2,0:1,0:3,0 0,30,243:10:0:5,0:5,0:10,0 17 435 . A <*> 0 . DP=29;ADF=15,0;ADR=14,0;AD=29,0;I16=15,14,0,0,1035,38091,0,0,1647,96123,0,0,562,12596,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:8,0:8,0:16,0 0,9,103:3:0:2,0:1,0:3,0 0,30,237:10:0:5,0:5,0:10,0 17 436 . T <*> 0 . DP=28;ADF=14,0;ADR=14,0;AD=28,0;I16=14,14,0,0,998,36220,0,0,1587,92523,0,0,564,12654,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:8,0:8,0:16,0 0,9,110:3:0:2,0:1,0:3,0 0,27,223:9:0:4,0:5,0:9,0 -17 437 . T G,<*> 0 . DP=28;ADF=13,1,0;ADR=14,0,0;AD=27,1,0;I16=13,14,1,0,990,36832,6,36,1558,91682,29,841,549,12435,16,256;QS=2.9781,0.0218978,0;SGB=-0.556633;RPBZ=-1.36195;MQBZ=-2.88675;MQSBZ=0.6;BQBZ=-1.67909;NMBZ=-0.19245;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255,48,255,255:16:0:8,0,0:8,0,0:16,0,0 0,9,109,9,109,109:3:0:2,0,0:1,0,0:3,0,0 0,17,200,24,203,201:9:0:3,1,0:5,0,0:8,1,0 +17 437 . T G,<*> 0 . DP=28;ADF=13,1,0;ADR=14,0,0;AD=27,1,0;I16=13,14,1,0,990,36832,6,36,1558,91682,29,841,549,12435,16,256;QS=2.9781,0.0218978,0;SGB=-0.556633;RPBZ=-1.36214;MQBZ=-2.88675;MQSBZ=0.6;BQBZ=-1.67909;NMBZ=-0.19245;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255,48,255,255:16:0:8,0,0:8,0,0:16,0,0 0,9,109,9,109,109:3:0:2,0,0:1,0,0:3,0,0 0,17,200,24,203,201:9:0:3,1,0:5,0,0:8,1,0 17 438 . A <*> 0 . DP=28;ADF=14,0;ADR=14,0;AD=28,0;I16=14,14,0,0,984,35784,0,0,1587,92523,0,0,565,12707,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:8,0:8,0:16,0 0,9,107:3:0:2,0:1,0:3,0 0,27,220:9:0:4,0:5,0:9,0 17 439 . C <*> 0 . DP=28;ADF=14,0;ADR=14,0;AD=28,0;I16=14,14,0,0,1055,40273,0,0,1587,92523,0,0,563,12649,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:8,0:8,0:16,0 0,9,107:3:0:2,0:1,0:3,0 0,27,224:9:0:4,0:5,0:9,0 17 440 . A <*> 0 . DP=28;ADF=14,0;ADR=14,0;AD=28,0;I16=14,14,0,0,1095,43251,0,0,1587,92523,0,0,561,12615,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:8,0:8,0:16,0 0,9,115:3:0:2,0:1,0:3,0 0,27,247:9:0:4,0:5,0:9,0 @@ -394,7 +394,7 @@ 17 462 . G <*> 0 . DP=32;ADF=18,0;ADR=13,0;AD=31,0;I16=18,13,0,0,1169,46001,0,0,1775,103851,0,0,577,12669,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:10,0:7,0:17,0 0,12,131:4:0:3,0:1,0:4,0 0,30,241:10:0:5,0:5,0:10,0 17 463 . G <*> 0 . DP=32;ADF=18,0;ADR=13,0;AD=31,0;I16=18,13,0,0,1095,41573,0,0,1775,103851,0,0,583,12729,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:10,0:7,0:17,0 0,12,126:4:0:3,0:1,0:4,0 0,30,221:10:0:5,0:5,0:10,0 17 464 . A <*> 0 . DP=32;ADF=18,0;ADR=13,0;AD=31,0;I16=18,13,0,0,1100,41724,0,0,1775,103851,0,0,589,12821,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:10,0:7,0:17,0 0,12,148:4:0:3,0:1,0:4,0 0,30,217:10:0:5,0:5,0:10,0 -17 465 . C T,<*> 0 . DP=33;ADF=19,0,0;ADR=12,1,0;AD=31,1,0;I16=19,12,0,1,1173,45601,4,16,1775,103851,60,3600,589,12909,6,36;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.67936;MQBZ=0.321288;MQSBZ=0.341466;BQBZ=-1.68493;NMBZ=3.21288;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255,51,255,255:17:0:10,0,0:7,0,0:17,0,0 0,15,158,15,158,158:5:0:4,0,0:1,0,0:5,0,0 0,20,224,27,227,224:10:0:5,0,0:4,1,0:9,1,0 +17 465 . C T,<*> 0 . DP=33;ADF=19,0,0;ADR=12,1,0;AD=31,1,0;I16=19,12,0,1,1173,45601,4,16,1775,103851,60,3600,589,12909,6,36;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.67982;MQBZ=0.321288;MQSBZ=0.341466;BQBZ=-1.68493;NMBZ=3.21288;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255,51,255,255:17:0:10,0,0:7,0,0:17,0,0 0,15,158,15,158,158:5:0:4,0,0:1,0,0:5,0,0 0,20,224,27,227,224:10:0:5,0,0:4,1,0:9,1,0 17 466 . A <*> 0 . DP=34;ADF=20,0;ADR=13,0;AD=33,0;I16=20,13,0,0,1268,49686,0,0,1895,111051,0,0,602,13102,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:11,0:7,0:18,0 0,15,173:5:0:4,0:1,0:5,0 0,30,255:10:0:5,0:5,0:10,0 17 467 . A <*> 0 . DP=34;ADF=20,0;ADR=13,0;AD=33,0;I16=20,13,0,0,1246,48610,0,0,1895,111051,0,0,608,13194,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:11,0:7,0:18,0 0,15,177:5:0:4,0:1,0:5,0 0,30,251:10:0:5,0:5,0:10,0 17 468 . A <*> 0 . DP=35;ADF=21,0;ADR=13,0;AD=34,0;I16=21,13,0,0,1253,48095,0,0,1955,114651,0,0,613,13273,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:12,0:7,0:19,0 0,15,174:5:0:4,0:1,0:5,0 0,30,251:10:0:5,0:5,0:10,0 @@ -417,7 +417,7 @@ 17 485 . G <*> 0 . DP=35;ADF=23,0;ADR=12,0;AD=35,0;I16=23,12,0,0,1329,51411,0,0,2015,118251,0,0,669,14931,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:12,0:6,0:18,0 0,18,160:6:0:5,0:1,0:6,0 0,33,255:11:0:6,0:5,0:11,0 17 486 . A <*> 0 . DP=34;ADF=22,0;ADR=12,0;AD=34,0;I16=22,12,0,0,1313,51667,0,0,1955,114651,0,0,671,14989,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:11,0:6,0:17,0 0,18,173:6:0:5,0:1,0:6,0 0,33,255:11:0:6,0:5,0:11,0 17 487 . G <*> 0 . DP=34;ADF=22,0;ADR=12,0;AD=34,0;I16=22,12,0,0,1300,50304,0,0,1955,114651,0,0,672,15030,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:11,0:6,0:17,0 0,18,169:6:0:5,0:1,0:6,0 0,33,255:11:0:6,0:5,0:11,0 -17 488 . A G,<*> 0 . DP=35;ADF=22,1,0;ADR=12,0,0;AD=34,1,0;I16=22,12,1,0,1278,48412,4,16,1986,117410,29,841,646,14380,25,625;QS=2.98947,0.0105263,0;SGB=-0.556633;RPBZ=0.544734;MQBZ=-3.36505;MQSBZ=0.10737;BQBZ=-1.69552;NMBZ=-0.171499;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255,54,255,255:18:0:12,0,0:6,0,0:18,0,0 0,18,177,18,177,177:6:0:5,0,0:1,0,0:6,0,0 0,23,255,30,255,255:11:0:5,1,0:5,0,0:10,1,0 +17 488 . A G,<*> 0 . DP=35;ADF=22,1,0;ADR=12,0,0;AD=34,1,0;I16=22,12,1,0,1278,48412,4,16,1986,117410,29,841,646,14380,25,625;QS=2.98947,0.0105263,0;SGB=-0.556633;RPBZ=0.594463;MQBZ=-3.36505;MQSBZ=0.10737;BQBZ=-1.69552;NMBZ=-0.171499;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255,54,255,255:18:0:12,0,0:6,0,0:18,0,0 0,18,177,18,177,177:6:0:5,0,0:1,0,0:6,0,0 0,23,255,30,255,255:11:0:5,1,0:5,0,0:10,1,0 17 489 . A <*> 0 . DP=35;ADF=23,0;ADR=12,0;AD=35,0;I16=23,12,0,0,1264,46916,0,0,2015,118251,0,0,671,15015,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:12,0:6,0:18,0 0,18,175:6:0:5,0:1,0:6,0 0,33,255:11:0:6,0:5,0:11,0 17 490 . A <*> 0 . DP=36;ADF=24,0;ADR=12,0;AD=36,0;I16=24,12,0,0,1332,50280,0,0,2075,121851,0,0,671,15061,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:12,0:6,0:18,0 0,21,188:7:0:6,0:1,0:7,0 0,33,255:11:0:6,0:5,0:11,0 17 491 . T <*> 0 . DP=36;ADF=24,0;ADR=12,0;AD=36,0;I16=24,12,0,0,1284,46802,0,0,2075,121851,0,0,671,15093,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:12,0:6,0:18,0 0,21,178:7:0:6,0:1,0:7,0 0,33,255:11:0:6,0:5,0:11,0 @@ -441,9 +441,9 @@ 17 509 . C <*> 0 . DP=34;ADF=24,0;ADR=10,0;AD=34,0;I16=24,10,0,0,1272,48272,0,0,1986,117410,0,0,640,14430,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:13,0:5,0:18,0 0,21,186:7:0:6,0:1,0:7,0 0,27,241:9:0:5,0:4,0:9,0 17 510 . A <*> 0 . DP=34;ADF=23,0;ADR=11,0;AD=34,0;I16=23,11,0,0,1211,44827,0,0,1986,117410,0,0,638,14398,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:13,0:6,0:19,0 0,21,187:7:0:6,0:1,0:7,0 0,24,221:8:0:4,0:4,0:8,0 17 511 . A <*> 0 . DP=34;ADF=23,0;ADR=11,0;AD=34,0;I16=23,11,0,0,1238,46516,0,0,1986,117410,0,0,637,14395,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:13,0:6,0:19,0 0,21,195:7:0:6,0:1,0:7,0 0,24,233:8:0:4,0:4,0:8,0 -17 512 . A C,<*> 0 . DP=33;ADF=22,0,0;ADR=10,1,0;AD=32,1,0;I16=22,10,0,1,1133,41513,13,169,1866,110210,60,3600,628,14340,9,81;QS=2.97766,0.0223368,0;SGB=-0.556633;RPBZ=-1.47091;MQBZ=0.253876;MQSBZ=-0.461593;BQBZ=-1.68442;NMBZ=2.68627;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255,51,255,255:18:0:12,0,0:5,1,0:17,1,0 0,21,183,21,183,183:7:0:6,0,0:1,0,0:7,0,0 0,24,231,24,231,231:8:0:4,0,0:4,0,0:8,0,0 -17 513 . A T,<*> 0 . DP=32;ADF=21,1,0;ADR=10,0,0;AD=31,1,0;I16=21,10,1,0,1125,42283,12,144,1806,106610,60,3600,623,14249,15,225;QS=2.97966,0.020339,0;SGB=-0.556633;RPBZ=-1.24598;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.57376;NMBZ=2.63913;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,37,255,48,255,255:17:0:11,1,0:5,0,0:16,1,0 0,21,177,21,177,177:7:0:6,0,0:1,0,0:7,0,0 0,24,233,24,233,233:8:0:4,0,0:4,0,0:8,0,0 -17 514 . A T,<*> 0 . DP=32;ADF=22,0,0;ADR=9,1,0;AD=31,1,0;I16=22,9,0,1,1086,40204,16,256,1806,106610,60,3600,627,14381,11,121;QS=2.97127,0.0287253,0;SGB=-0.556633;RPBZ=-1.46267;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.46657;NMBZ=2.63913;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,34,255,48,255,255:17:0:12,0,0:4,1,0:16,1,0 0,21,172,21,172,172:7:0:6,0,0:1,0,0:7,0,0 0,24,235,24,235,235:8:0:4,0,0:4,0,0:8,0,0 +17 512 . A C,<*> 0 . DP=33;ADF=22,0,0;ADR=10,1,0;AD=32,1,0;I16=22,10,0,1,1133,41513,13,169,1866,110210,60,3600,628,14340,9,81;QS=2.97766,0.0223368,0;SGB=-0.556633;RPBZ=-1.47079;MQBZ=0.253876;MQSBZ=-0.461593;BQBZ=-1.68442;NMBZ=2.68627;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255,51,255,255:18:0:12,0,0:5,1,0:17,1,0 0,21,183,21,183,183:7:0:6,0,0:1,0,0:7,0,0 0,24,231,24,231,231:8:0:4,0,0:4,0,0:8,0,0 +17 513 . A T,<*> 0 . DP=32;ADF=21,1,0;ADR=10,0,0;AD=31,1,0;I16=21,10,1,0,1125,42283,12,144,1806,106610,60,3600,623,14249,15,225;QS=2.97966,0.020339,0;SGB=-0.556633;RPBZ=-1.24609;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.57376;NMBZ=2.63913;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,37,255,48,255,255:17:0:11,1,0:5,0,0:16,1,0 0,21,177,21,177,177:7:0:6,0,0:1,0,0:7,0,0 0,24,233,24,233,233:8:0:4,0,0:4,0,0:8,0,0 +17 514 . A T,<*> 0 . DP=32;ADF=22,0,0;ADR=9,1,0;AD=31,1,0;I16=22,9,0,1,1086,40204,16,256,1806,106610,60,3600,627,14381,11,121;QS=2.97127,0.0287253,0;SGB=-0.556633;RPBZ=-1.4628;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.46657;NMBZ=2.63913;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,34,255,48,255,255:17:0:12,0,0:4,1,0:16,1,0 0,21,172,21,172,172:7:0:6,0,0:1,0,0:7,0,0 0,24,235,24,235,235:8:0:4,0,0:4,0,0:8,0,0 17 515 . C <*> 0 . DP=32;ADF=22,0;ADR=10,0;AD=32,0;I16=22,10,0,0,1050,37704,0,0,1866,110210,0,0,638,14554,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:12,0:5,0:17,0 0,21,169:7:0:6,0:1,0:7,0 0,24,211:8:0:4,0:4,0:8,0 17 516 . C <*> 0 . DP=32;ADF=22,0;ADR=10,0;AD=32,0;I16=22,10,0,0,1109,40651,0,0,1866,110210,0,0,637,14579,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:12,0:5,0:17,0 0,21,187:7:0:6,0:1,0:7,0 0,24,215:8:0:4,0:4,0:8,0 17 517 . T <*> 0 . DP=33;ADF=23,0;ADR=10,0;AD=33,0;I16=23,10,0,0,1269,49995,0,0,1926,113810,0,0,636,14626,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:13,0:5,0:18,0 0,21,201:7:0:6,0:1,0:7,0 0,24,242:8:0:4,0:4,0:8,0 @@ -452,7 +452,7 @@ 17 520 . T <*> 0 . DP=36;ADF=25,0;ADR=11,0;AD=36,0;I16=25,11,0,0,1243,45051,0,0,2106,124610,0,0,638,14818,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,63,255:21:0:15,0:6,0:21,0 0,21,180:7:0:6,0:1,0:7,0 0,24,223:8:0:4,0:4,0:8,0 17 521 . C <*> 0 . DP=34;ADF=25,0;ADR=9,0;AD=34,0;I16=25,9,0,0,1281,49527,0,0,1986,117410,0,0,641,14875,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,60,255:20:0:15,0:5,0:20,0 0,21,191:7:0:6,0:1,0:7,0 0,21,204:7:0:4,0:3,0:7,0 17 522 . A <*> 0 . DP=32;ADF=24,0;ADR=8,0;AD=32,0;I16=24,8,0,0,1158,43228,0,0,1897,112969,0,0,646,14960,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,60,255:20:0:15,0:5,0:20,0 0,21,185:7:0:6,0:1,0:7,0 0,15,170:5:0:3,0:2,0:5,0 -17 523 . T G,<*> 0 . DP=32;ADF=23,1,0;ADR=8,0,0;AD=31,1,0;I16=23,8,1,0,1184,45708,15,225,1837,109369,60,3600,626,14446,25,625;QS=2.9794,0.0206044,0;SGB=-0.556633;RPBZ=1.13753;MQBZ=0.179605;MQSBZ=-1.73205;BQBZ=-1.68805;NMBZ=2.89159;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,44,255,57,255,255:20:0:14,1,0:5,0,0:19,1,0 0,21,191,21,191,191:7:0:6,0,0:1,0,0:7,0,0 0,15,166,15,166,166:5:0:3,0,0:2,0,0:5,0,0 +17 523 . T G,<*> 0 . DP=32;ADF=23,1,0;ADR=8,0,0;AD=31,1,0;I16=23,8,1,0,1184,45708,15,225,1837,109369,60,3600,626,14446,25,625;QS=2.9794,0.0206044,0;SGB=-0.556633;RPBZ=1.13742;MQBZ=0.179605;MQSBZ=-1.73205;BQBZ=-1.68805;NMBZ=2.89159;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,44,255,57,255,255:20:0:14,1,0:5,0,0:19,1,0 0,21,191,21,191,191:7:0:6,0,0:1,0,0:7,0,0 0,15,166,15,166,166:5:0:3,0,0:2,0,0:5,0,0 17 524 . T <*> 0 . DP=32;ADF=24,0;ADR=8,0;AD=32,0;I16=24,8,0,0,1096,39618,0,0,1897,112969,0,0,654,15108,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,60,255:20:0:15,0:5,0:20,0 0,21,194:7:0:6,0:1,0:7,0 0,15,150:5:0:3,0:2,0:5,0 17 525 . G <*> 0 . DP=32;ADF=24,0;ADR=8,0;AD=32,0;I16=24,8,0,0,1188,45718,0,0,1897,112969,0,0,656,15120,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,60,255:20:0:15,0:5,0:20,0 0,21,188:7:0:6,0:1,0:7,0 0,15,133:5:0:3,0:2,0:5,0 17 526 . C <*> 0 . DP=32;ADF=24,0;ADR=8,0;AD=32,0;I16=24,8,0,0,1154,44014,0,0,1897,112969,0,0,658,15156,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,60,255:20:0:15,0:5,0:20,0 0,21,185:7:0:6,0:1,0:7,0 0,15,137:5:0:3,0:2,0:5,0 @@ -464,7 +464,7 @@ 17 532 . T <*> 0 . DP=32;ADF=25,0;ADR=7,0;AD=32,0;I16=25,7,0,0,1161,43607,0,0,1897,112969,0,0,649,14477,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:15,0:4,0:19,0 0,21,181:7:0:6,0:1,0:7,0 0,18,192:6:0:4,0:2,0:6,0 17 533 . C <*> 0 . DP=32;ADF=25,0;ADR=7,0;AD=32,0;I16=25,7,0,0,1154,44084,0,0,1897,112969,0,0,644,14274,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:15,0:4,0:19,0 0,21,178:7:0:6,0:1,0:7,0 0,18,180:6:0:4,0:2,0:6,0 17 534 . T <*> 0 . DP=31;ADF=24,0;ADR=7,0;AD=31,0;I16=24,7,0,0,1222,49526,0,0,1837,109369,0,0,640,14104,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:14,0:4,0:18,0 0,21,205:7:0:6,0:1,0:7,0 0,18,205:6:0:4,0:2,0:6,0 -17 535 . A G,<*> 0 . DP=31;ADF=24,0,0;ADR=6,1,0;AD=30,1,0;I16=24,6,0,1,1080,39870,8,64,1777,105769,60,3600,611,13341,25,625;QS=2.98623,0.0137694,0;SGB=-0.556633;RPBZ=-0.894608;MQBZ=0.182574;MQSBZ=-1.85164;BQBZ=-1.6854;NMBZ=2.94255;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,41,255,51,255,255:18:0:14,0,0:3,1,0:17,1,0 0,21,194,21,194,194:7:0:6,0,0:1,0,0:7,0,0 0,18,189,18,189,189:6:0:4,0,0:2,0,0:6,0,0 +17 535 . A G,<*> 0 . DP=31;ADF=24,0,0;ADR=6,1,0;AD=30,1,0;I16=24,6,0,1,1080,39870,8,64,1777,105769,60,3600,611,13341,25,625;QS=2.98623,0.0137694,0;SGB=-0.556633;RPBZ=-0.894788;MQBZ=0.182574;MQSBZ=-1.85164;BQBZ=-1.6854;NMBZ=2.94255;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,41,255,51,255,255:18:0:14,0,0:3,1,0:17,1,0 0,21,194,21,194,194:7:0:6,0,0:1,0,0:7,0,0 0,18,189,18,189,189:6:0:4,0,0:2,0,0:6,0,0 17 536 . C <*> 0 . DP=31;ADF=24,0;ADR=7,0;AD=31,0;I16=24,7,0,0,1095,40551,0,0,1837,109369,0,0,631,13809,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:14,0:4,0:18,0 0,21,184:7:0:6,0:1,0:7,0 0,18,157:6:0:4,0:2,0:6,0 17 537 . C <*> 0 . DP=31;ADF=24,0;ADR=7,0;AD=31,0;I16=24,7,0,0,1049,38677,0,0,1837,109369,0,0,626,13682,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:14,0:4,0:18,0 0,21,172:7:0:6,0:1,0:7,0 0,18,183:6:0:4,0:2,0:6,0 17 538 . A <*> 0 . DP=31;ADF=24,0;ADR=7,0;AD=31,0;I16=24,7,0,0,1138,42478,0,0,1837,109369,0,0,620,13536,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:14,0:4,0:18,0 0,21,189:7:0:6,0:1,0:7,0 0,18,181:6:0:4,0:2,0:6,0 @@ -511,7 +511,7 @@ 17 579 . G <*> 0 . DP=30;ADF=16,0;ADR=14,0;AD=30,0;I16=16,14,0,0,1038,38820,0,0,1769,105241,0,0,523,11335,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:8,0:9,0:17,0 0,24,224:8:0:4,0:4,0:8,0 0,15,144:5:0:4,0:1,0:5,0 17 580 . A C,<*> 0 . DP=30;ADF=15,1,0;ADR=14,0,0;AD=29,1,0;I16=15,14,1,0,1060,39178,16,256,1709,101641,60,3600,510,11078,17,289;QS=2.97338,0.0266223,0;SGB=-0.556633;RPBZ=1.32953;MQBZ=0.185695;MQSBZ=-1.06904;BQBZ=-1.69093;NMBZ=1.86885;SCBZ=-0.267102;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,34,255,48,255,255:17:0:7,1,0:9,0,0:16,1,0 0,24,221,24,221,221:8:0:4,0,0:4,0,0:8,0,0 0,15,155,15,155,155:5:0:4,0,0:1,0,0:5,0,0 17 581 . A <*> 0 . DP=31;ADF=16,0;ADR=15,0;AD=31,0;I16=16,15,0,0,1083,39215,0,0,1829,108841,0,0,530,11384,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:8,0:10,0:18,0 0,24,223:8:0:4,0:4,0:8,0 0,15,153:5:0:4,0:1,0:5,0 -17 582 . C G,<*> 0 . DP=31;ADF=15,1,0;ADR=15,0,0;AD=30,1,0;I16=15,15,1,0,1080,39870,8,64,1769,105241,60,3600,519,11211,15,225;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.34245;MQBZ=0.182574;MQSBZ=-1.0328;BQBZ=-1.68266;NMBZ=1.92049;SCBZ=-0.262467;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,41,255,51,255,255:18:0:7,1,0:10,0,0:17,1,0 0,24,207,24,207,207:8:0:4,0,0:4,0,0:8,0,0 0,15,151,15,151,151:5:0:4,0,0:1,0,0:5,0,0 +17 582 . C G,<*> 0 . DP=31;ADF=15,1,0;ADR=15,0,0;AD=30,1,0;I16=15,15,1,0,1080,39870,8,64,1769,105241,60,3600,519,11211,15,225;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.34259;MQBZ=0.182574;MQSBZ=-1.0328;BQBZ=-1.68266;NMBZ=1.92049;SCBZ=-0.262467;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,41,255,51,255,255:18:0:7,1,0:10,0,0:17,1,0 0,24,207,24,207,207:8:0:4,0,0:4,0,0:8,0,0 0,15,151,15,151,151:5:0:4,0,0:1,0,0:5,0,0 17 583 . T <*> 0 . DP=30;ADF=16,0;ADR=14,0;AD=30,0;I16=16,14,0,0,1135,43913,0,0,1769,105241,0,0,539,11523,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:8,0:9,0:17,0 0,24,238:8:0:4,0:4,0:8,0 0,15,163:5:0:4,0:1,0:5,0 17 584 . C <*> 0 . DP=31;ADF=17,0;ADR=14,0;AD=31,0;I16=17,14,0,0,1069,39521,0,0,1798,106082,0,0,544,11644,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:9,0:9,0:18,0 0,24,209:8:0:4,0:4,0:8,0 0,15,157:5:0:4,0:1,0:5,0 17 585 . A <*> 0 . DP=31;ADF=17,0;ADR=14,0;AD=31,0;I16=17,14,0,0,1096,39866,0,0,1798,106082,0,0,549,11751,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:9,0:9,0:18,0 0,24,211:8:0:4,0:4,0:8,0 0,15,157:5:0:4,0:1,0:5,0 @@ -522,10 +522,10 @@ 17 590 . C <*> 0 . DP=32;ADF=17,0;ADR=15,0;AD=32,0;I16=17,15,0,0,1103,41355,0,0,1858,109682,0,0,574,12576,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:9,0:9,0:18,0 0,24,194:8:0:4,0:4,0:8,0 0,18,175:6:0:4,0:2,0:6,0 17 591 . A <*> 0 . DP=31;ADF=16,0;ADR=15,0;AD=31,0;I16=16,15,0,0,1164,44088,0,0,1798,106082,0,0,579,12695,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:9,0:9,0:18,0 0,21,209:7:0:3,0:4,0:7,0 0,18,188:6:0:4,0:2,0:6,0 17 592 . A <*> 0 . DP=31;ADF=16,0;ADR=15,0;AD=31,0;I16=16,15,0,0,1121,42193,0,0,1798,106082,0,0,583,12795,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:9,0:9,0:18,0 0,21,215:7:0:3,0:4,0:7,0 0,18,182:6:0:4,0:2,0:6,0 -17 593 . C A,<*> 0 . DP=31;ADF=16,0,0;ADR=14,1,0;AD=30,1,0;I16=16,14,0,1,1071,39925,7,49,1769,105241,29,841,561,12253,25,625;QS=2.97021,0.0297872,0;SGB=-0.556633;RPBZ=0.559412;MQBZ=-3.80789;MQSBZ=-0.0464238;BQBZ=-1.57464;NMBZ=2.13779;SCBZ=3.67454;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255,54,255,255:18:0:9,0,0:9,0,0:18,0,0 0,12,184,18,187,185:7:0:3,0,0:3,1,0:6,1,0 0,18,174,18,174,174:6:0:4,0,0:2,0,0:6,0,0 +17 593 . C A,<*> 0 . DP=31;ADF=16,0,0;ADR=14,1,0;AD=30,1,0;I16=16,14,0,1,1071,39925,7,49,1769,105241,29,841,561,12253,25,625;QS=2.97021,0.0297872,0;SGB=-0.556633;RPBZ=0.559355;MQBZ=-3.80789;MQSBZ=-0.0464238;BQBZ=-1.57464;NMBZ=2.13779;SCBZ=3.67454;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255,54,255,255:18:0:9,0,0:9,0,0:18,0,0 0,12,184,18,187,185:7:0:3,0,0:3,1,0:6,1,0 0,18,174,18,174,174:6:0:4,0,0:2,0,0:6,0,0 17 594 . A G,<*> 0 . DP=33;ADF=16,1,0;ADR=16,0,0;AD=32,1,0;I16=16,16,1,0,1161,42757,4,16,1858,109682,60,3600,572,12672,15,225;QS=2.99359,0.00641026,0;SGB=-0.556633;RPBZ=-0.998367;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68954;NMBZ=1.76408;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,42,255,51,255,255:18:0:8,1,0:9,0,0:17,1,0 0,21,205,21,205,205:7:0:3,0,0:4,0,0:7,0,0 0,24,213,24,213,213:8:0:5,0,0:3,0,0:8,0,0 17 595 . A <*> 0 . DP=33;ADF=17,0;ADR=16,0;AD=33,0;I16=17,16,0,0,1136,40412,0,0,1918,113282,0,0,589,12905,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:9,0:9,0:18,0 0,21,198:7:0:3,0:4,0:7,0 0,24,218:8:0:5,0:3,0:8,0 -17 596 . A G,<*> 0 . DP=33;ADF=16,1,0;ADR=16,0,0;AD=32,1,0;I16=16,16,1,0,1061,37187,8,64,1858,109682,60,3600,590,12952,1,1;QS=2.98564,0.0143627,0;SGB=-0.556633;RPBZ=1.68132;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68357;NMBZ=1.61602;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,41,255,51,255,255:18:0:8,1,0:9,0,0:17,1,0 0,21,169,21,169,169:7:0:3,0,0:4,0,0:7,0,0 0,24,231,24,231,231:8:0:5,0,0:3,0,0:8,0,0 +17 596 . A G,<*> 0 . DP=33;ADF=16,1,0;ADR=16,0,0;AD=32,1,0;I16=16,16,1,0,1061,37187,8,64,1858,109682,60,3600,590,12952,1,1;QS=2.98564,0.0143627,0;SGB=-0.556633;RPBZ=1.68146;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68357;NMBZ=1.61602;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,41,255,51,255,255:18:0:8,1,0:9,0,0:17,1,0 0,21,169,21,169,169:7:0:3,0,0:4,0,0:7,0,0 0,24,231,24,231,231:8:0:5,0,0:3,0,0:8,0,0 17 597 . C <*> 0 . DP=33;ADF=17,0;ADR=16,0;AD=33,0;I16=17,16,0,0,1196,44890,0,0,1918,113282,0,0,592,12990,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:9,0:9,0:18,0 0,21,204:7:0:3,0:4,0:7,0 0,24,220:8:0:5,0:3,0:8,0 17 598 . T <*> 0 . DP=33;ADF=16,0;ADR=17,0;AD=33,0;I16=16,17,0,0,1219,47333,0,0,1918,113282,0,0,597,13029,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:8,0:9,0:17,0 0,21,217:7:0:3,0:4,0:7,0 0,27,242:9:0:5,0:4,0:9,0 17 599 . T <*> 0 . DP=33;ADF=16,0;ADR=17,0;AD=33,0;I16=16,17,0,0,1182,43598,0,0,1918,113282,0,0,599,13095,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:8,0:9,0:17,0 0,21,197:7:0:3,0:4,0:7,0 0,27,247:9:0:5,0:4,0:9,0 diff --git a/test/mpileup/mpileup.6.out b/test/mpileup/mpileup.6.out index 9b4cef2dc..7f43c300c 100644 --- a/test/mpileup/mpileup.6.out +++ b/test/mpileup/mpileup.6.out @@ -26,7 +26,7 @@ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00100 HG00101 HG00102 17 100 . C <*> . . END=102;MinDP=3;QS=3,0 PL:DP 0,27,182:9 0,9,108:3 0,15,132:5 17 103 . T C,<*> 0 . DP=18;I16=15,1,1,0,668,28542,6,36,929,54841,29,841,323,7035,6,36;QS=2.98256,0.0174419,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64924;NMBZ=2.45514;SCBZ=4;FS=0;MQ0F=0 PL:DP:DV 0,17,184,24,187,185:9:1 0,9,118,9,118,118:3:0 0,15,147,15,147,147:5:0 -17 104 . G C,<*> 0 . DP=18;I16=15,1,1,0,601,24163,3,9,929,54841,29,841,320,6884,7,49;QS=2.98726,0.0127389,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64309;NMBZ=2.45514;SCBZ=2.91548;FS=0;MQ0F=0 PL:DP:DV 0,18,173,24,176,173:9:1 0,9,101,9,101,101:3:0 0,15,133,15,133,133:5:0 +17 104 . G C,<*> 0 . DP=18;I16=15,1,1,0,601,24163,3,9,929,54841,29,841,320,6884,7,49;QS=2.98726,0.0127389,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64309;NMBZ=2.45514;SCBZ=4;FS=0;MQ0F=0 PL:DP:DV 0,18,173,24,176,173:9:1 0,9,101,9,101,101:3:0 0,15,133,15,133,133:5:0 17 105 . G <*> . . END=108;MinDP=3;QS=3,0 PL:DP 0,30,171:10 0,9,92:3 0,15,124:5 17 109 . T C,<*> 0 . DP=19;I16=16,1,1,0,716,30648,2,4,989,58441,29,841,309,6415,12,144;QS=2.98922,0.0107817,0;SGB=-0.556633;RPBZ=-0.674966;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.6661;NMBZ=2.52179;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV 0,20,191,27,194,191:10:1 0,9,120,9,120,120:3:0 0,15,150,15,150,150:5:0 17 110 . G <*> . . END=111;MinDP=3;QS=3,0 PL:DP 0,30,167:10 0,9,95:3 0,15,119:5 @@ -40,65 +40,65 @@ 17 121 . G <*> . . END=124;MinDP=2;QS=3,0 PL:DP 0,24,170:8 0,6,84:2 0,18,154:6 17 125 . A T,<*> 0 . DP=18;I16=14,2,1,0,589,22565,4,16,898,52082,29,841,272,5916,25,625;QS=2.98444,0.0155642,0;SGB=-0.556633;RPBZ=1.02125;MQBZ=-2.16025;MQSBZ=-1.23956;BQBZ=-1.64106;NMBZ=2.91548;SCBZ=2.91548;FS=0;MQ0F=0 PL:DP:DV 0,15,149,21,152,149:8:1 0,9,114,9,114,114:3:0 0,18,162,18,162,162:6:0 17 126 . A <*> . . END=158;MinDP=2;QS=3,0 PL:DP 0,18,128:6 0,6,81:2 0,15,102:5 -17 159 . A G,<*> 0 . DP=15;I16=12,2,1,0,519,19467,5,25,809,47641,60,3600,260,5880,0,0;QS=2.97076,0.0292398,0;SGB=-0.556633;RPBZ=-1.62163;MQBZ=0.267261;MQSBZ=-2.54951;BQBZ=-1.63041;NMBZ=0;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,21,157,21,157,157:7:0 0,6,83,6,83,83:2:0 0,10,129,15,132,129:6:1 +17 159 . A G,<*> 0 . DP=15;I16=12,2,1,0,519,19467,5,25,809,47641,60,3600,260,5880,0,0;QS=2.97076,0.0292398,0;SGB=-0.556633;RPBZ=-1.62019;MQBZ=0.267261;MQSBZ=-2.54951;BQBZ=-1.63041;NMBZ=0;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,21,157,21,157,157:7:0 0,6,83,6,83,83:2:0 0,10,129,15,132,129:6:1 17 160 . G <*> . . END=173;MinDP=2;QS=3,0 PL:DP 0,15,106:5 0,6,75:2 0,15,138:5 17 174 . G <*> . . END=188;MinDP=1;QS=3,0 PL:DP 0,15,111:5 0,3,27:1 0,21,116:7 17 189 . C <*> . . MinDP=2;QS=3,0 PL:DP 0,18,152:6 0,6,67:2 0,21,167:7 17 190 . A C,<*> 0 . DP=15;I16=12,2,1,0,500,18230,5,25,778,44882,60,3600,243,5381,25,625;QS=2.97664,0.0233645,0;SGB=-0.556633;RPBZ=0;MQBZ=0.392232;MQSBZ=-3.74166;BQBZ=-1.63041;NMBZ=-0.267261;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,18,138,18,138,138:6:0 0,6,68,6,68,68:2:0 0,12,153,18,156,153:7:1 17 191 . T <*> . . END=222;MinDP=2;QS=3,0 PL:DP 0,18,140:6 0,6,63:2 0,12,73:4 -17 223 . G T,<*> 0 . DP=13;I16=9,3,1,0,412,14782,8,64,627,34923,60,3600,243,5657,25,625;QS=2.96596,0.0340426,0;SGB=-0.556633;RPBZ=1.06904;MQBZ=0.547723;MQSBZ=-3.4641;BQBZ=-1.60577;NMBZ=-0.288675;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,11,166,18,169,167:7:1 0,6,53,6,53,53:2:0 0,12,81,12,81,81:4:0 +17 223 . G T,<*> 0 . DP=13;I16=9,3,1,0,412,14782,8,64,627,34923,60,3600,243,5657,25,625;QS=2.96596,0.0340426,0;SGB=-0.556633;RPBZ=1.07052;MQBZ=0.547723;MQSBZ=-3.4641;BQBZ=-1.60577;NMBZ=-0.288675;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,11,166,18,169,167:7:1 0,6,53,6,53,53:2:0 0,12,81,12,81,81:4:0 17 224 . G <*> . . END=225;MinDP=2;QS=3,0 PL:DP 0,18,165:6 0,6,48:2 0,12,70:4 -17 226 . A G,C,<*> 0 . DP=13;I16=8,3,1,1,381,13669,6,18,567,31323,89,4441,248,5894,44,986;QS=2.94293,0.0392157,0.0178571,0;VDB=0.84;SGB=-2.62246;RPBZ=-0.592972;MQBZ=-0.615457;MQSBZ=-3.4641;BQBZ=-2.17723;NMBZ=2.34521;SCBZ=2.34521;FS=0;MQ0F=0 PL:DP:DV 0,18,159,12,162,159,18,159,162,159:7:1 0,6,53,6,53,53,6,53,53,53:2:0 0,5,79,9,82,80,9,82,80,80:4:1 +17 226 . A G,C,<*> 0 . DP=13;I16=8,3,1,1,381,13669,6,18,567,31323,89,4441,248,5894,44,986;QS=2.94293,0.0392157,0.0178571,0;VDB=0.84;SGB=-2.62246;RPBZ=-0.592157;MQBZ=-0.615457;MQSBZ=-3.4641;BQBZ=-2.17723;NMBZ=2.34521;SCBZ=2.34521;FS=0;MQ0F=0 PL:DP:DV 0,18,159,12,162,159,18,159,162,159:7:1 0,6,53,6,53,53,6,53,53,53:2:0 0,5,79,9,82,80,9,82,80,80:4:1 17 227 . C <*> . . END=236;MinDP=2;QS=3,0 PL:DP 0,21,145:7 0,6,45:2 0,12,70:4 17 237 . A C,<*> 0 . DP=14;I16=9,4,1,0,465,16877,8,64,656,35764,60,3600,266,6282,25,625;QS=2.93162,0.0683761,0;SGB=-0.556633;RPBZ=1.11754;MQBZ=0.632456;MQSBZ=-3.60555;BQBZ=-1.61959;NMBZ=-0.27735;SCBZ=-0.27735;FS=0;MQ0F=0 PL:DP:DV 0,24,206,24,206,206:8:0 0,6,53,6,53,53:2:0 0,3,84,9,87,87:4:1 17 238 . C <*> . . END=255;MinDP=2;QS=3,0 PL:DP 0,24,211:8 0,6,50:2 0,12,64:4 17 256 . A <*> . . END=266;MinDP=5;QS=3,0 PL:DP 0,33,247:11 0,15,92:5 0,15,122:5 -17 267 . T G,<*> 0 . DP=21;I16=9,11,0,1,739,27465,8,64,960,50456,29,841,373,7935,25,625;QS=2.94203,0.057971,0;SGB=-0.556633;RPBZ=-0.330504;MQBZ=-1.23153;MQSBZ=-3.3021;BQBZ=-1.66282;NMBZ=2.4409;SCBZ=2.91633;FS=0;MQ0F=0 PL:DP:DV 0,33,254,33,254,254:11:0 0,6,93,12,96,96:5:1 0,15,149,15,149,149:5:0 +17 267 . T G,<*> 0 . DP=21;I16=9,11,0,1,739,27465,8,64,960,50456,29,841,373,7935,25,625;QS=2.94203,0.057971,0;SGB=-0.556633;RPBZ=-0.330396;MQBZ=-1.23153;MQSBZ=-3.3021;BQBZ=-1.66282;NMBZ=2.4409;SCBZ=2.91633;FS=0;MQ0F=0 PL:DP:DV 0,33,254,33,254,254:11:0 0,6,93,12,96,96:5:1 0,15,149,15,149,149:5:0 17 268 . T <*> . . END=272;MinDP=5;QS=3,0 PL:DP 0,33,238:11 0,15,91:5 0,15,143:5 17 273 . T C,<*> 0 . DP=22;I16=9,12,0,1,798,30664,5,25,989,51297,29,841,392,8620,25,625;QS=2.96094,0.0390625,0;SGB=-0.556633;RPBZ=-0.236567;MQBZ=-1.16701;MQSBZ=-3.42286;BQBZ=-1.66779;NMBZ=2.50862;SCBZ=3.00076;FS=0;MQ0F=0 PL:DP:DV 0,36,255,36,255,255:12:0 0,7,89,12,92,90:5:1 0,15,161,15,161,161:5:0 17 274 . C <*> . . MinDP=5;QS=3,0 PL:DP 0,36,255:12 0,15,101:5 0,15,144:5 17 275 . C <*> . . END=277;MinDP=4;QS=3,0 PL:DP 0,33,253:11 0,15,114:5 0,12,121:4 -17 278 . A C,<*> 0 . DP=21;I16=6,14,1,0,722,26452,7,49,867,42179,60,3600,415,9521,11,121;QS=2.97935,0.020649,0;SGB=-0.556633;RPBZ=1.56989;MQBZ=1.0247;MQSBZ=-3.24037;BQBZ=-1.66667;NMBZ=-0.406816;SCBZ=-0.324037;FS=0;MQ0F=0 PL:DP:DV 0,22,231,30,234,231:11:1 0,18,123,18,123,123:6:0 0,12,121,12,121,121:4:0 +17 278 . A C,<*> 0 . DP=21;I16=6,14,1,0,722,26452,7,49,867,42179,60,3600,415,9521,11,121;QS=2.97935,0.020649,0;SGB=-0.556633;RPBZ=1.65198;MQBZ=1.0247;MQSBZ=-3.24037;BQBZ=-1.66667;NMBZ=-0.406816;SCBZ=-0.324037;FS=0;MQ0F=0 PL:DP:DV 0,22,231,30,234,231:11:1 0,18,123,18,123,123:6:0 0,12,121,12,121,121:4:0 17 279 . A <*> . . END=282;MinDP=4;QS=3,0 PL:DP 0,36,253:12 0,18,122:6 0,12,119:4 17 283 . C <*> . . END=296;MinDP=5;QS=3,0 PL:DP 0,33,240:11 0,18,119:6 0,15,122:5 17 297 . C G,<*> 0 . DP=25;I16=9,15,1,0,901,34305,4,16,1138,59338,60,3600,445,9901,10,100;QS=2.98261,0.0173913,0;SGB=-0.556633;RPBZ=-1.24856;MQBZ=0.806872;MQSBZ=-3.22749;BQBZ=-1.67542;NMBZ=-0.434372;SCBZ=-0.368383;FS=0;MQ0F=0 PL:DP:DV 0,33,255,33,255,255:11:0 0,15,168,21,171,168:8:1 0,18,161,18,161,161:6:0 17 298 . A <*> . . END=301;MinDP=7;QS=3,0 PL:DP 0,30,231:10 0,21,172:7 0,21,189:7 -17 302 . T TA 0 . INDEL;IDV=7;IMF=1;DP=25;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.539485,2.46052;VDB=0.260546;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.22749;BQBZ=-1.67542;NMBZ=-0.199304;SCBZ=-0.268121;FS=0;MQ0F=0 PL:DP:DV 161,0,99:11:6 158,0,14:7:6 201,21,0:7:7 +17 302 . T TA 0 . INDEL;IDV=7;IMF=1;DP=25;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.539485,2.46052;VDB=0.241622;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.22749;BQBZ=-1.67542;NMBZ=-0.199304;SCBZ=-0.268121;FS=0;MQ0F=0 PL:DP:DV 161,0,99:11:6 158,0,14:7:6 201,21,0:7:7 17 303 . G <*> . . END=334;MinDP=7;QS=3,0 PL:DP 0,30,235:10 0,21,197:7 0,21,195:7 -17 335 . A G,<*> 0 . DP=32;I16=13,18,1,0,1084,40336,4,16,1589,87297,60,3600,555,11943,0,0;QS=2.98919,0.0108108,0;SGB=-0.556633;RPBZ=-1.67921;MQBZ=0.622171;MQSBZ=-2.25492;BQBZ=-1.68602;NMBZ=-0.428353;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV 0,33,252,33,252,252:11:0 0,27,219,27,219,219:9:0 0,25,245,33,248,245:12:1 +17 335 . A G,<*> 0 . DP=32;I16=13,18,1,0,1084,40336,4,16,1589,87297,60,3600,555,11943,0,0;QS=2.98919,0.0108108,0;SGB=-0.556633;RPBZ=-1.67936;MQBZ=0.622171;MQSBZ=-2.25492;BQBZ=-1.68602;NMBZ=-0.428353;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV 0,33,252,33,252,252:11:0 0,27,219,27,219,219:9:0 0,25,245,33,248,245:12:1 17 336 . A <*> . . MinDP=9;QS=3,0 PL:DP 0,33,255:11 0,27,212:9 0,36,255:12 -17 337 . C A,<*> 0 . DP=32;I16=14,17,0,1,1125,42481,5,25,1612,89528,37,1369,536,11590,18,324;QS=2.98113,0.0188679,0;SGB=-0.556633;RPBZ=0.812519;MQBZ=-1.03695;MQSBZ=-2.25492;BQBZ=-1.68353;NMBZ=-0.376914;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV 0,33,255,33,255,255:11:0 0,17,195,24,198,195:9:1 0,36,255,36,255,255:12:0 +17 337 . C A,<*> 0 . DP=32;I16=14,17,0,1,1125,42481,5,25,1612,89528,37,1369,536,11590,18,324;QS=2.98113,0.0188679,0;SGB=-0.556633;RPBZ=0.812593;MQBZ=-1.03695;MQSBZ=-2.25492;BQBZ=-1.68353;NMBZ=-0.376914;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV 0,33,255,33,255,255:11:0 0,17,195,24,198,195:9:1 0,36,255,36,255,255:12:0 17 338 . T <*> . . END=354;MinDP=8;QS=3,0 PL:DP 0,27,225:9 0,24,185:8 0,30,255:10 17 355 . G T,<*> 0 . DP=28;I16=14,13,0,1,1001,37907,41,1681,1442,81174,60,3600,547,12487,25,625;QS=2.875,0.125,0;SGB=-0.556633;RPBZ=0.185772;MQBZ=0.520126;MQSBZ=-1.7696;BQBZ=0.683978;NMBZ=2.33874;SCBZ=-0.27735;FS=0;MQ0F=0 PL:DP:DV 14,0,200,38,203,231:9:1 0,27,222,27,222,222:9:0 0,30,255,30,255,255:10:0 17 356 . G <*> . . END=358;MinDP=8;QS=3,0 PL:DP 0,27,228:9 0,24,197:8 0,30,252:10 -17 359 . G T,<*> 0 . DP=29;I16=15,13,0,1,1085,42761,10,100,1525,87005,60,3600,552,12620,25,625;QS=2.96032,0.0396825,0;SGB=-0.556633;RPBZ=-0.119567;MQBZ=0.456435;MQSBZ=-1.53333;BQBZ=-1.68246;NMBZ=3.0531;SCBZ=5.2915;FS=0;MQ0F=0 PL:DP:DV 0,30,255,30,255,255:10:0 0,13,178,21,181,180:8:1 0,33,255,33,255,255:11:0 +17 359 . G T,<*> 0 . DP=29;I16=15,13,0,1,1085,42761,10,100,1525,87005,60,3600,552,12620,25,625;QS=2.96032,0.0396825,0;SGB=-0.556633;RPBZ=-0.119611;MQBZ=0.456435;MQSBZ=-1.53333;BQBZ=-1.68246;NMBZ=3.0531;SCBZ=5.2915;FS=0;MQ0F=0 PL:DP:DV 0,30,255,30,255,255:10:0 0,13,178,21,181,180:8:1 0,33,255,33,255,255:11:0 17 360 . A <*> . . END=368;MinDP=8;QS=3,0 PL:DP 0,30,252:10 0,24,204:8 0,30,255:10 -17 369 . T G,<*> 0 . DP=28;I16=16,11,0,1,1037,40275,6,36,1496,86164,60,3600,548,12256,25,625;QS=2.97683,0.023166,0;SGB=-0.556633;RPBZ=0.123865;MQBZ=0.408248;MQSBZ=-1.37784;BQBZ=-1.68703;NMBZ=2.99794;SCBZ=5.19615;FS=0;MQ0F=0 PL:DP:DV 0,30,250,30,250,250:10:0 0,15,189,21,192,190:8:1 0,30,255,30,255,255:10:0 +17 369 . T G,<*> 0 . DP=28;I16=16,11,0,1,1037,40275,6,36,1496,86164,60,3600,548,12256,25,625;QS=2.97683,0.023166,0;SGB=-0.556633;RPBZ=0.12395;MQBZ=0.408248;MQSBZ=-1.37784;BQBZ=-1.68703;NMBZ=2.99794;SCBZ=5.19615;FS=0;MQ0F=0 PL:DP:DV 0,30,250,30,250,250:10:0 0,15,189,21,192,190:8:1 0,30,255,30,255,255:10:0 17 370 . C <*> . . END=374;MinDP=8;QS=3,0 PL:DP 0,30,255:10 0,24,201:8 0,30,255:10 -17 375 . A T,<*> 0 . DP=31;I16=17,13,0,1,1138,43798,14,196,1676,96964,60,3600,547,12177,4,16;QS=2.9661,0.0338983,0;SGB=-0.556633;RPBZ=-1.45462;MQBZ=0.3849;MQSBZ=-1.26404;BQBZ=-1.68488;NMBZ=2.30253;SCBZ=-0.182574;FS=0;MQ0F=0 PL:DP:DV 0,36,255,36,255,255:12:0 0,24,218,24,218,218:8:0 0,18,255,30,255,255:11:1 +17 375 . A T,<*> 0 . DP=31;I16=17,13,0,1,1138,43798,14,196,1676,96964,60,3600,547,12177,4,16;QS=2.9661,0.0338983,0;SGB=-0.556633;RPBZ=-1.45432;MQBZ=0.3849;MQSBZ=-1.26404;BQBZ=-1.68488;NMBZ=2.30253;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,36,255,36,255,255:12:0 0,24,218,24,218,218:8:0 0,18,255,30,255,255:11:1 17 376 . G <*> . . END=383;MinDP=7;QS=3,0 PL:DP 0,36,255:12 0,21,172:7 0,30,255:10 -17 384 . A C,<*> 0 . DP=31;I16=19,11,0,1,1077,39885,4,16,1738,102482,60,3600,504,10988,25,625;QS=2.98419,0.0158103,0;SGB=-0.556633;RPBZ=0.615415;MQBZ=0.262613;MQSBZ=-0.333409;BQBZ=-1.68746;NMBZ=3.26825;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,39,255,39,255,255:13:0 0,15,171,21,174,171:8:1 0,30,255,30,255,255:10:0 +17 384 . A C,<*> 0 . DP=31;I16=19,11,0,1,1077,39885,4,16,1738,102482,60,3600,504,10988,25,625;QS=2.98419,0.0158103,0;SGB=-0.556633;RPBZ=0.615229;MQBZ=0.262613;MQSBZ=-0.333409;BQBZ=-1.68746;NMBZ=3.26825;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,39,255,39,255,255:13:0 0,15,171,21,174,171:8:1 0,30,255,30,255,255:10:0 17 385 . C <*> . . END=400;MinDP=5;QS=3,0 PL:DP 0,36,255:12 0,15,133:5 0,30,255:10 17 401 . A C,<*> 0 . DP=29;I16=17,11,0,1,1063,41001,8,64,1587,92523,60,3600,501,11113,25,625;QS=2.97985,0.0201511,0;SGB=-0.556633;RPBZ=-0.478622;MQBZ=0.339683;MQSBZ=0.29364;BQBZ=-1.68267;NMBZ=3.53589;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,39,255,39,255,255:13:0 0,15,160,15,160,160:5:0 0,22,255,30,255,255:11:1 17 402 . T <*> . . END=404;MinDP=5;QS=3,0 PL:DP 0,39,255:13 0,15,131:5 0,33,255:11 17 405 . T <*> . . END=411;MinDP=4;QS=3,0 PL:DP 0,39,255:13 0,12,109:4 0,30,244:10 -17 412 . C T,<*> 0 . DP=30;I16=17,12,1,0,1094,42458,14,196,1678,98882,60,3600,495,10659,25,625;QS=2.97455,0.0254545,0;SGB=-0.556633;RPBZ=-0.404685;MQBZ=0.267261;MQSBZ=-0.293785;BQBZ=-1.6942;NMBZ=-0.267102;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,30,255,42,255,255:15:1 0,12,124,12,124,124:4:0 0,33,255,33,255,255:11:0 +17 412 . C T,<*> 0 . DP=30;I16=17,12,1,0,1094,42458,14,196,1678,98882,60,3600,495,10659,25,625;QS=2.97455,0.0254545,0;SGB=-0.556633;RPBZ=-0.40473;MQBZ=0.267261;MQSBZ=-0.293785;BQBZ=-1.6942;NMBZ=-0.267102;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,30,255,42,255,255:15:1 0,12,124,12,124,124:4:0 0,33,255,33,255,255:11:0 17 413 . A <*> . . END=436;MinDP=3;QS=3,0 PL:DP 0,45,255:15 0,9,98:3 0,27,223:9 -17 437 . T G,<*> 0 . DP=28;I16=13,14,1,0,990,36832,6,36,1558,91682,29,841,549,12435,16,256;QS=2.9781,0.0218978,0;SGB=-0.556633;RPBZ=-1.36195;MQBZ=-2.88675;MQSBZ=0.6;BQBZ=-1.67909;NMBZ=-0.19245;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,48,255,48,255,255:16:0 0,9,109,9,109,109:3:0 0,17,200,24,203,201:9:1 +17 437 . T G,<*> 0 . DP=28;I16=13,14,1,0,990,36832,6,36,1558,91682,29,841,549,12435,16,256;QS=2.9781,0.0218978,0;SGB=-0.556633;RPBZ=-1.36214;MQBZ=-2.88675;MQSBZ=0.6;BQBZ=-1.67909;NMBZ=-0.19245;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,48,255,48,255,255:16:0 0,9,109,9,109,109:3:0 0,17,200,24,203,201:9:1 17 438 . A <*> . . END=464;MinDP=2;QS=3,0 PL:DP 0,48,255:16 0,6,97:2 0,27,198:9 -17 465 . C T,<*> 0 . DP=33;I16=19,12,0,1,1173,45601,4,16,1775,103851,60,3600,589,12909,6,36;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.67936;MQBZ=0.321288;MQSBZ=0.341466;BQBZ=-1.68493;NMBZ=3.21288;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,51,255,51,255,255:17:0 0,15,158,15,158,158:5:0 0,20,224,27,227,224:10:1 +17 465 . C T,<*> 0 . DP=33;I16=19,12,0,1,1173,45601,4,16,1775,103851,60,3600,589,12909,6,36;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.67982;MQBZ=0.321288;MQSBZ=0.341466;BQBZ=-1.68493;NMBZ=3.21288;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,51,255,51,255,255:17:0 0,15,158,15,158,158:5:0 0,20,224,27,227,224:10:1 17 466 . A <*> . . END=470;MinDP=5;QS=3,0 PL:DP 0,54,255:18 0,15,165:5 0,30,238:10 17 471 . T G,C,<*> 0 . DP=36;I16=21,12,0,2,1220,46380,18,162,1918,113282,97,4969,611,13281,16,256;QS=2.94529,0.0273556,0.0273556,0;VDB=0.96;SGB=0.346553;RPBZ=0.497712;MQBZ=-1.9761;MQSBZ=0.312094;BQBZ=-2.35032;NMBZ=2.19566;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,57,255,57,255,255,57,255,255,255:19:0 0,15,169,15,169,169,15,169,169,169:5:0 0,19,219,19,221,219,27,222,222,221:11:2 17 472 . T <*> . . END=487;MinDP=5;QS=3,0 PL:DP 0,51,255:17 0,15,146:5 0,30,241:10 -17 488 . A G,<*> 0 . DP=35;I16=22,12,1,0,1278,48412,4,16,1986,117410,29,841,646,14380,25,625;QS=2.98947,0.0105263,0;SGB=-0.556633;RPBZ=0.544734;MQBZ=-3.36505;MQSBZ=0.10737;BQBZ=-1.69552;NMBZ=-0.171499;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,54,255,54,255,255:18:0 0,18,177,18,177,177:6:0 0,23,255,30,255,255:11:1 +17 488 . A G,<*> 0 . DP=35;I16=22,12,1,0,1278,48412,4,16,1986,117410,29,841,646,14380,25,625;QS=2.98947,0.0105263,0;SGB=-0.556633;RPBZ=0.594463;MQBZ=-3.36505;MQSBZ=0.10737;BQBZ=-1.69552;NMBZ=-0.171499;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,54,255,54,255,255:18:0 0,18,177,18,177,177:6:0 0,23,255,30,255,255:11:1 17 489 . A <*> . . END=511;MinDP=6;QS=3,0 PL:DP 0,51,255:17 0,18,175:6 0,24,221:8 -17 512 . A C,<*> 0 . DP=33;I16=22,10,0,1,1133,41513,13,169,1866,110210,60,3600,628,14340,9,81;QS=2.97766,0.0223368,0;SGB=-0.556633;RPBZ=-1.47091;MQBZ=0.253876;MQSBZ=-0.461593;BQBZ=-1.68442;NMBZ=2.68627;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,39,255,51,255,255:18:1 0,21,183,21,183,183:7:0 0,24,231,24,231,231:8:0 -17 513 . A T,<*> 0 . DP=32;I16=21,10,1,0,1125,42283,12,144,1806,106610,60,3600,623,14249,15,225;QS=2.97966,0.020339,0;SGB=-0.556633;RPBZ=-1.24598;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.57376;NMBZ=2.63913;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,37,255,48,255,255:17:1 0,21,177,21,177,177:7:0 0,24,233,24,233,233:8:0 -17 514 . A T,<*> 0 . DP=32;I16=22,9,0,1,1086,40204,16,256,1806,106610,60,3600,627,14381,11,121;QS=2.97127,0.0287253,0;SGB=-0.556633;RPBZ=-1.46267;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.46657;NMBZ=2.63913;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,34,255,48,255,255:17:1 0,21,172,21,172,172:7:0 0,24,235,24,235,235:8:0 +17 512 . A C,<*> 0 . DP=33;I16=22,10,0,1,1133,41513,13,169,1866,110210,60,3600,628,14340,9,81;QS=2.97766,0.0223368,0;SGB=-0.556633;RPBZ=-1.47079;MQBZ=0.253876;MQSBZ=-0.461593;BQBZ=-1.68442;NMBZ=2.68627;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,39,255,51,255,255:18:1 0,21,183,21,183,183:7:0 0,24,231,24,231,231:8:0 +17 513 . A T,<*> 0 . DP=32;I16=21,10,1,0,1125,42283,12,144,1806,106610,60,3600,623,14249,15,225;QS=2.97966,0.020339,0;SGB=-0.556633;RPBZ=-1.24609;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.57376;NMBZ=2.63913;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,37,255,48,255,255:17:1 0,21,177,21,177,177:7:0 0,24,233,24,233,233:8:0 +17 514 . A T,<*> 0 . DP=32;I16=22,9,0,1,1086,40204,16,256,1806,106610,60,3600,627,14381,11,121;QS=2.97127,0.0287253,0;SGB=-0.556633;RPBZ=-1.4628;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.46657;NMBZ=2.63913;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,34,255,48,255,255:17:1 0,21,172,21,172,172:7:0 0,24,235,24,235,235:8:0 17 515 . C <*> . . END=522;MinDP=5;QS=3,0 PL:DP 0,51,255:17 0,21,169:7 0,15,170:5 -17 523 . T G,<*> 0 . DP=32;I16=23,8,1,0,1184,45708,15,225,1837,109369,60,3600,626,14446,25,625;QS=2.9794,0.0206044,0;SGB=-0.556633;RPBZ=1.13753;MQBZ=0.179605;MQSBZ=-1.73205;BQBZ=-1.68805;NMBZ=2.89159;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,44,255,57,255,255:20:1 0,21,191,21,191,191:7:0 0,15,166,15,166,166:5:0 +17 523 . T G,<*> 0 . DP=32;I16=23,8,1,0,1184,45708,15,225,1837,109369,60,3600,626,14446,25,625;QS=2.9794,0.0206044,0;SGB=-0.556633;RPBZ=1.13742;MQBZ=0.179605;MQSBZ=-1.73205;BQBZ=-1.68805;NMBZ=2.89159;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,44,255,57,255,255:20:1 0,21,191,21,191,191:7:0 0,15,166,15,166,166:5:0 17 524 . T <*> . . END=534;MinDP=5;QS=3,0 PL:DP 0,54,255:18 0,21,172:7 0,15,133:5 -17 535 . A G,<*> 0 . DP=31;I16=24,6,0,1,1080,39870,8,64,1777,105769,60,3600,611,13341,25,625;QS=2.98623,0.0137694,0;SGB=-0.556633;RPBZ=-0.894608;MQBZ=0.182574;MQSBZ=-1.85164;BQBZ=-1.6854;NMBZ=2.94255;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,21,194,21,194,194:7:0 0,18,189,18,189,189:6:0 +17 535 . A G,<*> 0 . DP=31;I16=24,6,0,1,1080,39870,8,64,1777,105769,60,3600,611,13341,25,625;QS=2.98623,0.0137694,0;SGB=-0.556633;RPBZ=-0.894788;MQBZ=0.182574;MQSBZ=-1.85164;BQBZ=-1.6854;NMBZ=2.94255;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,21,194,21,194,194:7:0 0,18,189,18,189,189:6:0 17 536 . C <*> . . END=547;MinDP=6;QS=3,0 PL:DP 0,54,255:18 0,21,166:7 0,18,157:6 17 548 . A C,<*> 0 . DP=33;I16=23,9,1,0,1153,42673,9,81,1866,110210,60,3600,561,12489,3,9;QS=2.98607,0.0139319,0;SGB=-0.556633;RPBZ=1.57584;MQBZ=0.253876;MQSBZ=-2.34521;BQBZ=-1.68939;NMBZ=2.40838;SCBZ=3.80814;FS=0;MQ0F=0 PL:DP:DV 0,44,255,54,255,255:19:1 0,21,181,21,181,181:7:0 0,21,211,21,211,211:7:0 17 549 . T G,<*> 0 . DP=32;I16=23,8,0,1,1135,42143,20,400,1806,106610,60,3600,532,11720,25,625;QS=2.96918,0.0308166,0;SGB=-0.556633;RPBZ=-0.487556;MQBZ=0.258065;MQSBZ=-2.29695;BQBZ=-1.68602;NMBZ=2.45062;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV 0,34,255,51,255,255:18:1 0,21,168,21,168,168:7:0 0,21,208,21,208,208:7:0 @@ -112,10 +112,10 @@ 17 576 . G <*> . . END=579;MinDP=5;QS=3,0 PL:DP 0,48,255:16 0,24,198:8 0,15,144:5 17 580 . A C,<*> 0 . DP=30;I16=15,14,1,0,1060,39178,16,256,1709,101641,60,3600,510,11078,17,289;QS=2.97338,0.0266223,0;SGB=-0.556633;RPBZ=1.32953;MQBZ=0.185695;MQSBZ=-1.06904;BQBZ=-1.69093;NMBZ=1.86885;SCBZ=-0.267102;FS=0;MQ0F=0 PL:DP:DV 0,34,255,48,255,255:17:1 0,24,221,24,221,221:8:0 0,15,155,15,155,155:5:0 17 581 . A <*> . . MinDP=5;QS=3,0 PL:DP 0,54,255:18 0,24,223:8 0,15,153:5 -17 582 . C G,<*> 0 . DP=31;I16=15,15,1,0,1080,39870,8,64,1769,105241,60,3600,519,11211,15,225;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.34245;MQBZ=0.182574;MQSBZ=-1.0328;BQBZ=-1.68266;NMBZ=1.92049;SCBZ=-0.262467;FS=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,24,207,24,207,207:8:0 0,15,151,15,151,151:5:0 +17 582 . C G,<*> 0 . DP=31;I16=15,15,1,0,1080,39870,8,64,1769,105241,60,3600,519,11211,15,225;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.34259;MQBZ=0.182574;MQSBZ=-1.0328;BQBZ=-1.68266;NMBZ=1.92049;SCBZ=-0.262467;FS=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,24,207,24,207,207:8:0 0,15,151,15,151,151:5:0 17 583 . T <*> . . END=592;MinDP=5;QS=3,0 PL:DP 0,51,255:17 0,21,209:7 0,15,155:5 -17 593 . C A,<*> 0 . DP=31;I16=16,14,0,1,1071,39925,7,49,1769,105241,29,841,561,12253,25,625;QS=2.97021,0.0297872,0;SGB=-0.556633;RPBZ=0.559412;MQBZ=-3.80789;MQSBZ=-0.0464238;BQBZ=-1.57464;NMBZ=2.13779;SCBZ=3.67454;FS=0;MQ0F=0 PL:DP:DV 0,54,255,54,255,255:18:0 0,12,184,18,187,185:7:1 0,18,174,18,174,174:6:0 +17 593 . C A,<*> 0 . DP=31;I16=16,14,0,1,1071,39925,7,49,1769,105241,29,841,561,12253,25,625;QS=2.97021,0.0297872,0;SGB=-0.556633;RPBZ=0.559355;MQBZ=-3.80789;MQSBZ=-0.0464238;BQBZ=-1.57464;NMBZ=2.13779;SCBZ=3.67454;FS=0;MQ0F=0 PL:DP:DV 0,54,255,54,255,255:18:0 0,12,184,18,187,185:7:1 0,18,174,18,174,174:6:0 17 594 . A G,<*> 0 . DP=33;I16=16,16,1,0,1161,42757,4,16,1858,109682,60,3600,572,12672,15,225;QS=2.99359,0.00641026,0;SGB=-0.556633;RPBZ=-0.998367;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68954;NMBZ=1.76408;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:DV 0,42,255,51,255,255:18:1 0,21,205,21,205,205:7:0 0,24,213,24,213,213:8:0 17 595 . A <*> . . MinDP=7;QS=3,0 PL:DP 0,54,255:18 0,21,198:7 0,24,218:8 -17 596 . A G,<*> 0 . DP=33;I16=16,16,1,0,1061,37187,8,64,1858,109682,60,3600,590,12952,1,1;QS=2.98564,0.0143627,0;SGB=-0.556633;RPBZ=1.68132;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68357;NMBZ=1.61602;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,21,169,21,169,169:7:0 0,24,231,24,231,231:8:0 +17 596 . A G,<*> 0 . DP=33;I16=16,16,1,0,1061,37187,8,64,1858,109682,60,3600,590,12952,1,1;QS=2.98564,0.0143627,0;SGB=-0.556633;RPBZ=1.68146;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68357;NMBZ=1.61602;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,21,169,21,169,169:7:0 0,24,231,24,231,231:8:0 17 597 . C <*> . . END=600;MinDP=7;QS=3,0 PL:DP 0,51,255:17 0,21,194:7 0,24,220:8 From f5a1ef58ab34f9ddc061cfbd79c6f01a1125dfe3 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Thu, 20 Oct 2022 11:15:47 +0200 Subject: [PATCH 35/84] New options `-g, --gene-list` and `--gene-list-fields` which allow to prioritize consequences from a list of genes, or restrict output to the listed genes --- NEWS | 5 ++ plugins/split-vep.c | 153 +++++++++++++++++++++++++++------ test/split-vep.gene-list.1.out | 10 +++ test/split-vep.gene-list.2.out | 3 + test/split-vep.gene-list.3.out | 5 ++ test/split-vep.gene-list.txt | 3 + test/split-vep.gene-list.vcf | 8 ++ test/test.pl | 17 +++- 8 files changed, 176 insertions(+), 28 deletions(-) create mode 100644 test/split-vep.gene-list.1.out create mode 100644 test/split-vep.gene-list.2.out create mode 100644 test/split-vep.gene-list.3.out create mode 100644 test/split-vep.gene-list.txt create mode 100644 test/split-vep.gene-list.vcf diff --git a/NEWS b/NEWS index bbcfbdcc4..641c4f238 100644 --- a/NEWS +++ b/NEWS @@ -26,6 +26,11 @@ Changes affecting specific commands: - Add new `--new-gt X` option (#1800) +* bcftools +split-vep + + - New options `-g, --gene-list` and `--gene-list-fields` which allow to prioritize + consequences from a list of genes, or restrict output to the listed genes + * bcftools +trio-dnm2 - New -n, --strictly-novel option to downplay alleles which violate Mendelian diff --git a/plugins/split-vep.c b/plugins/split-vep.c index 7aa96b765..e45d11636 100644 --- a/plugins/split-vep.c +++ b/plugins/split-vep.c @@ -53,6 +53,9 @@ #define SELECT_TR_PRIMARY 2 #define SELECT_CSQ_ANY -1 +#define GENES_RESTRICT 0 +#define GENES_PRIORITIZE 1 + typedef struct { regex_t *regex; @@ -99,11 +102,16 @@ typedef struct *select, // the --select option *column_str, // the --columns option *column_types, // the --columns-types option - *annot_prefix; // the --annot-prefix option + *annot_prefix, // the --annot-prefix option + *genes_fname, // the --gene-list option + *gene_fields_str; // the --gene-list-fields option + int *gene_fields, ngene_fields; // the indices of --gene-list-fields names void *field2idx, // VEP field name to index, used in initialization - *csq2severity; // consequence type to severity score + *csq2severity, // consequence type to severity score + *genes; // hashed --gene-list genes cols_t *cols_tr, // the current CSQ tag split into transcripts - *cols_csq; // the current CSQ transcript split into fields + **cols_csq; // the current CSQ transcripts split into fields + int ncols_csq,mcols_csq; // the number of cols_csq transcripts and the high-water mark int min_severity, max_severity; // ignore consequences outside this severity range int drop_sites; // the -x, --drop-sites option int select_tr; // one of SELECT_TR_* @@ -117,6 +125,7 @@ typedef struct int ncolumn2type; int raw_vep_request; // raw VEP tag requested and will need subsetting int allow_undef_tags; + int genes_mode; // --gene-list +FILE, one of GENES_* mode, prioritize or restrict int print_header; } args_t; @@ -198,6 +207,8 @@ static const char *usage_text(void) " -d, --duplicate Output per transcript/allele consequences on a new line rather rather than\n" " as comma-separated fields on a single line\n" " -f, --format STR Create non-VCF output; similar to `bcftools query -f` but drops lines w/o consequence\n" + " -g, --gene-list [+]FILE Consider only genes listed in FILE, or prioritize them if prefixed with \"+\"\n" + " --gene-list-fields LIST Use these fields when matching genes from the -g list [SYMBOL,Gene,gene]\n" " -H, --print-header Print header\n" " -l, --list Parse the VCF header and list the annotation fields\n" " -p, --annot-prefix STR Before doing anything else, prepend STR to all CSQ fields to avoid tag name conflicts\n" @@ -447,6 +458,36 @@ char *strdup_annot_prefix(args_t *args, const char *str) free(tmp); return out; } +static void init_gene_list(args_t *args) +{ + int i,j,ngene = 0; + args->genes_mode = args->genes_fname[0]=='+' ? GENES_PRIORITIZE : GENES_RESTRICT; + char *fname = args->genes_fname[0]=='+' ? args->genes_fname+1 : args->genes_fname; + char **gene = hts_readlines(fname, &ngene); + if ( !ngene || !gene ) error("Could not read the file provided with --gene-list %s\n",fname); + args->genes = khash_str2int_init(); + for (i=0; igenes,tmp,1) < 0 ) free(tmp); // duplicate gene name + free(gene[i]); + } + free(gene); + + if ( !args->gene_fields_str ) args->gene_fields_str = "SYMBOL,Gene,gene"; + gene = hts_readlist(args->gene_fields_str,0,&ngene); + args->gene_fields = (int*)malloc(ngene*sizeof(*args->gene_fields)); + for (i=0,j=0; ifield2idx,tmp,&args->gene_fields[j])==0 ) j++; + free(tmp); + free(gene[i]); + } + free(gene); + args->ngene_fields = j; + if ( !args->ngene_fields ) error("None of the \"%s\" fields is present in INFO/%s\n",args->gene_fields_str,args->vep_tag); +} static void init_data(args_t *args) { args->sr = bcf_sr_init(); @@ -764,6 +805,7 @@ static void init_data(args_t *args) if ( args->convert && (max_unpack & BCF_UN_FMT) ) convert_set_option(args->convert, subset_samples, &args->smpl_pass); } + if ( args->genes_fname ) init_gene_list(args); free(str.s); } @@ -774,9 +816,11 @@ static void destroy_data(args_t *args) free(args->kstr.s); free(args->column_str); free(args->format_str); - cols_destroy(args->cols_csq); cols_destroy(args->cols_tr); int i; + for (i=0; imcols_csq; i++) + cols_destroy(args->cols_csq[i]); + free(args->cols_csq); for (i=0; inscale; i++) free(args->scale[i]); free(args->scale); for (i=0; infield; i++) free(args->field[i]); @@ -789,6 +833,8 @@ static void destroy_data(args_t *args) free(ann->str.s); } free(args->annot); + free(args->gene_fields); + if ( args->genes ) khash_str2int_destroy_free(args->genes); if ( args->field2idx ) khash_str2int_destroy(args->field2idx); if ( args->csq2severity ) khash_str2int_destroy(args->csq2severity); bcf_sr_destroy(args->sr); @@ -870,27 +916,27 @@ static int csq_severity_pass(args_t *args, char *csq) return 1; } -static int get_primary_transcript(args_t *args, bcf1_t *rec, cols_t *cols_tr) // modifies args->cols_csq! +static int get_primary_transcript(args_t *args, bcf1_t *rec) { int i; - for (i=0; in; i++) + for (i=0; incols_csq; i++) { - args->cols_csq = cols_split(cols_tr->off[i], args->cols_csq, '|'); - if ( args->primary_id >= args->cols_csq->n ) - error("Too few columns at %s:%"PRId64" .. %d (Consequence) >= %d\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1,args->primary_id,args->cols_csq->n); - if ( !strcmp("YES",args->cols_csq->off[args->primary_id]) ) return i; + cols_t *cols_csq = args->cols_csq[i]; + if ( args->primary_id >= cols_csq->n ) + error("Too few columns at %s:%"PRId64" .. %d (Consequence) >= %d\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1,args->primary_id,cols_csq->n); + if ( !strcmp("YES",cols_csq->off[args->primary_id]) ) return i; } return -1; } -static int get_worst_transcript(args_t *args, bcf1_t *rec, cols_t *cols_tr) // modifies args->cols_csq! +static int get_worst_transcript(args_t *args, bcf1_t *rec) { int i, max_severity = -1, imax_severity = 0; - for (i=0; in; i++) + for (i=0; incols_csq; i++) { - args->cols_csq = cols_split(cols_tr->off[i], args->cols_csq, '|'); - if ( args->csq_idx >= args->cols_csq->n ) - error("Too few columns at %s:%"PRId64" .. %d (Consequence) >= %d\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1,args->csq_idx,args->cols_csq->n); - char *csq = args->cols_csq->off[args->csq_idx]; + cols_t *cols_csq = args->cols_csq[i]; + if ( args->csq_idx >= cols_csq->n ) + error("Too few columns at %s:%"PRId64" .. %d (Consequence) >= %d\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1,args->csq_idx,cols_csq->n); + char *csq = cols_csq->off[args->csq_idx]; int min, max; csq_to_severity(args, csq, &min, &max, -1); @@ -1005,6 +1051,46 @@ static void filter_and_output(args_t *args, bcf1_t *rec, int severity_pass, int if ( bcf_write(args->fh_vcf, args->hdr_out,rec)!=0 ) error("Failed to write to %s\n", args->output_fname); } +static void restrict_csqs_to_genes(args_t *args) +{ + int i,j, nhit = 0; + + // use iarr to mark transcripts from interesting genes + hts_expand(int32_t,args->cols_tr->n,args->miarr,args->iarr); + for (i=0; icols_tr->n; i++) + { + cols_t *cols_csq = args->cols_csq[i]; + for (j=0; jngene_fields; j++) + { + int idx = args->gene_fields[j]; + if ( idx >= cols_csq->n ) continue; + if ( khash_str2int_has_key(args->genes,cols_csq->off[idx]) ) break; + } + if ( j < args->ngene_fields ) + args->iarr[i] = 1, nhit++; + else + args->iarr[i] = 0; + } + if ( !nhit ) + { + if ( args->genes_mode==GENES_RESTRICT ) args->ncols_csq = 0; // no gene of interest + return; + } + + // remove all uninteresting genes by putting all cols_csq hits first + i = 0, j = args->cols_tr->n - 1; + while ( i < j ) + { + if ( args->iarr[i]==1 ) { i++; continue; } + if ( args->iarr[j]==0 ) { j--; continue; } + cols_t *tmp = args->cols_csq[i]; + args->cols_csq[i] = args->cols_csq[j]; + args->cols_csq[j] = tmp; + i++; + j--; + } + args->ncols_csq = nhit; +} static void process_record(args_t *args, bcf1_t *rec) { int len = bcf_get_info_string(args->hdr,rec,args->vep_tag,&args->csq_str,&args->ncsq_str); @@ -1018,16 +1104,27 @@ static void process_record(args_t *args, bcf1_t *rec) return; } + int i; args->cols_tr = cols_split(args->csq_str, args->cols_tr, ','); + if ( args->cols_tr->n > args->mcols_csq ) + { + args->cols_csq = (cols_t**)realloc(args->cols_csq,args->cols_tr->n*sizeof(*args->cols_csq)); + for (i=args->mcols_csq; icols_tr->n; i++) args->cols_csq[i] = NULL; + args->mcols_csq = args->cols_tr->n; + } + args->ncols_csq = args->cols_tr->n; + for (i=0; icols_tr->n; i++) + args->cols_csq[i] = cols_split(args->cols_tr->off[i], args->cols_csq[i], '|'); + if ( args->genes ) restrict_csqs_to_genes(args); - int i,j, itr_min = 0, itr_max = args->cols_tr->n - 1; + int j, itr_min = 0, itr_max = args->ncols_csq - 1; if ( args->select_tr==SELECT_TR_PRIMARY ) { - itr_min = itr_max = get_primary_transcript(args, rec, args->cols_tr); + itr_min = itr_max = get_primary_transcript(args, rec); if ( itr_min<0 ) itr_max = itr_min - 1; } else if ( args->select_tr==SELECT_TR_WORST ) - itr_min = itr_max = get_worst_transcript(args, rec, args->cols_tr); + itr_min = itr_max = get_worst_transcript(args, rec); annot_reset(args->annot, args->nannot); int severity_pass = 0; // consequence severity requested via the -s option (BCF record may be output but not annotated) @@ -1035,18 +1132,18 @@ static void process_record(args_t *args, bcf1_t *rec) static int too_few_fields_warned = 0; for (i=itr_min; i<=itr_max; i++) { - args->cols_csq = cols_split(args->cols_tr->off[i], args->cols_csq, '|'); - if ( args->csq_idx >= args->cols_csq->n ) - error("Too few columns at %s:%"PRId64" .. %d (Consequence) >= %d\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1,args->csq_idx,args->cols_csq->n); + cols_t *cols_csq = args->cols_csq[i]; + if ( args->csq_idx >= cols_csq->n ) + error("Too few columns at %s:%"PRId64" .. %d (Consequence) >= %d\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1,args->csq_idx,cols_csq->n); - char *csq = args->cols_csq->off[args->csq_idx]; + char *csq = cols_csq->off[args->csq_idx]; if ( !csq_severity_pass(args, csq) ) continue; severity_pass = 1; for (j=0; jnannot; j++) { annot_t *ann = &args->annot[j]; - if ( ann->idx >= args->cols_csq->n ) + if ( ann->idx >= cols_csq->n ) { if ( !too_few_fields_warned ) { @@ -1059,7 +1156,7 @@ static void process_record(args_t *args, bcf1_t *rec) char *ann_str = NULL; if ( ann->idx==-1 ) ann_str = args->cols_tr->off[i]; - else if ( *args->cols_csq->off[ann->idx] ) ann_str = args->cols_csq->off[ann->idx]; + else if ( *cols_csq->off[ann->idx] ) ann_str = cols_csq->off[ann->idx]; if ( ann_str ) { annot_append(ann, ann_str); @@ -1099,6 +1196,8 @@ int run(int argc, char **argv) {"all-fields",no_argument,0,'A'}, {"duplicate",no_argument,0,'d'}, {"format",required_argument,0,'f'}, + {"gene-list",required_argument,0,'g'}, + {"gene-list-fields",required_argument,0,5}, {"annotation",required_argument,0,'a'}, {"annot-prefix",required_argument,0,'p'}, {"columns",required_argument,0,'c'}, @@ -1122,7 +1221,7 @@ int run(int argc, char **argv) }; int c; char *tmp; - while ((c = getopt_long(argc, argv, "o:O:i:e:r:R:t:T:lS:s:c:p:a:f:dA:xuH",loptions,NULL)) >= 0) + while ((c = getopt_long(argc, argv, "o:O:i:e:r:R:t:T:lS:s:c:p:a:f:dA:xuHg:",loptions,NULL)) >= 0) { switch (c) { @@ -1137,6 +1236,7 @@ int run(int argc, char **argv) case 'x': args->drop_sites = 1; break; case 'd': args->duplicate = 1; break; case 'f': args->format_str = strdup(optarg); break; + case 'g': args->genes_fname = optarg; break; case 'a': args->vep_tag = optarg; break; case 'p': args->annot_prefix = optarg; break; case 'c': args->column_str = strdup(optarg); break; @@ -1181,6 +1281,7 @@ int run(int argc, char **argv) args->targets_overlap = parse_overlap_option(optarg); if ( args->targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg); break; + case 5 : args->gene_fields_str = optarg; break; case 'h': case '?': default: error("%s", usage_text()); break; diff --git a/test/split-vep.gene-list.1.out b/test/split-vep.gene-list.1.out new file mode 100644 index 000000000..94fbcac83 --- /dev/null +++ b/test/split-vep.gene-list.1.out @@ -0,0 +1,10 @@ +1:1000 ENSG00000082996 missense_variant +1:1000 ENSG00000206199 splice_acceptor_variant&non_coding_transcript_variant +1:2000 ENSG00000104936 downstream_gene_variant +1:2000 ENSG00000177045 missense_variant +1:2000 ENSG00000237452 downstream_gene_variant +1:2000 ENSG00000267395 upstream_gene_variant +1:3000 ENSG00000285314 splice_donor_variant&non_coding_transcript_variant +1:3000 ENSG00000099949 splice_donor_variant&non_coding_transcript_variant +1:4000 ENSG00000013563 splice_donor_variant +1:4000 ENSG00000147403 missense_variant diff --git a/test/split-vep.gene-list.2.out b/test/split-vep.gene-list.2.out new file mode 100644 index 000000000..24d456e72 --- /dev/null +++ b/test/split-vep.gene-list.2.out @@ -0,0 +1,3 @@ +1:1000 ENSG00000082996 missense_variant +1:2000 ENSG00000177045 missense_variant +1:4000 ENSG00000147403 missense_variant diff --git a/test/split-vep.gene-list.3.out b/test/split-vep.gene-list.3.out new file mode 100644 index 000000000..7d321fd4a --- /dev/null +++ b/test/split-vep.gene-list.3.out @@ -0,0 +1,5 @@ +1:1000 ENSG00000082996 missense_variant +1:2000 ENSG00000177045 missense_variant +1:3000 ENSG00000285314 splice_donor_variant&non_coding_transcript_variant +1:3000 ENSG00000099949 splice_donor_variant&non_coding_transcript_variant +1:4000 ENSG00000147403 missense_variant diff --git a/test/split-vep.gene-list.txt b/test/split-vep.gene-list.txt new file mode 100644 index 000000000..d94504352 --- /dev/null +++ b/test/split-vep.gene-list.txt @@ -0,0 +1,3 @@ +RNF13 +SIX5 +RPL10 diff --git a/test/split-vep.gene-list.vcf b/test/split-vep.gene-list.vcf new file mode 100644 index 000000000..d1a01c082 --- /dev/null +++ b/test/split-vep.gene-list.vcf @@ -0,0 +1,8 @@ +##fileformat=VCFv4.2 +##contig= +##INFO= +#CHROM POS ID REF ALT QUAL FILTER INFO +1 1000 . C T . . CSQ=T|missense_variant|MODERATE|RNF13|ENSG00000082996|Transcript|ENST00000344229|protein_coding|3/11||ENST00000344229.7:c.92C>T|ENSP00000341361.3:p.Pro31Leu|794|92|31|P/L|cCt/cTt||1||1||SNV|HGNC|HGNC:10057||||1|P1|CCDS3146.1|ENSP00000341361|O43567.157||UPI0000134318|O43567-1|1|tolerated(0.09)|benign(0.007)|CDD:cd02123&PANTHER:PTHR22765:SF34&PANTHER:PTHR22765&Gene3D:3.50.30.30||||||||||||||||||||||||||||||||||||||27.4|4.062662|ENST00000392894&ENST00000344229&ENST00000470151&ENST00000466478&ENST00000468648&ENST00000459632&ENST00000466795&ENST00000490631|D|D&D|B&B&.&.&.&.&.&.|B&B&.&.&.&.&.&.|T&T&D&D&T&D&D&T|O43567&O43567&C9JYY4&C9JU37&C9JRV0&C9JYN7&C9J8T4&C9J383|.&YES&.&.&.&.&.&.|||||0.323|9|6|31|22|0.00|0.00|0.00|0.00|RNF13,T|splice_acceptor_variant&non_coding_transcript_variant|HIGH|ANKUB1|ENSG00000206199|Transcript|ENST00000473672|processed_transcript||1/1|ENST00000473672.1:n.487-1G>A||||||||1||-1||SNV|HGNC|HGNC:29642||||4||||||||||||||||||||||||||||||||||||||||||extended_intronic_splice_region_variant|loss/acceptor/149846117-149846118/Medium/6.247071||||||27.4|4.062662||||||||||||||9|6|31|22|0.00|0.00|0.00|0.00|RNF13 +1 2000 . G A . . CSQ=A|downstream_gene_variant|MODIFIER|DMPK|ENSG00000104936|Transcript|ENST00000291270|protein_coding||||||||||rs767172612|1|886|-1||SNV|HGNC|HGNC:2933|YES|NM_004409.5||5|A2|CCDS12674.1|ENSP00000291270|Q09013.209|E5KR06.76|UPI0000223FEB|Q09013-9|1||||||||||||||3.968e-05|0|0|0|9.843e-05|0|0|0|0.0001825|0.0001825|gnomAD_SAS|||||||||||||||||24.5|3.428627||||||||||||||-13|-38|24|-11|0.00|0.00|0.00|0.00|SIX5,A|missense_variant|MODERATE|SIX5|ENSG00000177045|Transcript|ENST00000317578|protein_coding|1/3||ENST00000317578.7:c.14C>T|ENSP00000316842.4:p.Pro5Leu|422|14|5|P/L|cCt/cTt|rs767172612|1||-1||SNV|HGNC|HGNC:10891|YES|NM_175875.5||1|P1|CCDS12673.1|ENSP00000316842|Q8N196.159||UPI0000366E2B||1|deleterious_low_confidence(0)|benign(0.093)|PANTHER:PTHR10390&PANTHER:PTHR10390:SF40&MobiDB_lite:mobidb-lite&Low_complexity_(Seg):seg|||||||||||3.968e-05|0|0|0|9.843e-05|0|0|0|0.0001825|0.0001825|gnomAD_SAS|||||||||||||||||24.5|3.428627|ENST00000643139&ENST00000317578&ENST00000622857&ENST00000560168||D|B&B&.&.|B&B&.&.|.&D&.&.|Q8N196&Q8N196&A0A087WXX3&H0YLF6|.&YES&.&.|||||0.405|-13|-38|24|-11|0.00|0.00|0.00|0.00|SIX5,A|downstream_gene_variant|MODIFIER|MEIOSIN|ENSG00000237452|Transcript|ENST00000457052|protein_coding||||||||||rs767172612|1|4290|1||SNV|HGNC|HGNC:44318|YES|NM_001310124.2||5|P1|CCDS82368.1|ENSP00000402674|C9JSJ3.79||UPI0002840CC6||||||||||||||||3.968e-05|0|0|0|9.843e-05|0|0|0|0.0001825|0.0001825|gnomAD_SAS|||||||||||||||||24.5|3.428627||||||||||||||-13|-38|24|-11|0.00|0.00|0.00|0.00|SIX5,A|upstream_gene_variant|MODIFIER|DM1-AS|ENSG00000267395|Transcript|ENST00000586251|lncRNA||||||||||rs767172612|1|2151|1||SNV|HGNC|HGNC:53125||||2||||||||||||||||||||||3.968e-05|0|0|0|9.843e-05|0|0|0|0.0001825|0.0001825|gnomAD_SAS|||||||||||||||||24.5|3.428627||||||||||||||-13|-38|24|-11|0.00|0.00|0.00|0.00|SIX5 +1 3000 . G T . . CSQ=T|splice_donor_variant&non_coding_transcript_variant|HIGH||ENSG00000285314|Transcript|ENST00000479606|lncRNA||11/21|ENST00000479606.5:n.1295+1G>T|||||||rs767191322&COSV53149291|1||1||SNV|||YES|||2||||||||||||||||||||||4.057e-06|0|0|0|0|0|8.998e-06|0|0|8.998e-06|gnomAD_NFE||0&1|1&1|||||||extended_intronic_splice_region_variant|loss/donor/20992370-20992371/Medium/6.672249||||||33|5.100843||||||||||||||46|-29|45|-1|0.00|0.00|0.42|1.00|LZTR1,T|splice_donor_variant&non_coding_transcript_variant|HIGH|LZTR1|ENSG00000099949|Transcript|ENST00000492480|retained_intron||2/5|ENST00000492480.1:n.205+1G>T|||||||rs767191322&COSV53149291|1||1||SNV|HGNC|HGNC:6742||||3||||||||1||||||||||||||4.057e-06|0|0|0|0|0|8.998e-06|0|0|8.998e-06|gnomAD_NFE||0&1|1&1|||||||extended_intronic_splice_region_variant|loss/donor/20992370-20992371/Medium/6.672249||||||33|5.100843||||||||||||||46|-29|45|-1|0.00|0.00|0.42|1.00|LZTR1 +1 4000 . C G . . CSQ=G|splice_donor_variant|HIGH|DNASE1L1|ENSG00000013563|Transcript|ENST00000014935|protein_coding||7/8|ENST00000014935.7:c.525+1G>C||||||||1||-1||SNV|HGNC|HGNC:2957||||2|P1|CCDS14747.1|ENSP00000014935|P49184.181||UPI0000129891||||||||||||||||||||||||||||||||||||extended_intronic_splice_region_variant|loss/donor/154403268-154403269/Medium/9.500494||||||24.2|3.326590|||||||||HC|||INTRON_SIZE:78||-23|24|25|1|0.00|0.06|0.00|0.99|DNASE1L1,G|missense_variant|MODERATE|RPL10|ENSG00000147403|Transcript|ENST00000451365|protein_coding|4/4||ENST00000451365.1:c.284C>G|ENSP00000406125.1:p.Thr95Ser|284|284|95|T/S|aCc/aGc||1||1|cds_start_NF|SNV|HGNC|HGNC:10298||||1|||ENSP00000406125||B8A6G2.66|UPI000173A19B||1|tolerated_low_confidence(0.2)|possibly_damaging(0.722)|Gene3D:3.90.1170.10||||||||||||||||||||||||||||||||||||||24.2|3.326590|ENST00000393638&ENST00000369809&ENST00000369807&ENST00000369808&ENST00000014935&ENST00000309585&ENST00000451865||D&D&D&D&D&D|.&.&.&.&.&.&.|.&.&.&.&.&.&.|.&.&.&.&.&.&.|P49184&P49184&P49184&P49184&P49184&P49184&A6QRJ0|.&YES&.&.&.&.&.|||||0.444|-23|24|25|1|0.00|0.06|0.00|0.99|DNASE1L1 diff --git a/test/test.pl b/test/test.pl index f15eda3d7..0497ecda5 100755 --- a/test/test.pl +++ b/test/test.pl @@ -639,6 +639,9 @@ run_test(\&test_vcf_plugin,$opts,in=>'split-vep.9',out=>'split-vep.24.out',cmd=>'+split-vep',args=>qq[-a BCSQ -f '%xPOS %xConsequence\\n' -p x | grep -v ^#]); run_test(\&test_vcf_plugin,$opts,in=>'split-vep.10',out=>'split-vep.25.out',cmd=>'+split-vep',args=>qq[-a CSQ -f '%M_CAP_pred %M_CAP_score\\n' | grep -v ^#]); run_test(\&test_vcf_plugin,$opts,in=>'split-vep.10',out=>'split-vep.25.out',cmd=>'+split-vep',args=>qq[-a CSQ -f '%xM_CAP_pred %xM_CAP_score\\n' -p x | grep -v ^#]); +run_test(\&test_vcf_plugin,$opts,in=>'split-vep.gene-list',out=>'split-vep.gene-list.1.out',cmd=>'+split-vep',args=>qq[-d -f '%CHROM:%POS %Gene %Consequence\\n']); +run_test(\&test_vcf_plugin,$opts,in=>'split-vep.gene-list',out=>'split-vep.gene-list.2.out',cmd=>'+split-vep',args=>qq[-d -f '%CHROM:%POS %Gene %Consequence\\n' -g {PATH}/split-vep.gene-list.txt]); +run_test(\&test_vcf_plugin,$opts,in=>'split-vep.gene-list',out=>'split-vep.gene-list.3.out',cmd=>'+split-vep',args=>qq[-d -f '%CHROM:%POS %Gene %Consequence\\n' -g +{PATH}/split-vep.gene-list.txt]); run_test(\&test_vcf_plugin,$opts,in=>'parental-origin',out=>'parental-origin.1.out',cmd=>'+parental-origin',args=>qq[-r 20:100 -p proband,father,mother -t del | grep -v ^#]); run_test(\&test_vcf_plugin,$opts,in=>'parental-origin',out=>'parental-origin.2.out',cmd=>'+parental-origin',args=>qq[-r 20:101 -p proband,father,mother -t del | grep -v ^#]); run_test(\&test_vcf_plugin,$opts,in=>'parental-origin',out=>'parental-origin.3.out',cmd=>'+parental-origin',args=>qq[-r 20:102 -p proband,father,mother -t del | grep -v ^#]); @@ -852,7 +855,7 @@ sub error "About: htslib consistency test script\n", "Usage: test.pl [OPTIONS]\n", "Options:\n", - " -f, --function LIST Run only the listed test functions (e.g. 'test_mpileup,test_vcf_call')\n", + " -f, --function LIST Run only the listed tests (e.g. 'test_mpileup,split-vep')\n", " -p, --plugins Test also plugins, requires libhts.so.\n", " -r, --redo-outputs Recreate expected output files.\n", " -t, --temp-dir When given, temporary files will not be removed.\n", @@ -922,7 +925,17 @@ sub run_test use B qw(svref_2object); } my $name = svref_2object($func)->GV->NAME; - if ( !exists($$opts{run_function}{$name}) ) { return; } + my %args = @args; + my $run = 0; + if ( exists($$opts{run_function}{$name}) ) { $run = 1; } + if ( !$run && exists($args{cmd}) ) + { + for my $func (keys %{$$opts{run_function}}) + { + if ( $args{cmd}=~/$func/ ) { $run = 1; last; } + } + } + if ( !$run ) { return; } } &$func($opts,@args); } From 0fc8bf13452196bffbb438636c75c98c18cc52f0 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Thu, 20 Oct 2022 16:41:31 +0200 Subject: [PATCH 36/84] [minor] Remove unused variable --- plugins/trio-dnm2.c | 2 -- 1 file changed, 2 deletions(-) diff --git a/plugins/trio-dnm2.c b/plugins/trio-dnm2.c index ee4e13014..8928046b1 100644 --- a/plugins/trio-dnm2.c +++ b/plugins/trio-dnm2.c @@ -128,8 +128,6 @@ typedef struct } args_t; -args_t args; - const char *about(void) { return "Screen variants for possible de-novo mutations in trios.\n"; From 6f4732b6c4922026c7bcb48a49378c0a958ea25b Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Fri, 21 Oct 2022 17:11:46 +0200 Subject: [PATCH 37/84] Fix gene restricting when combined with -s --- plugins/split-vep.c | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/plugins/split-vep.c b/plugins/split-vep.c index e45d11636..5914d27c4 100644 --- a/plugins/split-vep.c +++ b/plugins/split-vep.c @@ -207,7 +207,7 @@ static const char *usage_text(void) " -d, --duplicate Output per transcript/allele consequences on a new line rather rather than\n" " as comma-separated fields on a single line\n" " -f, --format STR Create non-VCF output; similar to `bcftools query -f` but drops lines w/o consequence\n" - " -g, --gene-list [+]FILE Consider only genes listed in FILE, or prioritize them if prefixed with \"+\"\n" + " -g, --gene-list [+]FILE Consider only genes listed in FILE, or prioritize if FILE is prefixed with \"+\"\n" " --gene-list-fields LIST Use these fields when matching genes from the -g list [SYMBOL,Gene,gene]\n" " -H, --print-header Print header\n" " -l, --list Parse the VCF header and list the annotation fields\n" @@ -1086,6 +1086,9 @@ static void restrict_csqs_to_genes(args_t *args) cols_t *tmp = args->cols_csq[i]; args->cols_csq[i] = args->cols_csq[j]; args->cols_csq[j] = tmp; + char *tmp2 = args->cols_tr->off[i]; + args->cols_tr->off[i] = args->cols_tr->off[j]; + args->cols_tr->off[j] = tmp2; i++; j--; } @@ -1093,7 +1096,7 @@ static void restrict_csqs_to_genes(args_t *args) } static void process_record(args_t *args, bcf1_t *rec) { - int len = bcf_get_info_string(args->hdr,rec,args->vep_tag,&args->csq_str,&args->ncsq_str); + int i,len = bcf_get_info_string(args->hdr,rec,args->vep_tag,&args->csq_str,&args->ncsq_str); if ( len<=0 ) { if ( !args->drop_sites ) @@ -1104,7 +1107,7 @@ static void process_record(args_t *args, bcf1_t *rec) return; } - int i; + // split by transcript and by field args->cols_tr = cols_split(args->csq_str, args->cols_tr, ','); if ( args->cols_tr->n > args->mcols_csq ) { @@ -1115,10 +1118,15 @@ static void process_record(args_t *args, bcf1_t *rec) args->ncols_csq = args->cols_tr->n; for (i=0; icols_tr->n; i++) args->cols_csq[i] = cols_split(args->cols_tr->off[i], args->cols_csq[i], '|'); + + // restrict to -g genes if ( args->genes ) restrict_csqs_to_genes(args); + // select transcripts of interest int j, itr_min = 0, itr_max = args->ncols_csq - 1; - if ( args->select_tr==SELECT_TR_PRIMARY ) + if ( !args->ncols_csq ) + itr_min = itr_max + 1; // no transcripts left after -g applied + else if ( args->select_tr==SELECT_TR_PRIMARY ) { itr_min = itr_max = get_primary_transcript(args, rec); if ( itr_min<0 ) itr_max = itr_min - 1; From c9aed47e407e14d345cee9dca023ec47c92a7254 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Wed, 26 Oct 2022 09:23:37 +0100 Subject: [PATCH 38/84] Make the --af-annots argument optional --- misc/run-roh.pl | 61 ++++++++++++++++++++++++++----------------------- 1 file changed, 32 insertions(+), 29 deletions(-) diff --git a/misc/run-roh.pl b/misc/run-roh.pl index 3a1ca1100..057d5839a 100755 --- a/misc/run-roh.pl +++ b/misc/run-roh.pl @@ -1,21 +1,21 @@ #!/usr/bin/env perl # # The MIT License -# -# Copyright (c) 2017-2018, 2020 Genome Research Ltd. -# +# +# Copyright (c) 2017-2022 Genome Research Ltd. +# # Author: Petr Danecek -# +# # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal # in the Software without restriction, including without limitation the rights # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: -# +# # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. -# +# # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE @@ -41,7 +41,7 @@ sub error { my (@msg) = @_; if ( scalar @msg ) { confess @msg,"\n"; } - print + print "About: This is a convenience wrapper for \"bcftools roh\" which takes multiple VCF/BCF files\n", " and locates regions private to a sample or shared across multiple samples. On input it\n", " expects a directory with .vcf, .vcf.gz or .bcf files, a file with allele frequencies\n", @@ -49,7 +49,7 @@ sub error " for details\n", "Usage: run-roh.pl [OPTIONS]\n", "Options:\n", - " -a, --af-annots Allele frequency annotations [1000GP-AFs/AFs.tab.gz]\n", + " -a, --af-annots Allele frequency annotations (optional)\n", " -i, --indir Input directory with VCF files\n", " --include Select sites for which the expression is true\n", " --exclude Exclude sites for which the epxression is true\n", @@ -69,7 +69,6 @@ sub parse_params { my $opts = { - af_annots => '1000GP-AFs/AFs.tab.gz', verbose => 1, min_length => 1e6, min_markers => 100, @@ -95,9 +94,12 @@ sub parse_params } if ( !exists($$opts{outdir}) ) { error("Missing the -o, --outdir option.\n") } if ( !exists($$opts{indir}) ) { error("Missing the -i, --indir option.\n") } - if ( ! -e $$opts{af_annots} ) { error("The annotation file does not exist: $$opts{af_annots}\n"); } - if ( ! -e "$$opts{af_annots}.tbi" ) { error("The annotation file is not indexed: $$opts{af_annots}.tbi\n"); } - if ( ! -e "$$opts{af_annots}.hdr" ) { error("The annotation file has no header: $$opts{af_annots}.hdr\n"); } + if ( exists($$opts{af_annots}) ) + { + if ( ! -e $$opts{af_annots} ) { error("The annotation file does not exist: $$opts{af_annots}\n"); } + if ( ! -e "$$opts{af_annots}.tbi" ) { error("The annotation file is not indexed: $$opts{af_annots}.tbi\n"); } + if ( ! -e "$$opts{af_annots}.hdr" ) { error("The annotation file has no header: $$opts{af_annots}.hdr\n"); } + } if ( exists($$opts{genmap}) && ! -d "$$opts{genmap}" ) { error("The directory with genetic maps does not exist: $$opts{genmap}\n"); } if ( exists($$opts{include_expr}) ) { $$opts{include_expr} =~ s/\'/\'\\\'\'/g; $$opts{inc_exc} .= qq[ -i '$$opts{include_expr}']; } if ( exists($$opts{exclude_expr}) ) { $$opts{exclude_expr} =~ s/\'/\'\\\'\'/g; $$opts{inc_exc} .= qq[ -e '$$opts{exclude_expr}']; } @@ -118,14 +120,14 @@ sub cmd if ( !defined $pid ) { error("Cannot fork: $!"); } my @out; - if ($pid) + if ($pid) { # parent @out = <$kid_io>; close($kid_io); - } - else - { + } + else + { # child exec('bash', '-o','pipefail','-c', $cmd) or error("Failed to run the command [bash -o pipefail -c $cmd]: $!"); } @@ -134,7 +136,7 @@ sub cmd my $exit_status = $?; my $status = exists($args{require_status}) ? $args{require_status} : 0; - if ( $status ne $exit_status ) + if ( $status ne $exit_status ) { my $msg; if ( $? & 0xff ) @@ -147,7 +149,7 @@ sub cmd } $msg .= ":\n\t$cmd\n\n"; if ( @out ) { $msg .= join('',@out,"\n\n"); } - error($msg); + error($msg); } return @out; } @@ -179,7 +181,7 @@ sub parse_genmap_path if ( !length($suffix) ) { last; } } my @test = glob("$prefix*$suffix"); - if ( @test != @files ) + if ( @test != @files ) { error( "Error: Could not determine the genetic map files in \"$$opts{genmap}\". The directory must contain only\n" . @@ -213,16 +215,17 @@ sub run_roh push @files,$outfile; if ( -e $outfile ) { next; } - my $cmd = - "bcftools annotate --rename-chrs $chr_fname '$$opts{indir}/$file' -Ou | " . - "bcftools annotate -c CHROM,POS,REF,ALT,AF1KG -h $$opts{af_annots}.hdr -a $$opts{af_annots} "; - + my $cmd = "bcftools annotate --rename-chrs $chr_fname '$$opts{indir}/$file'"; + if ( exists($$opts{af_annots}) ) + { + $cmd .= " -Ou | bcftools annotate -c CHROM,POS,REF,ALT,AF1KG -h $$opts{af_annots}.hdr -a $$opts{af_annots} "; + } if ( exists($$opts{inc_exc}) ) { $cmd .= " -Ou | bcftools view $$opts{inc_exc} "; } - $cmd .= "-Ob -o $outfile.part && "; - $cmd .= "mv $outfile.part $outfile"; + $cmd .= " -Ob -o $outfile.part && "; + $cmd .= " mv $outfile.part $outfile"; cmd($cmd, %$opts); } @@ -243,7 +246,7 @@ sub run_roh if ( !$total or $used/$total < 0.3 ) { print STDERR @out; - print STDERR "WARNING: Less than 30% of sites was used!\n\n"; + print STDERR "WARNING: Less than 30% of sites was used!\n\n"; } } cmd(qq[bcftools query -f'GT\\t%CHROM\\t%POS[\\t%SAMPLE\\t%GT]\\n' $file | gzip -c >> $file.txt.gz.part && mv $file.txt.gz.part $file.txt.gz],%$opts); @@ -267,7 +270,7 @@ sub next_region { if ( !exists($$regions{$chr}{$smpl}) ) { next; } my $reg = $$regions{$chr}{$smpl}[0]; - if ( !%min ) + if ( !%min ) { $min{chr} = $chr; $min{beg} = $$reg{beg}; @@ -316,7 +319,7 @@ sub eval_roh my @samples = sort keys %samples; print $fh "# [1]chrom\t[2]beg\t[3]end\t[4]length (Mb)"; my $i = 5; - for my $smpl (@samples) { print $fh "\t[$i]$smpl"; $i++; } + for my $smpl (@samples) { print $fh "\t[$i]$smpl"; $i++; } print $fh "\n"; while (my $min = next_region(\%regions)) { @@ -345,7 +348,7 @@ sub eval_roh { if ( $lengths{$smpl}!=0 ) { - print STDERR "ERROR: a bug detected, sanity check failed, expected zero length : $smpl .. $lengths{$smpl}\n"; + print STDERR "ERROR: a bug detected, sanity check failed, expected zero length : $smpl .. $lengths{$smpl}\n"; } } print STDERR "The merged regions are in $$opts{outdir}/merged.txt\n"; From 4cfa4c81bfc3ed4bf8b007c615e1da26b5e41869 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Fri, 28 Oct 2022 10:18:30 +0100 Subject: [PATCH 39/84] Make variantkey conversion work for ALT=. sites. Resolves #1806 --- convert.c | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/convert.c b/convert.c index 5317cb8fd..4ae57b7d4 100644 --- a/convert.c +++ b/convert.c @@ -1117,14 +1117,21 @@ static void process_rsid_hex(convert_t *convert, bcf1_t *line, fmt_t *fmt, int i static void process_variantkey_hex(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { + const char *alt = NULL; + size_t sizealt = 0; + if ( line->n_allele>1 ) + { + alt = line->d.allele[1]; + sizealt = strlen(line->d.allele[1]); + } uint64_t vk = variantkey( convert->header->id[BCF_DT_CTG][line->rid].key, strlen(convert->header->id[BCF_DT_CTG][line->rid].key), line->pos, line->d.allele[0], strlen(line->d.allele[0]), - line->d.allele[1], - strlen(line->d.allele[1])); + alt, + sizealt); ksprintf(str, "%016" PRIx64 "", vk); } From 6042f7aff4252293c23e13927b887dc2e3ae86c7 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Fri, 28 Oct 2022 10:35:20 +0100 Subject: [PATCH 40/84] [DOCS] Add usage page warning for combining filtering with sample subsetting. Resolves #1807 --- vcfview.c | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/vcfview.c b/vcfview.c index cc0205814..96dcbc7b5 100644 --- a/vcfview.c +++ b/vcfview.c @@ -1,6 +1,6 @@ /* vcfview.c -- VCF/BCF conversion, view, subset and filter VCF/BCF files. - Copyright (C) 2013-2021 Genome Research Ltd. + Copyright (C) 2013-2022 Genome Research Ltd. Author: Shane McCarthy @@ -512,7 +512,9 @@ static void usage(args_t *args) fprintf(stderr, "Subset options:\n"); fprintf(stderr, " -a, --trim-alt-alleles Trim ALT alleles not seen in the genotype fields (or their subset with -s/-S)\n"); fprintf(stderr, " -I, --no-update Do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)\n"); - fprintf(stderr, " -s, --samples [^]LIST Comma separated list of samples to include (or exclude with \"^\" prefix)\n"); + fprintf(stderr, " -s, --samples [^]LIST Comma separated list of samples to include (or exclude with \"^\" prefix). Be careful\n"); + fprintf(stderr, " when combining filtering with sample subsetting as filtering comes (usually) first.\n"); + fprintf(stderr, " If unsure, split sample subsetting and filtering in two commands, using -Ou when piping.\n"); fprintf(stderr, " -S, --samples-file [^]FILE File of samples to include (or exclude with \"^\" prefix)\n"); fprintf(stderr, " --force-samples Only warn about unknown subset samples\n"); fprintf(stderr, "\n"); @@ -623,7 +625,7 @@ int main_vcfview(int argc, char *argv[]) case 'l': args->clevel = strtol(optarg,&tmp,10); if ( *tmp ) error("Could not parse argument: --compression-level %s\n", optarg); - args->output_type |= FT_GZ; + args->output_type |= FT_GZ; break; case 'o': args->fn_out = optarg; break; case 'H': args->print_header = 0; break; @@ -649,7 +651,7 @@ int main_vcfview(int argc, char *argv[]) args->min_alleles = strtol(optarg,&tmp,10); if ( *tmp ) error("Could not parse argument: --min-alleles %s\n", optarg); break; - case 'M': + case 'M': args->max_alleles = strtol(optarg,&tmp,10); if ( *tmp ) error("Could not parse argument: --max-alleles %s\n", optarg); break; From 34217913032ac8fd4df879f1ff451bcfad292236 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Fri, 28 Oct 2022 13:39:26 +0100 Subject: [PATCH 41/84] [MINOR] update NEWS --- NEWS | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/NEWS b/NEWS index 641c4f238..65bf61c64 100644 --- a/NEWS +++ b/NEWS @@ -11,6 +11,10 @@ Changes affecting specific commands: - Fix a bug where too many alleles passed to `-C alleles` via `-T` caused memory corruption (#1790) +* bcftools convert + + - Make variantkey conversion work for sites without an ALT allele (#1806) + * bcftools norm - New --multi-overlaps option allows to set overlapping alleles either to the From f5c8b4e9a820bd01478c9f8df5367fb4e082255c Mon Sep 17 00:00:00 2001 From: Andrew Whitwham Date: Mon, 31 Oct 2022 14:36:13 +0000 Subject: [PATCH 42/84] Added error checks. One error check if the interactive gui cannot be set, another when the input format is incorrect. --- misc/plot-roh.py | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/misc/plot-roh.py b/misc/plot-roh.py index cde5f519e..654c4d77a 100755 --- a/misc/plot-roh.py +++ b/misc/plot-roh.py @@ -133,15 +133,22 @@ def wrap_hash(**args): return args import matplotlib.pyplot as plt import matplotlib.patches as patches else: + gui_set = False; + for gui in ['TKAgg','GTKAgg','Qt4Agg','WXAgg','MacOSX']: try: mpl.use(gui,warn=False, force=True) import matplotlib.pyplot as plt import matplotlib.patches as patches + gui_set = True; break except: continue + if gui_set==False: + usage("Unable to set GUI for interactive plot") + + cols = [ '#337ab7', '#5cb85c', '#5bc0de', '#f0ad4e', '#d9534f', 'grey', 'black' ] globstr = os.path.join(dir, '*.txt.gz') @@ -352,6 +359,16 @@ def parse_samples(fname,highlight): off = 0 off_sep = 0 dat_rg1 = {} + +if not chrs: + print("No GT tags found in input file.\n\nPlease try rerunning using run-roh.pl with --roh-args \"-G 30\"") + print("\nAlternatively run these commands manually:") + print("bcftools annotate --rename-chrs chr-names.txt in.bcf -Ob -o annotated.bcf") + print("bcftools roh -G 30 --AF-tag AF1KG annotated.bcf -Orz -o out.file.txt.gz") + print("bcftools query -f'GT\\t%CHROM\\t%POS[\\t%SAMPLE\\t%GT]\\n' annotated.bcf | gzip -c >> out.file.txt.gz") + print("\nWhere chr-names.txt can be created by:") + usage("for i in `seq 1 22`; do printf \"chr$i\\t$i\\n\" >> test_char.txt; done; printf \"chrX\\tX\\n\" >> test_char.txt") + for chr in chrs: if chr in dat_rg: rg1 = merge_regions(dat_rg[chr]) From 20ce302b44dbf1d4558adb5588dff4ea1e50daad Mon Sep 17 00:00:00 2001 From: Andrew Whitwham Date: Tue, 1 Nov 2022 11:25:09 +0000 Subject: [PATCH 43/84] Error comments changed on review. --- misc/plot-roh.py | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/misc/plot-roh.py b/misc/plot-roh.py index 654c4d77a..9c6bb02f0 100755 --- a/misc/plot-roh.py +++ b/misc/plot-roh.py @@ -361,13 +361,7 @@ def parse_samples(fname,highlight): dat_rg1 = {} if not chrs: - print("No GT tags found in input file.\n\nPlease try rerunning using run-roh.pl with --roh-args \"-G 30\"") - print("\nAlternatively run these commands manually:") - print("bcftools annotate --rename-chrs chr-names.txt in.bcf -Ob -o annotated.bcf") - print("bcftools roh -G 30 --AF-tag AF1KG annotated.bcf -Orz -o out.file.txt.gz") - print("bcftools query -f'GT\\t%CHROM\\t%POS[\\t%SAMPLE\\t%GT]\\n' annotated.bcf | gzip -c >> out.file.txt.gz") - print("\nWhere chr-names.txt can be created by:") - usage("for i in `seq 1 22`; do printf \"chr$i\\t$i\\n\" >> test_char.txt; done; printf \"chrX\\tX\\n\" >> test_char.txt") + usage("No GT lines found in input file. Was it generated using the run-roh.pl script?") for chr in chrs: if chr in dat_rg: From c056692edd418421e4a104770d811a8c07fa56e7 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Tue, 1 Nov 2022 13:25:18 +0000 Subject: [PATCH 44/84] New +mendelian2 plugin, deprecates the original +mendelian Note that command line options have changed and the output format has changed as well. Hopefully resolves #1729 and #1738 --- NEWS | 6 + doc/bcftools.txt | 3 + plugins/mendelian.c | 7 +- plugins/mendelian2.c | 878 +++++++++++++++++++++++++++++++++++++++++++ test/mendelian.4.out | 2 +- test/mendelian.6.out | 26 ++ test/mendelian.7.out | 18 + test/mendelian.8.out | 13 + test/test.pl | 6 + 9 files changed, 955 insertions(+), 4 deletions(-) create mode 100644 plugins/mendelian2.c create mode 100644 test/mendelian.6.out create mode 100644 test/mendelian.7.out create mode 100644 test/mendelian.8.out diff --git a/NEWS b/NEWS index 65bf61c64..93cbd898b 100644 --- a/NEWS +++ b/NEWS @@ -15,6 +15,12 @@ Changes affecting specific commands: - Make variantkey conversion work for sites without an ALT allele (#1806) +* bcftools +mendelian + + - The +mendelian plugin has been deprecated and replaced with +mendelian2. The + function of the plugin is the same but the command line options and the output + format has changed, and for this was introduced as a new plugin. + * bcftools norm - New --multi-overlaps option allows to set overlapping alleles either to the diff --git a/doc/bcftools.txt b/doc/bcftools.txt index 457bde783..47222bed9 100644 --- a/doc/bcftools.txt +++ b/doc/bcftools.txt @@ -2588,6 +2588,9 @@ By default, appropriate system directories are searched for installed plugins. compare two files and set non-identical genotypes to missing *mendelian*:: + count Mendelian consistent / inconsistent genotypes (deprecated, use +mendelian2 instead) + +*mendelian2*:: count Mendelian consistent / inconsistent genotypes. *missing2ref*:: diff --git a/plugins/mendelian.c b/plugins/mendelian.c index 3f5128448..65a65fe1c 100644 --- a/plugins/mendelian.c +++ b/plugins/mendelian.c @@ -85,7 +85,7 @@ static bcf1_t *process(bcf1_t *rec); const char *about(void) { - return "Count Mendelian consistent / inconsistent genotypes.\n"; + return "Count Mendelian consistent / inconsistent genotypes [DEPRECATED, use mendelian2 instead]\n"; } typedef struct @@ -142,7 +142,8 @@ const char *usage(void) { return "\n" - "About: Count Mendelian consistent / inconsistent genotypes.\n" + "About: Count Mendelian consistent / inconsistent genotypes. Note that this plugin is DEPRECATED and\n" + " will not be supported in the future. Please use the newer plugin +mendelian2 instead.\n" "Usage: bcftools +mendelian [Options]\n" "Options:\n" " -c, --count Count the number of consistent sites [DEPRECATED, use `-m c` instead]\n" @@ -463,7 +464,7 @@ int run(int argc, char **argv) args.out_fh = hts_open(args.output_fname ? args.output_fname : "-", wmode); if ( args.out_fh == NULL ) error("Can't write to \"%s\": %s\n", args.output_fname, strerror(errno)); if ( args.mode&MODE_ANNOTATE ) - bcf_hdr_append(args.hdr, "##INFO="); + bcf_hdr_append(args.hdr, "##INFO="); if ( bcf_hdr_write(args.out_fh, args.hdr)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args.output_fname); } diff --git a/plugins/mendelian2.c b/plugins/mendelian2.c new file mode 100644 index 000000000..f1d5c7b02 --- /dev/null +++ b/plugins/mendelian2.c @@ -0,0 +1,878 @@ +/* The MIT License + + Copyright (c) 2015-2022 Genome Research Ltd. + + Author: Petr Danecek + + Permission is hereby granted, free of charge, to any person obtaining a copy + of this software and associated documentation files (the "Software"), to deal + in the Software without restriction, including without limitation the rights + to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + copies of the Software, and to permit persons to whom the Software is + furnished to do so, subject to the following conditions: + + The above copyright notice and this permission notice shall be included in + all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + THE SOFTWARE. + + */ + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include // for isatty +#include "bcftools.h" +#include "regidx.h" +#include "filter.h" + +// Logic of the filters: include or exclude sites which match the filters? +#define FLT_INCLUDE 1 +#define FLT_EXCLUDE 2 + +#define MODE_ANNOTATE (1<<0) // -m a +#define MODE_COUNT (1<<1) // -m c +#define MODE_DELETE (1<<2) // -m d +#define MODE_LIST_ERR (1<<3) // -m e +#define MODE_DROP_ERR (1<<4) // -m E +#define MODE_LIST_GOOD (1<<5) // -m g +#define MODE_LIST_MISS (1<<6) // -m m +#define MODE_DROP_MISS (1<<7) // -m M +#define MODE_LIST_SKIP (1<<8) // -m s +#define MODE_DROP_SKIP (1<<9) // -m S +#define LIST_MODES (MODE_LIST_ERR|MODE_LIST_GOOD|MODE_LIST_MISS|MODE_LIST_SKIP) + +#define iMOM 0 +#define iDAD 1 +#define iKID 2 + +typedef struct +{ + int nno_gt, // number of rows with no FMT/GT + nnot_diploid, // FMT/GT2 not diploid + nfail, // number of -i/-e filters failed + nmiss, // number of genotypes with a missing allele in the trio + ngood, // number of good genotypes (after any -i/-e filters applied) + nmerr; // number of mendelian errors +} +stats_t; + +typedef struct +{ + int idx[3]; // VCF sample index of mom,dad,kid, in that order + stats_t stats; // per trio stats collected over all sites + int fail, has_merr; // per site filtering and mendeian error info + int sex_id; // implicitly defined by rules (typically 1X=0, 2X=1), see str2sex_id +} +trio_t; + +typedef struct +{ + uint8_t + ploidy:4, // 0,1,2 + sex_id:2, // id given by str2sex_id mapping + inherits:2; // one of the M,F,MF,. inheritance modes given as combination of 1<,proband,father,mother,sex(1:male,2:female)\n" + " --rules ASSEMBLY[?] Predefined inheritance rules, \"list\" to print available settings, \"list?\" for detailed information\n" + " --rules-file FILE Inheritance rules, run with `--rules list?` for examples\n" + "\n" + "Example:\n" + " # Print number of good, erroneous and missing genotypes\n" + " bcftools +mendelian2 in.vcf -p 1X:Child,Father,Mother -c\n" + "\n"; +} + +typedef struct +{ + const char *alias, *about, *rules; +} +rules_predef_t; + +static rules_predef_t rules_predefs[] = +{ + { .alias = "GRCh37", + .about = "Human Genome reference assembly GRCh37 / hg19, both chr naming conventions", + .rules = + " # Unlisted regions inherit from both parents (MF)\n" + " 1X X:1-60000 M\n" + " 1X X:2699521-154931043 M\n" + " 1X Y:1-59373566 F\n" + " 2X Y:1-59373566 .\n" + " 1X MT:1-16569 M\n" + " 2X MT:1-16569 M\n" + "\n" + " 1X chrX:1-60000 M\n" + " 1X chrX:2699521-154931043 M\n" + " 1X chrY:1-59373566 F\n" + " 2X chrY:1-59373566 .\n" + " 1X chrM:1-16569 M\n" + " 2X chrM:1-16569 M\n" + }, + { .alias = "GRCh38", + .about = "Human Genome reference assembly GRCh38 / hg38, both chr naming conventions", + .rules = + " # Unlisted regions inherit from both parents (MF)\n" + " 1X X:1-9999 M\n" + " 1X X:2781480-155701381 M\n" + " 1X Y:1-57227415 F\n" + " 2X Y:1-57227415 .\n" + " 1X MT:1-16569 M\n" + " 2X MT:1-16569 M\n" + "\n" + " 1X chrX:1-9999 M\n" + " 1X chrX:2781480-155701381 M\n" + " 1X chrY:1-57227415 F\n" + " 2X chrY:1-57227415 .\n" + " 1X chrMT:1-16569 M\n" + " 2X chrMT:1-16569 M\n" + }, + { + .alias = NULL, + .about = NULL, + .rules = NULL, + } +}; + +static int parse_rules(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr) +{ + args_t *args = (args_t*)usr; + + // e.g + // 1X Y:1-59373566 F # son + // 2X Y:1-59373566 . # daughter + + if ( line[0]=='#' ) return -1; // skip comment lines + + // eat any leading spaces + char *ss = (char*) line; + while ( *ss && isspace(*ss) ) ss++; + if ( !*ss ) return -1; // skip empty lines + + // sex id, e.g. 1X or 2X + char keep, *tmp, *se = ss; + while ( *se && !isspace(*se) ) se++; + if ( !*se ) error("Could not parse the sex ID in the region line: %s\n", line); + keep = *se; + *se = 0; + int sex_id = 0; + if ( khash_str2int_get(args->str2sex_id,ss,&sex_id)!=0 ) + { + tmp = strdup(ss); + if ( khash_str2int_set(args->str2sex_id,tmp,args->nsex_id) < 0 ) error("Could not insert into a hash\n"); + sex_id = args->nsex_id++; + } + *se = keep; + while ( *se && isdigit(*se) ) se++; + while ( *se && isspace(*se) ) se++; + ss = se; + + // chromosome name, beg, end + while ( se[1] && !isspace(se[1]) ) se++; + while ( se > ss && isdigit(*se) ) se--; + if ( *se!='-' ) error("Could not parse the region: %s\n",line); + *end = strtol(se+1, &tmp, 10) - 1; + if ( tmp==se+1 ) error("Could not parse the region: %s\n",line); + while ( se > ss && *se!=':' ) se--; + *beg = strtol(se+1, &tmp, 10) - 1; + if ( tmp==se+1 ) error("Could not parse the region: %s\n",line); + + *chr_beg = ss; + *chr_end = se-1; + + // skip region + while ( *ss && !isspace(*ss) ) ss++; + while ( *ss && isspace(*ss) ) ss++; + + rule_t *rule = (rule_t*) payload; + rule->sex_id = sex_id; + rule->inherits = 0; + rule->ploidy = 0; + + // alleles inherited from mother (M), father (F), both (MF), none (.) + while ( *ss && !isspace(*ss) ) + { + if ( *ss=='M' ) { rule->inherits |= 1<ploidy++; } + else if ( *ss=='F' ) { rule->inherits |= 1<ploidy++; } + else if ( *ss=='.' ) { rule->inherits = 0; rule->ploidy = 0; } + else error("Could not parse the region: %s\n", line); + ss++; + if ( rule->ploidy > 2 ) error("Todo: not ready for ploidy > 2: %s\n", line); + } + return 0; +} +regidx_t *init_rules(args_t *args, char *alias) +{ + const rules_predef_t *rules = rules_predefs; + if ( !alias ) alias = "GRCh37"; + + int detailed = 0, len = strlen(alias); + if ( alias[len-1]=='?' ) { detailed = 1; alias[len-1] = 0; } + + while ( rules->alias && strcasecmp(alias,rules->alias) ) rules++; + + if ( !rules->alias ) + { + fprintf(stderr,"\nPRE-DEFINED INHERITANCE RULES\n\n"); + fprintf(stderr," * Columns are: SEX_ID CHROM:BEG-END INHERITED_FROM\n"); + fprintf(stderr," * Coordinates are 1-based inclusive.\n\n"); + rules = rules_predefs; + while ( rules->alias ) + { + fprintf(stderr,"%s\n .. %s\n\n", rules->alias,rules->about); + if ( detailed ) + fprintf(stderr,"%s\n", rules->rules); + rules++; + } + fprintf(stderr,"Run as --rules (e.g. --rules GRCh37).\n"); + fprintf(stderr,"To see the detailed ploidy definition, append a question mark (e.g. --rules GRCh37?).\n"); + fprintf(stderr,"\n"); + exit(-1); + } + else if ( detailed ) + { + fprintf(stderr,"%s", rules->rules); + exit(-1); + } + return regidx_init_string(rules->rules, parse_rules, NULL, sizeof(rule_t), args); +} + +static int cmp_trios(const void *_a, const void *_b) +{ + trio_t *a = (trio_t *) _a; + trio_t *b = (trio_t *) _b; + int i; + int amin = a->idx[0]; + for (i=1; i<3; i++) + if ( amin > a->idx[i] ) amin = a->idx[i]; + int bmin = b->idx[0]; + for (i=1; i<3; i++) + if ( bmin > b->idx[i] ) bmin = b->idx[i]; + if ( amin < bmin ) return -1; + if ( amin > bmin ) return 1; + return 0; +} +static void parse_ped(args_t *args, char *fname) +{ + htsFile *fp = hts_open(fname, "r"); + if ( !fp ) error("Could not read: %s\n", fname); + + kstring_t str = {0,0,0}; + if ( hts_getline(fp, KS_SEP_LINE, &str) <= 0 ) error("Empty file: %s\n", fname); + + int moff = 0, *off = NULL, mtrio = 0; + do + { + // familyID sampleID paternalID maternalID sex phenotype population relationship siblings secondOrder thirdOrder children comment + // BB03 HG01884 HG01885 HG01956 2 0 ACB child 0 0 0 0 + int ncols = ksplit_core(str.s,0,&moff,&off); + if ( ncols<4 ) error("Could not parse the ped file: %s\n", str.s); + + int dad = bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,&str.s[off[2]]); + if ( dad < 0 ) continue; + int mom = bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,&str.s[off[3]]); + if ( mom < 0 ) continue; + int kid = bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,&str.s[off[1]]); + if ( kid < 0 ) continue; + + int sex = 0; + if ( ncols>=5 ) + { + char *tmp; + sex = strtol(&str.s[off[4]],&tmp,10); + if ( tmp==&str.s[off[4]] || *tmp ) error("Could not parse the PED file, the 5th column should be numeric: %s\n",str.s); + if ( sex!=1 && sex!=2 ) sex = 0; + } + + args->ntrio++; + hts_expand0(trio_t,args->ntrio,mtrio,args->trio); + trio_t *trio = &args->trio[args->ntrio-1]; + trio->idx[iDAD] = dad; + trio->idx[iMOM] = mom; + trio->idx[iKID] = kid; + if ( khash_str2int_get(args->str2sex_id, sex==1 ? "1X" : "2X", &trio->sex_id)<0 ) + error("Missing the sex \"%s\", it's not in the rules :-/\n",sex==1 ? "1X" : "2X"); + } + while ( hts_getline(fp, KS_SEP_LINE, &str)>=0 ); + + // sort the sample by index so that they are accessed more or less sequentially + qsort(args->trio,args->ntrio,sizeof(trio_t),cmp_trios); + + // check for duplicates + int i; + for (i=1; intrio; i++) + { + trio_t *ta = &args->trio[i-1]; + trio_t *tb = &args->trio[i]; + if ( ta->idx[0]==tb->idx[0] && ta->idx[1]==tb->idx[1] && ta->idx[2]==tb->idx[2] ) + error("Error: duplicate trio entries detected in the PED file: %s\n",fname); + } + + fprintf(stderr,"Identified %d complete trio%s in the VCF file\n", args->ntrio,args->ntrio==1?"":"s"); + + free(str.s); + free(off); + if ( hts_close(fp)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,fname); +} + +static void init_data(args_t *args) +{ + args->sr = bcf_sr_init(); + if ( args->regions ) + { + args->sr->require_index = 1; + bcf_sr_set_opt(args->sr,BCF_SR_REGIONS_OVERLAP,args->regions_overlap); + if ( bcf_sr_set_regions(args->sr, args->regions, args->regions_is_file)<0 ) error("Failed to read the regions: %s\n",args->regions); + } + if ( args->targets ) + { + bcf_sr_set_opt(args->sr,BCF_SR_TARGETS_OVERLAP,args->targets_overlap); + if ( bcf_sr_set_targets(args->sr, args->targets, args->targets_is_file, 0)<0 ) error("Failed to read the targets: %s\n",args->targets); + } + if ( !bcf_sr_add_reader(args->sr,args->fname) ) error("Error: %s\n", bcf_sr_strerror(args->sr->errnum)); + args->hdr = bcf_sr_get_header(args->sr,0); + + if ( args->filter_str ) args->filter = filter_init(args->hdr, args->filter_str); + + args->str2sex_id = khash_str2int_init(); + if ( args->rules_fname ) + args->rules = regidx_init(args->rules_fname, parse_rules, NULL, sizeof(rule_t), args); + else + args->rules = init_rules(args, args->rules_str); + if ( !args->rules ) error("Coud not parse the Mendelian rules\n"); + args->itr = regitr_init(args->rules); + args->rule = (rule_t*) malloc(sizeof(*args->rule)*args->nsex_id); + + int i, n = 0; + char **list; + if ( args->pfm ) + { + args->ntrio = 1; + args->trio = (trio_t*) calloc(1,sizeof(trio_t)); + list = hts_readlist(args->pfm, 0, &n); + if ( n!=3 ) error("Expected three sample names with -t\n"); + args->trio[0].idx[iKID] = bcf_hdr_id2int(args->hdr, BCF_DT_SAMPLE, list[0]); + args->trio[0].idx[iDAD] = bcf_hdr_id2int(args->hdr, BCF_DT_SAMPLE, list[1]); + args->trio[0].idx[iMOM] = bcf_hdr_id2int(args->hdr, BCF_DT_SAMPLE, list[2]); + if ( args->trio[0].idx[iKID] < 0 ) + { + if ( strlen(list[0])>3 && !strncasecmp(list[0],"1X:",3) ) + { + args->trio[0].idx[iKID] = bcf_hdr_id2int(args->hdr, BCF_DT_SAMPLE, list[0]+3); + args->trio[0].sex_id = iDAD; + } + else if ( strlen(list[0])>3 && !strncasecmp(list[0],"2X:",3) ) + { + args->trio[0].idx[iKID] = bcf_hdr_id2int(args->hdr, BCF_DT_SAMPLE, list[0]+3); + args->trio[0].sex_id = iMOM; + } + } + for (i=0; itrio[0].idx[i] < 0 ) error("The sample is not present: %s\n", list[i]); + free(list[i]); + } + free(list); + } + else + { + parse_ped(args,args->ped_fname); + if ( !args->ntrio ) error("No complete trio present\n"); + } + + args->hdr_out = bcf_hdr_dup(args->hdr); + if ( args->mode&MODE_ANNOTATE ) + bcf_hdr_append(args->hdr_out,"##INFO="); + if ( args->record_cmd_line ) + bcf_hdr_append_version(args->hdr_out, args->argc, args->argv, "bcftools_trio-dnm2"); + + if ( args->mode!=MODE_COUNT ) + { + char wmode[8]; + set_wmode(wmode,args->output_type,args->output_fname,args->clevel); + args->out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode); + if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno)); + if ( bcf_hdr_write(args->out_fh, args->hdr_out)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); + } +} + +static void destroy_data(args_t *args) +{ + if ( args->filter ) filter_destroy(args->filter); + regidx_destroy(args->rules); + regitr_destroy(args->itr); + khash_str2int_destroy_free(args->str2sex_id); + free(args->trio); + free(args->gt_arr); + free(args->rule); + if ( args->out_fh && hts_close(args->out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname); + bcf_hdr_destroy(args->hdr_out); + bcf_sr_destroy(args->sr); + free(args); +} + +static int test_filters(args_t *args, bcf1_t *rec) +{ + uint8_t *smpl_pass; + int i,j, pass_site = filter_test(args->filter, rec, (const uint8_t**) &smpl_pass); + if ( args->filter_logic & FLT_EXCLUDE ) + { + if ( pass_site ) + { + if ( !smpl_pass ) return 0; // no samples, -e mode, the expression failed + pass_site = 0; + for (i=0; intrio; i++) + { + int pass_trio = 1; + for (j=0; j<3; j++) + { + int idx = args->trio[i].idx[j]; + if ( smpl_pass[idx] ) { pass_trio = 0; break; } // with -e one sample passes, the whole trio fails + } + args->trio[i].fail = pass_trio ? 0 : 1; + if ( pass_trio ) pass_site = 1; + } + return pass_site; + } + for (i=0; intrio; i++) args->trio[i].fail = 0; + return 1; + } + if ( !pass_site ) return 0; + if ( smpl_pass ) + { + pass_site = 0; + for (i=0; intrio; i++) + { + int pass_trio = 1; + for (j=0; j<3; j++) + { + int idx = args->trio[i].idx[j]; + if ( !smpl_pass[idx] ) { pass_trio = 0; break; } + } + args->trio[i].fail = pass_trio ? 0 : 1; + if ( pass_trio ) pass_site = 1; + } + return pass_site; + } + for (i=0; intrio; i++) args->trio[i].fail = 0; + return 1; +} + +static int parse_gt(int32_t *gt, int ngt, uint64_t *a, uint64_t *b) +{ + *a = *b = 0; + + if ( gt[0]==bcf_gt_missing || gt[0]==bcf_int32_vector_end ) return 0; + *a |= 1<nmerr = 0; + + int ret = 0; + int ngt = bcf_get_genotypes(args->hdr, rec, &args->gt_arr, &args->ngt_arr); + if ( ngt<0 ) + { + args->stats.nno_gt++; + return ret; + } + if ( ngt!=2*bcf_hdr_nsamples(args->hdr) && ngt!=bcf_hdr_nsamples(args->hdr) ) + { + args->stats.nnot_diploid++; + return ret; + } + ngt /= bcf_hdr_nsamples(args->hdr); + + int i,j,itr_set = regidx_overlap(args->rules, bcf_seqname(args->hdr,rec),rec->pos,rec->pos+rec->rlen-1, args->itr); + for (i=0; insex_id; i++) + { + args->rule[i].sex_id = i; + args->rule[i].inherits = (1<rule[i].ploidy = 2; + } + while ( itr_set && regitr_overlap(args->itr) ) + { + rule_t *rule = ®itr_payload(args->itr,rule_t); + args->rule[rule->sex_id] = *rule; + } + + for (i=0; intrio; i++) + { + trio_t *trio = &args->trio[i]; + trio->has_merr = 0; + if ( trio->fail ) + { + trio->stats.nfail++; + continue; + } + rule_t *rule = &args->rule[trio->sex_id]; + if ( !rule->inherits ) continue; // should have some stats for this? + uint64_t kid1, kid2, parent, mom, dad; + int nal = parse_gt(&args->gt_arr[ngt*trio->idx[iKID]],ngt,&kid1,&kid2); + if ( nal < rule->ploidy ) { ret |= HAS_MISS; trio->stats.nmiss++; continue; } + if ( nal==1 ) + { + for (j=0; jnsex_id; j++) + { + if ( rule->inherits & (1<gt_arr[ngt*trio->idx[j]],ngt,&parent,&parent); + if ( !nal ) { ret |= HAS_MISS; trio->stats.nmiss++; continue; } + if ( parent&kid1 ) { ret |= HAS_GOOD; trio->stats.ngood++; continue; } + ret |= HAS_MERR; + trio->stats.nmerr++; + trio->has_merr = 1; + args->nmerr++; + continue; + } + int nal_mom = parse_gt(&args->gt_arr[ngt*trio->idx[iMOM]],ngt,&mom,&mom); + int nal_dad = parse_gt(&args->gt_arr[ngt*trio->idx[iDAD]],ngt,&dad,&dad); + if ( (kid1&dad && kid2&mom) || (kid1&mom && kid2&dad) ) { ret |= HAS_GOOD; trio->stats.ngood++; continue; } // both children's alleles phased + if ( !nal_mom || !nal_dad ) { ret |= HAS_MISS; trio->stats.nmiss++; } // one or both parents missing + if ( !nal_mom && !nal_dad ) continue; // both parents missing + if ( !nal_mom && ((kid1|kid2)&dad) ) continue; // one parent missing but the kid is consistent with the other + if ( !nal_dad && ((kid1|kid2)&mom) ) continue; + ret |= HAS_MERR; + trio->stats.nmerr++; + trio->has_merr = 1; + args->nmerr++; + } + + if ( !(args->mode&MODE_DELETE) || !(ret&HAS_MERR) ) return ret; + for (i=0; intrio; i++) + { + trio_t *trio = &args->trio[i]; + if ( !trio->has_merr ) continue; + delete_gt(&args->gt_arr[ngt*trio->idx[iKID]],ngt); + delete_gt(&args->gt_arr[ngt*trio->idx[iDAD]],ngt); + delete_gt(&args->gt_arr[ngt*trio->idx[iMOM]],ngt); + } + bcf_update_genotypes(args->hdr_out, rec, args->gt_arr, ngt*bcf_hdr_nsamples(args->hdr)); + return ret; +} + +static int process_record(args_t *args, bcf1_t *rec) // returns 1 to print rec, 0 to suppress printing +{ + int skip_site = 0; + if ( rec->n_allele==1 || bcf_get_variant_types(rec)==VCF_REF ) + { + args->nref_only++; + skip_site = 1; + } + else if ( rec->n_allele > 64 ) // we use uint64_t bitmask in collect_stats() + { + args->nmany_als++; + skip_site = 1; + } + else if ( args->filter && !test_filters(args,rec) ) + { + args->stats.nfail++; + skip_site = 1; + } + if ( skip_site ) return args->mode&MODE_DROP_SKIP ? 1 : 0; + + int ret = collect_stats(args, rec); + if ( ret&HAS_MERR ) args->stats.nmerr++; + if ( ret&HAS_MISS ) args->stats.nmiss++; + if ( ret&HAS_GOOD ) args->stats.ngood++; + if ( args->mode&MODE_COUNT ) return 0; + if ( args->mode&MODE_DROP_ERR && ret&HAS_MERR ) return 0; + if ( args->mode&MODE_DROP_MISS && ret&HAS_MISS ) return 0; + + if ( args->mode&MODE_ANNOTATE ) + { + bcf_update_info_int32(args->hdr_out,rec,"MERR",&args->nmerr,1); + } + + if ( args->mode&LIST_MODES ) + { + if ( args->mode&MODE_LIST_ERR && ret&HAS_MERR ) return 1; + if ( args->mode&MODE_LIST_MISS && ret&HAS_MISS ) return 1; + if ( args->mode&MODE_LIST_GOOD && ret&HAS_GOOD ) return 1; + return 0; + } + return 1; +} + +static void print_stats(args_t *args) +{ + if ( !(args->mode & MODE_COUNT) ) return; + + FILE *log_fh = stderr; + if ( args->mode==MODE_COUNT ) + { + log_fh = strcmp("-",args->output_fname) ? fopen(args->output_fname,"w") : stdout; + if ( !log_fh ) error("Error: cannot write to %s\n", args->output_fname); + } + + fprintf(log_fh,"# Summary stats\n"); + fprintf(log_fh,"sites_ref_only\t%d\t# sites skipped because there was no ALT allele\n", args->nref_only); + fprintf(log_fh,"sites_many_als\t%d\t# skipped because of too many ALT alleles\n", args->nmany_als); + fprintf(log_fh,"sites_fail\t%d\t# skipped because of failed -i/-e filter\n", args->stats.nfail); + fprintf(log_fh,"sites_no_GT\t%d\t# skipped because of absent FORMAT/GT field\n", args->stats.nno_gt); + fprintf(log_fh,"sites_not_diploid\t%d\t# skipped because FORMAT/GT not formatted diploid\n", args->stats.nnot_diploid); + fprintf(log_fh,"sites_missing\t%d\t# number of sites with at least one trio GT missing\n", args->stats.nmiss); + fprintf(log_fh,"sites_merr\t%d\t# number of sites with at least one Mendelian error\n", args->stats.nmerr); + fprintf(log_fh,"sites_good\t%d\t# number of sites with at least one good trio\n", args->stats.ngood); + + int i; + fprintf(log_fh,"# Per-trio stats, each column corresponds to one trio. List of trios is below.\n"); + fprintf(log_fh,"ngood"); + for (i=0; intrio; i++) fprintf(log_fh,"\t%d",args->trio[i].stats.ngood); + fprintf(log_fh,"\n"); + + fprintf(log_fh,"nmerr"); + for (i=0; intrio; i++) fprintf(log_fh,"\t%d",args->trio[i].stats.nmerr); + fprintf(log_fh,"\n"); + + fprintf(log_fh,"nmissing"); + for (i=0; intrio; i++) fprintf(log_fh,"\t%d",args->trio[i].stats.nmiss); + fprintf(log_fh,"\n"); + + fprintf(log_fh,"nfail"); + for (i=0; intrio; i++) fprintf(log_fh,"\t%d",args->trio[i].stats.nfail); + fprintf(log_fh,"\n"); + + fprintf(log_fh,"# List of trios. Their ids are in the same order as the values listed in the stats lines above. For\n"); + fprintf(log_fh,"# example, the values for the first trio (id=1) and the third trio (id=3) are in the 2nd and the 4th\n"); + fprintf(log_fh,"# column and their stats can be obtained with the unix command\n"); + fprintf(log_fh,"# cat stats.txt | grep ^n | cut -f1,2,4\n"); + fprintf(log_fh,"# TRIO\t[2]id\t[3]child\t[4]father\t[5]mother\n"); + for (i=0; intrio; i++) + { + trio_t *trio = &args->trio[i]; + fprintf(log_fh,"TRIO\t%d\t%s\t%s\t%s\n", i+1, + bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,trio->idx[iKID]), + bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,trio->idx[iDAD]), + bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,trio->idx[iMOM])); + } + + if ( log_fh!=stderr && log_fh!=stdout && fclose(log_fh) ) error("Error: close failed for %s\n", args->output_fname); +} + +int run(int argc, char **argv) +{ + args_t *args = (args_t*) calloc(1,sizeof(args_t)); + args->argc = argc; args->argv = argv; + args->output_fname = "-"; + args->record_cmd_line = 1; + args->regions_overlap = 1; + args->targets_overlap = 0; + args->clevel = -1; + + static struct option loptions[] = + { + {"trio",1,0,'t'}, + {"trio-file",1,0,'T'}, + {"ped",1,0,'p'}, + {"delete",0,0,'d'}, + {"list",1,0,'l'}, + {"mode",1,0,'m'}, + {"count",0,0,'c'}, + {"rules",1,0,1}, + {"rules-file",1,0,2}, + {"output",required_argument,NULL,'o'}, + {"output-type",required_argument,NULL,'O'}, + {"regions",1,0,'r'}, + {"regions-file",1,0,'R'}, + {"regions-overlap",required_argument,NULL,14}, + {"targets",1,0,'t'}, + {"targets-file",1,0,'T'}, + {"targets-overlap",required_argument,NULL,15}, + {"include",required_argument,0,'i'}, + {"exclude",required_argument,0,'e'}, + {0,0,0,0} + }; + int c; + char *tmp; + while ((c = getopt_long(argc, argv, "?ht:T:p:m:o:O:i:e:t:T:r:R:",loptions,NULL)) >= 0) + { + switch (c) + { + case 'e': + if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); + args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; + case 'i': + if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); + args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break; + case 't': args->targets = optarg; break; + case 'T': args->targets = optarg; args->targets_is_file = 1; break; + case 'r': args->regions = optarg; break; + case 'R': args->regions = optarg; args->regions_is_file = 1; break; + case 'o': args->output_fname = optarg; break; + case 'O': + switch (optarg[0]) { + case 'b': args->output_type = FT_BCF_GZ; break; + case 'u': args->output_type = FT_BCF; break; + case 'z': args->output_type = FT_VCF_GZ; break; + case 'v': args->output_type = FT_VCF; break; + default: + { + args->clevel = strtol(optarg,&tmp,10); + if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg); + } + }; + if ( optarg[1] ) + { + args->clevel = strtol(optarg+1,&tmp,10); + if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1); + } + break; + case 'm': + tmp = optarg; + while ( *tmp ) + { + if ( *tmp=='+' || *tmp=='g' ) args->mode |= MODE_LIST_GOOD; + else if ( *tmp=='x' || *tmp=='e' ) args->mode |= MODE_LIST_ERR; + else if ( *tmp=='a' ) args->mode |= MODE_ANNOTATE; + else if ( *tmp=='d' ) args->mode |= MODE_DELETE; + else if ( *tmp=='c' ) args->mode |= MODE_COUNT; + else if ( *tmp=='E' ) args->mode |= MODE_DROP_ERR; + else if ( *tmp=='u' || *tmp=='m' ) args->mode |= MODE_LIST_MISS; + else if ( *tmp=='M' ) args->mode |= MODE_DROP_MISS; + else if ( *tmp=='s' ) args->mode |= MODE_LIST_SKIP; + else if ( *tmp=='S' ) args->mode |= MODE_DROP_SKIP; + else error("The argument \"%c\" not recognised: --mode %s\n", *tmp,optarg); + tmp++; + } + break; + case 'P': args->ped_fname = optarg; break; + case 'p': args->pfm = optarg; break; + case 1 : args->rules_str = optarg; break; + case 2 : args->rules_fname = optarg; break; + case 'h': + case '?': + default: error("%s",usage_text()); break; + } + } + + if ( optind==argc ) + { + if ( !isatty(fileno((FILE *)stdin)) ) args->fname = "-"; // reading from stdin + else { error("%s", usage_text()); } + } + else if ( optind+1!=argc ) error("%s", usage_text()); + else args->fname = argv[optind]; + + if ( !args->ped_fname && !args->pfm ) error("Missing the -p or -P option\n"); + if ( args->ped_fname && args->pfm ) error("Expected only -p or -P option, not both\n"); + if ( !args->mode ) args->mode = MODE_COUNT; + + init_data(args); + + while ( bcf_sr_next_line(args->sr) ) + { + bcf1_t *rec = bcf_sr_get_line(args->sr,0); + if ( !process_record(args, rec) ) continue; + if ( bcf_write(args->out_fh, args->hdr_out, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); + } + + print_stats(args); + destroy_data(args); + + return 0; +} + diff --git a/test/mendelian.4.out b/test/mendelian.4.out index 5426613f4..0d3469b73 100644 --- a/test/mendelian.4.out +++ b/test/mendelian.4.out @@ -9,7 +9,7 @@ ##contig= ##contig= ##contig= -##INFO= +##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT mom1 dad1 child1 1 100 . A G 100 PASS MERR=0 GT 0/0 0/0 0/0 1 101 . A G 100 PASS MERR=1 GT 0/0 0/0 0/1 diff --git a/test/mendelian.6.out b/test/mendelian.6.out new file mode 100644 index 000000000..c5832f30f --- /dev/null +++ b/test/mendelian.6.out @@ -0,0 +1,26 @@ +##fileformat=VCFv4.2 +##FILTER= +##FORMAT= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT mom1 dad1 child1 +1 100 . A G 100 PASS . GT 0/0 0/0 0/0 +2 200 . A G 100 PASS . GT 0/0 0/1 0/0 +2 201 . A G 100 PASS . GT 0/0 0/1 0/1 +3 301 . A G 100 PASS . GT 0/0 1/1 0/1 +4 400 . A G 100 PASS . GT 0/1 0/0 0/0 +4 401 . A G 100 PASS . GT 0/1 0/0 0/1 +5 500 . A G 100 PASS . GT 0/1 0/1 0/0 +5 501 . A G 100 PASS . GT 0/1 0/1 0/1 +5 502 . A G 100 PASS . GT 0/1 0/1 1/1 +6 601 . A G 100 PASS . GT 0/1 1/1 0/1 +6 602 . A G 100 PASS . GT 0/1 1/1 1/1 +X 100 . A G 100 PASS . GT 0/0 1 0 +X 102 . A G 100 PASS . GT 0/0 1 0/1 +Y 101 . A G 100 PASS . GT . 0 0 diff --git a/test/mendelian.7.out b/test/mendelian.7.out new file mode 100644 index 000000000..ed748ae44 --- /dev/null +++ b/test/mendelian.7.out @@ -0,0 +1,18 @@ +##fileformat=VCFv4.2 +##FILTER= +##FORMAT= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT mom1 dad1 child1 +1 103 . A G 100 PASS . GT ./. 0/0 1/1 +1 104 . A G 100 PASS . GT . 0/0 1/1 +1 105 . A G 100 PASS . GT . 0/0 0/1 +X 104 . A G 100 PASS . GT . 0 1 +X 105 . A G 100 PASS . GT . 0 0/1 +Y 103 . A G 100 PASS . GT . 0 . diff --git a/test/mendelian.8.out b/test/mendelian.8.out new file mode 100644 index 000000000..28f9df8a7 --- /dev/null +++ b/test/mendelian.8.out @@ -0,0 +1,13 @@ +sites_ref_only 0 # sites skipped because there was no ALT allele +sites_many_als 0 # skipped because of too many ALT alleles +sites_fail 0 # skipped because of failed -i/-e filter +sites_no_GT 0 # skipped because of absent FORMAT/GT field +sites_not_diploid 0 # skipped because FORMAT/GT not formatted diploid +sites_missing 6 # number of sites with at least one trio GT missing +sites_merr 12 # number of sites with at least one Mendelian error +sites_good 14 # number of sites with at least one good trio +ngood 14 +nmerr 12 +nmissing 6 +nfail 0 +TRIO 1 child1 dad1 mom1 diff --git a/test/test.pl b/test/test.pl index 0497ecda5..17e1df3da 100755 --- a/test/test.pl +++ b/test/test.pl @@ -581,6 +581,12 @@ run_test(\&test_vcf_plugin,$opts,in=>'mendelian',out=>'mendelian.3.out',cmd=>'+mendelian',args=>'-t mom1,dad1,child1 -mx'); run_test(\&test_vcf_plugin,$opts,in=>'mendelian',out=>'mendelian.4.out',cmd=>'+mendelian',args=>'-t mom1,dad1,child1 -ma'); run_test(\&test_vcf_plugin,$opts,in=>'mendelian',out=>'mendelian.5.out',cmd=>'+mendelian',args=>'-t mom1,dad1,child1 -mu'); +run_test(\&test_vcf_plugin,$opts,in=>'mendelian',out=>'mendelian.1.out',cmd=>'+mendelian2',args=>'-p child1,dad1,mom1 -md'); +run_test(\&test_vcf_plugin,$opts,in=>'mendelian',out=>'mendelian.6.out',cmd=>'+mendelian2',args=>'-p child1,dad1,mom1 -mg'); +run_test(\&test_vcf_plugin,$opts,in=>'mendelian',out=>'mendelian.3.out',cmd=>'+mendelian2',args=>'-p child1,dad1,mom1 -me'); +run_test(\&test_vcf_plugin,$opts,in=>'mendelian',out=>'mendelian.4.out',cmd=>'+mendelian2',args=>'-p child1,dad1,mom1 -ma'); +run_test(\&test_vcf_plugin,$opts,in=>'mendelian',out=>'mendelian.7.out',cmd=>'+mendelian2',args=>'-p child1,dad1,mom1 -mm'); +run_test(\&test_vcf_plugin,$opts,in=>'mendelian',out=>'mendelian.8.out',cmd=>'+mendelian2',args=>'-p child1,dad1,mom1 | grep -v ^#'); run_test(\&test_vcf_plugin,$opts,in=>'contrast',out=>'contrast.out',cmd=>'+contrast',args=>'-a PASSOC,FASSOC,NOVELAL,NOVELGT -0 a,b -1 c'); run_test(\&test_vcf_plugin,$opts,in=>'contrast',out=>'contrast.out',cmd=>'+contrast',args=>'-a PASSOC,FASSOC,NOVELAL,NOVELGT -0 {PATH}/contrast0.txt -1 {PATH}/contrast1.txt'); run_test(\&test_vcf_plugin,$opts,in=>'contrast',out=>'contrast.1.out',cmd=>'+contrast',args=>'-a NASSOC -0 a,b,c -1 d --force-samples'); From fe0dfe3fbb869bf5ead555ed1eca8bc3222945e8 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Tue, 1 Nov 2022 15:14:07 +0000 Subject: [PATCH 45/84] Fix a bug which under-reports MNV consequences A MNV with multiple consequences (e.g. missense + stop_gained) be reported only as the less severe one (missense). Fixes #1810 --- NEWS | 5 + csq.c | 268 ++++++++++--------- test/csq/ENST00000360372/ENST00000360372.fa | 240 +++++++++++++++++ test/csq/ENST00000360372/ENST00000360372.gff | 30 +++ test/csq/ENST00000360372/mnp.txt | 3 + test/csq/ENST00000360372/mnp.vcf | 7 + 6 files changed, 423 insertions(+), 130 deletions(-) create mode 100644 test/csq/ENST00000360372/ENST00000360372.fa create mode 100644 test/csq/ENST00000360372/ENST00000360372.gff create mode 100644 test/csq/ENST00000360372/mnp.txt create mode 100644 test/csq/ENST00000360372/mnp.vcf diff --git a/NEWS b/NEWS index 93cbd898b..e7806cb39 100644 --- a/NEWS +++ b/NEWS @@ -15,6 +15,11 @@ Changes affecting specific commands: - Make variantkey conversion work for sites without an ALT allele (#1806) +* bcftool csq + + - Fix a bug where a MNV with multiple consequences (e.g. missense + stop_gained) + would report only the less severe one (#1810) + * bcftools +mendelian - The +mendelian plugin has been deprecated and replaced with +mendelian2. The diff --git a/csq.c b/csq.c index de0d7a9bb..7105a4be1 100644 --- a/csq.c +++ b/csq.c @@ -1,19 +1,19 @@ /* The MIT License - Copyright (c) 2016-2021 Genome Research Ltd. + Copyright (c) 2016-2022 Genome Research Ltd. Author: Petr Danecek - + Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: - + The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. - + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE @@ -76,12 +76,12 @@ B.ID=~/^transcript:/ && B.Parent=~/^gene:A.ID/ C .. corresponding CDS, exon, and UTR lines: - C[3] in {"CDS","exon","three_prime_UTR","five_prime_UTR"} && C.Parent=~/^transcript:B.ID/ + C[3] in {"CDS","exon","three_prime_UTR","five_prime_UTR"} && C.Parent=~/^transcript:B.ID/ For coding biotypes ("protein_coding" or "polymorphic_pseudogene") the complete chain link C -> B -> A is required. For the rest, link B -> A suffices. - - + + The supported consequence types, sorted by impact: splice_acceptor_variant .. end region of an intron changed (2bp at the 3' end of an intron) splice_donor_variant .. start region of an intron changed (2bp at the 5' end of an intron) @@ -119,18 +119,18 @@ (based on biotype) which maps from transcript_id to a transcript. At the same time also build the hash "gid2gene" which maps from gene_id to gf_gene_t pointer. - + 2. build "idx_cds", "idx_tscript", "idx_utr" and "idx_exon" indexes. Use only features from "ftr" which are present in "id2tr". 3. clean data that won't be needed anymore: ftr, id2tr, gid2gene. - + Data structures. idx_cds, idx_utr, idx_exon, idx_tscript: as described above, regidx structures for fast lookup of exons/transcripts overlapping a region, the payload is a pointer to tscript.cds */ - + #include #include #include @@ -163,9 +163,9 @@ #define FLT_EXCLUDE 2 // Definition of splice_region, splice_acceptor and splice_donor -#define N_SPLICE_DONOR 2 -#define N_SPLICE_REGION_EXON 3 -#define N_SPLICE_REGION_INTRON 8 +#define N_SPLICE_DONOR 2 +#define N_SPLICE_REGION_EXON 3 +#define N_SPLICE_REGION_INTRON 8 #define N_REF_PAD 10 // number of bases to avoid boundary effects @@ -186,7 +186,7 @@ // Node types in the haplotype tree #define HAP_CDS 0 -#define HAP_ROOT 1 +#define HAP_ROOT 1 #define HAP_SSS 2 // start/stop/splice #define CSQ_PRINTED_UPSTREAM (1<<0) @@ -226,25 +226,25 @@ #define CSQ_PRN_BIOTYPE CSQ_NON_CODING // see kput_vcsq() -const char *csq_strings[] = +const char *csq_strings[] = { - NULL, - "synonymous", - "missense", - "stop_lost", - "stop_gained", - "inframe_deletion", - "inframe_insertion", - "frameshift", - "splice_acceptor", - "splice_donor", - "start_lost", - "splice_region", - "stop_retained", - "5_prime_utr", - "3_prime_utr", - "non_coding", - "intron", + NULL, + "synonymous", + "missense", + "stop_lost", + "stop_gained", + "inframe_deletion", + "inframe_insertion", + "frameshift", + "splice_acceptor", + "splice_donor", + "start_lost", + "splice_region", + "stop_retained", + "5_prime_utr", + "3_prime_utr", + "non_coding", + "intron", "intergenic", "inframe_altering", NULL, @@ -260,7 +260,7 @@ const char *csq_strings[] = #define GFF_GENE_LINE 2 -/* +/* Genomic features, for fast lookup by position to overlapping features */ #define GF_coding_bit 6 @@ -505,9 +505,9 @@ hap_t; /* Helper structures, only for initialization - + ftr_t - temporary list of all exons, CDS, UTRs + temporary list of all exons, CDS, UTRs */ KHASH_MAP_INIT_INT(int2tscript, tscript_t*) KHASH_MAP_INIT_INT(int2gene, gf_gene_t*) @@ -596,7 +596,7 @@ typedef struct _args_t int ncsq2_max, nfmt_bcsq; // maximum number of csq per site that can be accessed from FORMAT/BCSQ (*2 and 1 bit skipped to avoid BCF missing values) int ncsq2_small_warned; int brief_predictions; - + int rid; // current chromosome tr_heap_t *active_tr; // heap of active transcripts for quick flushing hap_t *hap; // transcript haplotype recursion @@ -644,13 +644,13 @@ const uint8_t cnt4[] = #define dna2aa(x) gencode[ nt4[(uint8_t)(x)[0]]<<4 | nt4[(uint8_t)(x)[1]]<<2 | nt4[(uint8_t)(x)[2]] ] #define cdna2aa(x) gencode[ cnt4[(uint8_t)(x)[2]]<<4 | cnt4[(uint8_t)(x)[1]]<<2 | cnt4[(uint8_t)(x)[0]] ] -static const char *gf_strings_noncoding[] = -{ +static const char *gf_strings_noncoding[] = +{ "MT_rRNA", "MT_tRNA", "lincRNA", "miRNA", "misc_RNA", "rRNA", "snRNA", "snoRNA", "processed_transcript", "antisense", "macro_lncRNA", "ribozyme", "sRNA", "scRNA", "scaRNA", "sense_intronic", "sense_overlapping", - "pseudogene", "processed_pseudogene", "artifact", "IG_pseudogene", "IG_C_pseudogene", "IG_J_pseudogene", - "IG_V_pseudogene", "TR_V_pseudogene", "TR_J_pseudogene", "MT_tRNA_pseudogene", "misc_RNA_pseudogene", - "miRNA_pseudogene", "ribozyme", "retained_intron", "retrotransposed", "Trna_pseudogene", "transcribed_processed_pseudogene", + "pseudogene", "processed_pseudogene", "artifact", "IG_pseudogene", "IG_C_pseudogene", "IG_J_pseudogene", + "IG_V_pseudogene", "TR_V_pseudogene", "TR_J_pseudogene", "MT_tRNA_pseudogene", "misc_RNA_pseudogene", + "miRNA_pseudogene", "ribozyme", "retained_intron", "retrotransposed", "Trna_pseudogene", "transcribed_processed_pseudogene", "transcribed_unprocessed_pseudogene", "transcribed_unitary_pseudogene", "translated_unprocessed_pseudogene", "translated_processed_pseudogene", "known_ncRNA", "unitary_pseudogene", "unprocessed_pseudogene", "LRG_gene", "3_prime_overlapping_ncRNA", "disrupted_domain", "vaultRNA", "bidirectional_promoter_lncRNA", "ambiguous_orf" @@ -795,7 +795,7 @@ static inline int gff_parse_biotype(char *_line) line += 8; switch (*line) { - case 'p': + case 'p': if ( !strncmp(line,"protein_coding",14) ) return GF_PROTEIN_CODING; else if ( !strncmp(line,"pseudogene",10) ) return GF_PSEUDOGENE; else if ( !strncmp(line,"processed_transcript",20) ) return GF_PROCESSED_TRANSCRIPT; @@ -859,7 +859,7 @@ static inline int gff_parse_biotype(char *_line) case 't': if ( !strncmp(line,"tRNA_pseudogene",15) ) return GF_tRNA_PSEUDOGENE; else if ( !strncmp(line,"transcribed_processed_pseudogene",32) ) return GF_TRANSCRIBED_PROCESSED_PSEUDOGENE; - else if ( !strncmp(line,"transcribed_unprocessed_pseudogene",34) ) return GF_TRANSCRIBED_UNPROCESSED_PSEUDOGENE; + else if ( !strncmp(line,"transcribed_unprocessed_pseudogene",34) ) return GF_TRANSCRIBED_UNPROCESSED_PSEUDOGENE; else if ( !strncmp(line,"transcribed_unitary_pseudogene",30) ) return GF_TRANSCRIBED_UNITARY_PSEUDOGENE; else if ( !strncmp(line,"translated_unprocessed_pseudogene",33) ) return GF_TRANSLATED_UNPROCESSED_PSEUDOGENE; else if ( !strncmp(line,"translated_processed_pseudogene",31) ) return GF_TRANSLATED_PROCESSED_PSEUDOGENE; @@ -987,7 +987,7 @@ void gff_parse_gene(args_t *args, const char *line, char *ss, char *chr_beg, cha int gff_parse(args_t *args, char *line, ftr_t *ftr) { // - skip empty lines and commented lines - // - columns + // - columns // 1. chr // 2. // 3. CDS, transcript, gene, ... @@ -1016,7 +1016,7 @@ int gff_parse(args_t *args, char *line, ftr_t *ftr) ss = gff_parse_beg_end(line, ss, &ftr->beg,&ftr->end); ss = gff_skip(line, ss); int type = gff_parse_type(ss); - if ( type!=GFF_TSCRIPT_LINE && type!=GFF_GENE_LINE ) + if ( type!=GFF_TSCRIPT_LINE && type!=GFF_GENE_LINE ) { // we ignore these, debug print to see new types: ss = strstr(ss,"ID="); @@ -1090,14 +1090,14 @@ void register_cds(args_t *args, ftr_t *ftr) tscript_t *tr = tscript_init(aux, ftr->trid); if ( tr->strand != ftr->strand ) error("Conflicting strand in transcript %"PRIu32" .. %d vs %d\n",ftr->trid,tr->strand,ftr->strand); - + gf_cds_t *cds = (gf_cds_t*) malloc(sizeof(gf_cds_t)); cds->tr = tr; cds->beg = ftr->beg; cds->len = ftr->end - ftr->beg + 1; cds->icds = 0; // to keep valgrind on mac happy cds->phase = ftr->phase; - + hts_expand(gf_cds_t*,tr->ncds+1,tr->mcds,tr->cds); tr->cds[tr->ncds++] = cds; } @@ -1186,7 +1186,7 @@ void tscript_init_cds(args_t *args) error("Error: GFF3 assumption failed for transcript %s, CDS=%d: phase!=len%%3 (phase=%d, len=%d). Use the --force option to proceed anyway (at your own risk).\n", args->tscript_ids.str[tr->id],tr->cds[i]->beg+1,phase,len); } - len += tr->cds[i]->len; + len += tr->cds[i]->len; } if ( !tscript_ok ) continue; // skip this transcript } @@ -1245,12 +1245,12 @@ void tscript_init_cds(args_t *args) for (i=0; incds; i++) { tr->cds[i]->icds = i; - len += tr->cds[i]->len; + len += tr->cds[i]->len; if ( !i ) continue; gf_cds_t *a = tr->cds[i-1]; gf_cds_t *b = tr->cds[i]; - if ( a->beg + a->len - 1 >= b->beg ) + if ( a->beg + a->len - 1 >= b->beg ) { if ( args->force ) { @@ -1259,7 +1259,7 @@ void tscript_init_cds(args_t *args) } else error("Error: CDS overlap in the transcript %s: %"PRIu32"-%"PRIu32" and %"PRIu32"-%"PRIu32", is this intended (e.g. ribosomal slippage)?\n" - " Use the --force option to override (at your own risk).\n", + " Use the --force option to override (at your own risk).\n", args->tscript_ids.str[tr->id], a->beg+1,a->beg+a->len, b->beg+1,b->beg+b->len); } } @@ -1360,7 +1360,7 @@ void init_gff(args_t *args) continue; } - // populate regidx by category: + // populate regidx by category: // ftr->type .. GF_CDS, GF_EXON, GF_UTR3, GF_UTR5 // gene->type .. GF_PROTEIN_CODING, GF_MT_rRNA, GF_IG_C, ... if ( ftr->type==GF_CDS ) register_cds(args, ftr); @@ -1374,7 +1374,7 @@ void init_gff(args_t *args) if ( args->verbosity > 0 ) { - fprintf(stderr,"Indexed %d transcripts, %d exons, %d CDSs, %d UTRs\n", + fprintf(stderr,"Indexed %d transcripts, %d exons, %d CDSs, %d UTRs\n", regidx_nregs(args->idx_tscript), regidx_nregs(args->idx_exon), regidx_nregs(args->idx_cds), @@ -1437,7 +1437,7 @@ void init_data(args_t *args) if ( args->sample_list && !strcmp("-",args->sample_list) ) { // ignore all samples - if ( args->output_type==FT_TAB_TEXT ) + if ( args->output_type==FT_TAB_TEXT ) { // significant speedup for plain VCFs if (bcf_hdr_set_samples(args->hdr,NULL,0) < 0) @@ -1479,7 +1479,7 @@ void init_data(args_t *args) hts_set_opt(args->out_fh, HTS_OPT_THREAD_POOL, args->sr->p); if ( args->record_cmd_line ) bcf_hdr_append_version(args->hdr,args->argc,args->argv,"bcftools/csq"); bcf_hdr_printf(args->hdr,"##INFO=",args->bcsq_tag, args->local_csq ? "Local" : "Haplotype-aware"); - if ( args->hdr_nsmpl ) + if ( args->hdr_nsmpl ) bcf_hdr_printf(args->hdr,"##FORMAT=",args->bcsq_tag); if ( bcf_hdr_write(args->out_fh, args->hdr)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->output_fname?args->output_fname:"standard output"); } @@ -1556,7 +1556,7 @@ void destroy_data(args_t *args) */ #define SPLICE_VAR_REF 0 // ref: ACGT>ACGT, csq not applicable, skip completely #define SPLICE_OUTSIDE 1 // splice acceptor or similar; csq set and is done, does not overlap the region -#define SPLICE_INSIDE 2 // overlaps coding region; csq can be set but coding prediction is needed +#define SPLICE_INSIDE 2 // overlaps coding region; csq can be set but coding prediction is needed #define SPLICE_OVERLAP 3 // indel overlaps region boundary, csq set but could not determine csq typedef struct { @@ -1567,16 +1567,16 @@ typedef struct bcf1_t *rec; } vcf; uint16_t check_acceptor:1, // check distance from exon start (fwd) or end (rev) - check_start:1, // this is the first coding exon (relative to transcript orientation), check first (fwd) or last (rev) codon + check_start:1, // this is the first coding exon (relative to transcript orientation), check first (fwd) or last (rev) codon check_stop:1, // this is the last coding exon (relative to transcript orientation), check last (fwd) or first (rev) codon check_donor:1, // as with check_acceptor check_region_beg:1, // do/don't check for splices at this end, eg. in the first or last exon - check_region_end:1, // + check_region_end:1, // check_utr:1, // check splice sites (acceptor/donor/region_*) only if not in utr set_refalt:1; // set kref,kalt, if set, check also for synonymous events uint32_t csq; int tbeg, tend; // number of trimmed bases from beg and end of ref,alt allele - uint32_t ref_beg, // ref coordinates with spurious bases removed, ACC>AC can become AC>A or CC>C, whichever gives + uint32_t ref_beg, // ref coordinates with spurious bases removed, ACC>AC can become AC>A or CC>C, whichever gives ref_end; // a more conservative csq (the first and last base in kref.s) kstring_t kref, kalt; // trimmed alleles, set only with SPLICE_OLAP } @@ -1615,7 +1615,7 @@ static inline void splice_build_hap(splice_t *splice, uint32_t beg, int len) #define XDBG 0 #if XDBG fprintf(stderr,"build_hap: rbeg=%d + %d abeg=%d \n",rbeg,rlen,abeg); -#endif +#endif splice->kref.l = 0; splice->kalt.l = 0; @@ -1703,7 +1703,7 @@ static inline int csq_stage_utr(args_t *args, regitr_t *itr, bcf1_t *rec, uint32 gf_utr_t *utr = regitr_payload(itr, gf_utr_t*); tscript_t *tr = utr->tr; if ( tr->id != trid ) continue; - csq_t csq; + csq_t csq; memset(&csq, 0, sizeof(csq_t)); csq.pos = rec->pos; csq.type.type = (utr->which==prime5 ? CSQ_UTR5 : CSQ_UTR3) | type; @@ -1723,7 +1723,7 @@ static inline void csq_stage_splice(args_t *args, bcf1_t *rec, tscript_t *tr, ui fprintf(stderr,"csq_stage_splice %d: type=%d\n",rec->pos+1,type); #endif if ( !type ) return; - csq_t csq; + csq_t csq; memset(&csq, 0, sizeof(csq_t)); csq.pos = rec->pos; csq.type.type = type; @@ -1763,7 +1763,7 @@ fprintf(stderr,"ins: %s>%s .. ex=%d,%d beg,end=%d,%d tbeg,tend=%d,%d check_ut if ( regidx_overlap(args->idx_utr,chr,splice->ref_beg+1,splice->ref_beg+1, itr) ) // adjacent utr { ret = csq_stage_utr(args, itr, splice->vcf.rec, splice->tr->id, splice->csq, splice->vcf.ial); - if ( ret!=0 ) + if ( ret!=0 ) { regitr_destroy(itr); return SPLICE_OUTSIDE; // overlaps utr @@ -1910,7 +1910,7 @@ int shifted_del_synonymous(args_t *args, splice_t *splice, uint32_t ex_beg, uint while ( ptr_vcf[i] && ptr_vcf[i]==ptr_ref[i] ) i++; if ( ptr_vcf[i] ) return 0; // the deleted sequence cannot be replaced } - else + else { // STRAND_FWD int32_t vcf_block_beg = splice->vcf.pos + ref_len - 2*ndel; // the position of the first base of the ref block that could potentially replace the deletion @@ -2008,7 +2008,7 @@ fprintf(stderr,"splice_csq_del: %s>%s .. ex=%d,%d beg,end=%d,%d tbeg,tend=%d,% } } } - if ( splice->ref_end >= ex_beg ) + if ( splice->ref_end >= ex_beg ) { splice->tbeg = splice->ref_beg - splice->vcf.pos + 1; splice->ref_beg = ex_beg - 1; @@ -2058,7 +2058,7 @@ fprintf(stderr,"splice_csq_del: %s>%s .. ex=%d,%d beg,end=%d,%d tbeg,tend=%d,% } } } - if ( splice->ref_beg < ex_end ) + if ( splice->ref_beg < ex_end ) { splice->tend = splice->vcf.rlen - (splice->ref_end - splice->vcf.pos + 1); splice->ref_end = ex_end; @@ -2089,8 +2089,8 @@ fprintf(stderr,"splice_csq_del: %s>%s .. ex=%d,%d beg,end=%d,%d tbeg,tend=%d,% splice->vcf.rlen -= splice->tbeg + splice->tend; splice->vcf.alen -= splice->tbeg + splice->tend; } - splice->kref.l = 0; kputsn(splice->vcf.ref + splice->tbeg, splice->vcf.rlen, &splice->kref); - splice->kalt.l = 0; kputsn(splice->vcf.alt + splice->tbeg, splice->vcf.alen, &splice->kalt); + splice->kref.l = 0; kputsn(splice->vcf.ref + splice->tbeg, splice->vcf.rlen, &splice->kref); + splice->kalt.l = 0; kputsn(splice->vcf.alt + splice->tbeg, splice->vcf.alen, &splice->kalt); if ( (splice->ref_beg+1 < ex_beg && splice->ref_end >= ex_beg) || (splice->ref_beg+1 < ex_end && splice->ref_end >= ex_end) ) // ouch, ugly ENST00000409523/long-overlapping-del.vcf { splice->csq |= (splice->ref_end - splice->ref_beg)%3 ? CSQ_FRAMESHIFT_VARIANT : CSQ_INFRAME_DELETION; @@ -2137,7 +2137,7 @@ fprintf(stderr,"mnp: %s>%s .. ex=%d,%d beg,end=%d,%d tbeg,tend=%d,%d check_ut } } } - if ( splice->ref_end >= ex_beg ) + if ( splice->ref_end >= ex_beg ) { splice->tbeg = splice->ref_beg - splice->vcf.pos; splice->ref_beg = ex_beg; @@ -2167,7 +2167,7 @@ fprintf(stderr,"mnp: %s>%s .. ex=%d,%d beg,end=%d,%d tbeg,tend=%d,%d check_ut } } } - if ( splice->ref_beg <= ex_end ) + if ( splice->ref_beg <= ex_end ) { splice->tend = splice->vcf.rlen - (splice->ref_end - splice->vcf.pos + 1); splice->ref_end = ex_end; @@ -2194,8 +2194,8 @@ fprintf(stderr,"mnp: %s>%s .. ex=%d,%d beg,end=%d,%d tbeg,tend=%d,%d check_ut if ( splice->set_refalt ) { splice->vcf.rlen -= splice->tbeg + splice->tend; - splice->kref.l = 0; kputsn(splice->vcf.ref + splice->tbeg, splice->vcf.rlen, &splice->kref); - splice->kalt.l = 0; kputsn(splice->vcf.alt + splice->tbeg, splice->vcf.rlen, &splice->kalt); + splice->kref.l = 0; kputsn(splice->vcf.ref + splice->tbeg, splice->vcf.rlen, &splice->kref); + splice->kalt.l = 0; kputsn(splice->vcf.alt + splice->tbeg, splice->vcf.rlen, &splice->kalt); } csq_stage_splice(args, splice->vcf.rec, splice->tr, splice->csq, splice->vcf.ial); return SPLICE_INSIDE; @@ -2311,7 +2311,7 @@ fprintf(stderr,"cds splice_csq: %d [%s][%s] .. beg,end=%d %d, ret=%d, csq=%d\n\n } assert( parent->type!=HAP_SSS ); - if ( parent->type==HAP_CDS ) + if ( parent->type==HAP_CDS ) { i = parent->icds; if ( i!=cds->icds ) @@ -2393,7 +2393,7 @@ void hap_destroy(hap_node_t *hap) /* ref: spliced reference and its length (ref.l) - seq: part of the spliced query transcript on the reference strand to translate, its + seq: part of the spliced query transcript on the reference strand to translate, its length (seq.l) and the total length of the complete transcript (seq.m) sbeg: seq offset within the spliced query transcript rbeg: seq offset within ref, 0-based @@ -2501,7 +2501,7 @@ fprintf(stderr,"\ntranslate: %d %d %d fill=%d seq.l=%d\n",sbeg,rbeg,rend,fill, else // STRAND_REV { // right padding - number of bases to take from ref - npad = (seq.m - (sbeg + seq.l)) % 3; + npad = (seq.m - (sbeg + seq.l)) % 3; #if DBG>1 fprintf(stderr," npad: %d\n",npad); #endif @@ -2546,12 +2546,12 @@ fprintf(stderr,"\ntranslate: %d %d %d fill=%d seq.l=%d\n",sbeg,rbeg,rend,fill, } if ( seq.s-codon==2 ) { - tmp[2] = seq.s[0]; + tmp[2] = seq.s[0]; i = 1; } else if ( seq.s-codon==1 ) { - tmp[1] = seq.s[0]; + tmp[1] = seq.s[0]; tmp[2] = seq.s[1]; i = 0; } @@ -2594,7 +2594,7 @@ fprintf(stderr,"\ntranslate: %d %d %d fill=%d seq.l=%d\n",sbeg,rbeg,rend,fill, void tscript_splice_ref(tscript_t *tr) { int i, len = 0; - for (i=0; incds; i++) + for (i=0; incds; i++) len += tr->cds[i]->len; tr->nsref = len + 2*N_REF_PAD; @@ -2632,7 +2632,7 @@ fprintf(stderr,"csq_push: %d .. %d\n",rec->pos+1,csq->type.type); vrec_t *vrec = vbuf->vrec[i]; // if the variant overlaps donor/acceptor and also splice region, report only donor/acceptor - if ( csq->type.type & CSQ_SPLICE_REGION && csq->type.type & (CSQ_SPLICE_DONOR|CSQ_SPLICE_ACCEPTOR) ) + if ( csq->type.type & CSQ_SPLICE_REGION && csq->type.type & (CSQ_SPLICE_DONOR|CSQ_SPLICE_ACCEPTOR) ) csq->type.type &= ~CSQ_SPLICE_REGION; if ( csq->type.type & CSQ_PRINTED_UPSTREAM ) @@ -2661,7 +2661,7 @@ fprintf(stderr,"csq_push: %d .. %d\n",rec->pos+1,csq->type.type); if ( csq->type.gene != vrec->vcsq[i].gene ) continue; if ( csq->type.vcf_ial != vrec->vcsq[i].vcf_ial ) continue; if ( (csq->type.type&CSQ_UPSTREAM_STOP)^(vrec->vcsq[i].type&CSQ_UPSTREAM_STOP) ) continue; // both must or mustn't have upstream_stop - if ( csq->type.vstr.s || vrec->vcsq[i].vstr.s ) + if ( csq->type.vstr.s || vrec->vcsq[i].vstr.s ) { // This is a bit hacky, but we want a simpler and more predictable output. The splice_csq() function // can trigger stop/start events based on indel overlap, then another stop/start event can be triggered @@ -2669,14 +2669,14 @@ fprintf(stderr,"csq_push: %d .. %d\n",rec->pos+1,csq->type.type); // consequences: // stop_lost|AL627309.1|ENST00000423372|protein_coding|- // stop_lost&inframe_insertion|AL627309.1|ENST00000423372|protein_coding|-|260*>260CL|3630T>TAAA - if ( !csq->type.vstr.s || !vrec->vcsq[i].vstr.s ) + if ( !csq->type.vstr.s || !vrec->vcsq[i].vstr.s ) { if ( csq->type.type&CSQ_START_STOP && vrec->vcsq[i].type&CSQ_START_STOP ) { vrec->vcsq[i].type |= csq->type.type; // remove stop_lost&synonymous if stop_retained set - if ( vrec->vcsq[i].type&CSQ_STOP_RETAINED ) + if ( vrec->vcsq[i].type&CSQ_STOP_RETAINED ) vrec->vcsq[i].type &= ~(CSQ_STOP_LOST|CSQ_SYNONYMOUS_VARIANT); if ( !vrec->vcsq[i].vstr.s ) vrec->vcsq[i].vstr = csq->type.vstr; @@ -2686,7 +2686,7 @@ fprintf(stderr,"csq_push: %d .. %d\n",rec->pos+1,csq->type.type); } if ( strcmp(csq->type.vstr.s,vrec->vcsq[i].vstr.s) ) continue; } - vrec->vcsq[i].type |= csq->type.type; + vrec->vcsq[i].type |= csq->type.type; goto exit_duplicate; } } @@ -2696,7 +2696,7 @@ fprintf(stderr,"csq_push: %d .. %d\n",rec->pos+1,csq->type.type); { if ( csq->type.trid != vrec->vcsq[i].trid && (csq->type.type|vrec->vcsq[i].type)&CSQ_PRN_TSCRIPT) continue; if ( csq->type.biotype != vrec->vcsq[i].biotype ) continue; - if ( !(vrec->vcsq[i].type & CSQ_COMPOUND) ) + if ( !(vrec->vcsq[i].type & CSQ_COMPOUND) ) { vrec->vcsq[i].type |= csq->type.type; goto exit_duplicate; @@ -2799,7 +2799,7 @@ void hap_add_csq(args_t *args, hap_t *hap, hap_node_t *node, int tlen, int ibeg, csq->type.biotype = tr->type; // only now we see the translated sequence and can determine if the stop/start changes are real - int rm_csq = 0; + int rm_csq = 0; csq->type.type = 0; for (i=ibeg; i<=iend; i++) csq->type.type |= hap->stack[i].node->csq & CSQ_COMPOUND; @@ -2826,7 +2826,7 @@ void hap_add_csq(args_t *args, hap_t *hap, hap_node_t *node, int tlen, int ibeg, } if ( csq->type.type & CSQ_STOP_LOST ) { - if ( hap->tref.s[hap->tref.l-1]=='*' && hap->tref.s[hap->tref.l-1] == hap->tseq.s[hap->tseq.l-1] ) + if ( hap->tref.s[hap->tref.l-1]=='*' && hap->tref.s[hap->tref.l-1] == hap->tseq.s[hap->tseq.l-1] ) { rm_csq |= CSQ_STOP_LOST; csq->type.type |= CSQ_STOP_RETAINED; @@ -2862,16 +2862,20 @@ void hap_add_csq(args_t *args, hap_t *hap, hap_node_t *node, int tlen, int ibeg, } else { - for (i=0; itref.l; i++) - if ( hap->tref.s[i] != hap->tseq.s[i] ) break; - if ( i==hap->tref.l ) + int aa_change = 0; + for (i=0; itref.l; i++) + { + if ( hap->tref.s[i] == hap->tseq.s[i] ) continue; + aa_change = 1; + if ( hap->tref.s[i] == '*' ) + csq->type.type |= CSQ_STOP_LOST; + else if ( hap->tseq.s[i] == '*' ) + csq->type.type |= CSQ_STOP_GAINED; + else + csq->type.type |= CSQ_MISSENSE_VARIANT; + } + if ( !aa_change ) csq->type.type |= CSQ_SYNONYMOUS_VARIANT; - else if ( hap->tref.s[i] == '*' ) - csq->type.type |= CSQ_STOP_LOST; - else if ( hap->tseq.s[i] == '*' ) - csq->type.type |= CSQ_STOP_GAINED; - else - csq->type.type |= CSQ_MISSENSE_VARIANT; } } // Check if compound inframe variants are real inframes, or if the stop codon occurs before the frameshift can be restored @@ -3009,7 +3013,7 @@ void hap_finalize(args_t *args, hap_t *hap) // The spliced sequence has been built for the current haplotype and stored // in hap->sseq. Now we break it and output as independent parts - + kstring_t sseq; sseq.m = sref.m - 2*N_REF_PAD + hap->stack[istack].dlen; // total length of the spliced query transcript hap->upstream_stop = 0; @@ -3267,7 +3271,7 @@ vbuf_t *vbuf_push(args_t *args, bcf1_t **rec_ptr) // check for duplicate records i = args->vcf_rbuf.n ? rbuf_last(&args->vcf_rbuf) : -1; - if ( i<0 || args->vcf_buf[i]->vrec[0]->line->pos!=rec->pos ) + if ( i<0 || args->vcf_buf[i]->vrec[0]->line->pos!=rec->pos ) { // vcf record with a new pos rbuf_expand0(&args->vcf_rbuf, vbuf_t*, args->vcf_rbuf.n+1, args->vcf_buf); @@ -3333,7 +3337,7 @@ void vbuf_flush(args_t *args, uint32_t pos) vrec->line->pos = save_pos; // this is necessary for compound variants continue; } - + args->str.l = 0; kput_vcsq(args, &vrec->vcsq[0], &args->str); for (j=1; jnvcsq; j++) @@ -3411,7 +3415,7 @@ static void sanity_check_ref(args_t *args, tscript_t *tr, bcf1_t *rec) int i = 0; while ( ref[i] && vcf[i] ) { - if ( ref[i]!=vcf[i] && toupper(ref[i])!=toupper(vcf[i]) ) + if ( ref[i]!=vcf[i] && toupper(ref[i])!=toupper(vcf[i]) ) error("Error: the fasta reference does not match the VCF REF allele at %s:%"PRId64" .. fasta=%c vcf=%c\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+vbeg+1,ref[i],vcf[i]); i++; @@ -3456,7 +3460,7 @@ int test_cds_local(args_t *args, bcf1_t *rec) if ( rec->d.allele[i][0]=='<' || rec->d.allele[i][0]=='*' ) { continue; } if ( hap_init(args, &root, &node, cds, rec, i)!=0 ) continue; - csq_t csq; + csq_t csq; memset(&csq, 0, sizeof(csq_t)); csq.pos = rec->pos; csq.type.biotype = tr->type; @@ -3504,7 +3508,7 @@ int test_cds_local(args_t *args, bcf1_t *rec) } if ( csq_type & CSQ_STOP_LOST ) { - if ( tref->s[tref->l-1]=='*' && tref->s[tref->l-1] == tseq->s[tseq->l-1] ) + if ( tref->s[tref->l-1]=='*' && tref->s[tref->l-1] == tseq->s[tseq->l-1] ) { csq_type &= ~CSQ_STOP_LOST; csq_type |= CSQ_STOP_RETAINED; @@ -3537,16 +3541,20 @@ int test_cds_local(args_t *args, bcf1_t *rec) } else { - for (j=0; jl; j++) - if ( tref->s[j] != tseq->s[j] ) break; - if ( j==tref->l ) + int aa_change = 0; + for (j=0; jl; j++) + { + if ( tref->s[j] == tseq->s[j] ) continue; + aa_change = 1; + if ( tref->s[j] == '*' ) + csq_type |= CSQ_STOP_LOST; + else if ( tseq->s[j] == '*' ) + csq_type |= CSQ_STOP_GAINED; + else + csq_type |= CSQ_MISSENSE_VARIANT; + } + if ( !aa_change ) csq_type |= CSQ_SYNONYMOUS_VARIANT; - else if ( tref->s[j] == '*' ) - csq_type |= CSQ_STOP_LOST; - else if ( tseq->s[j] == '*' ) - csq_type |= CSQ_STOP_GAINED; - else - csq_type |= CSQ_MISSENSE_VARIANT; } if ( csq_type & CSQ_COMPOUND ) { @@ -3576,7 +3584,7 @@ int test_cds_local(args_t *args, bcf1_t *rec) tr->root->ncsq_list++; hts_expand0(csq_t,tr->root->ncsq_list,tr->root->mcsq_list,tr->root->csq_list); csq_t *rm_csq = tr->root->csq_list + tr->root->ncsq_list - 1; - rm_csq->type.vstr = str; + rm_csq->type.vstr = str; } if ( csq_type & ~CSQ_COMPOUND ) { @@ -3644,7 +3652,7 @@ int test_cds(args_t *args, bcf1_t *rec, vbuf_t *vbuf) fprintf(stderr," This message is printed only once, the verbosity can be increased with `--verbose 2`\n"); overlaps_warned = 1; } - if ( args->out ) + if ( args->out ) fprintf(args->out,"LOG\tWarning: Skipping overlapping variants at %s:%"PRId64"\t%s>%s\n", chr,(int64_t) rec->pos+1,rec->d.allele[0],rec->d.allele[1]); } else ret = 1; // prevent reporting as intron in test_tscript @@ -3653,7 +3661,7 @@ int test_cds(args_t *args, bcf1_t *rec, vbuf_t *vbuf) } if ( child->type==HAP_SSS ) { - csq_t csq; + csq_t csq; memset(&csq, 0, sizeof(csq_t)); csq.pos = rec->pos; csq.type.biotype = tr->type; @@ -3680,7 +3688,7 @@ int test_cds(args_t *args, bcf1_t *rec, vbuf_t *vbuf) // apply the VCF variants and extend the haplotype tree int j, ismpl, ihap, ngts = bcf_get_genotypes(args->hdr, rec, &args->gt_arr, &args->mgt_arr); ngts /= bcf_hdr_nsamples(args->hdr); - if ( ngts!=1 && ngts!=2 ) + if ( ngts!=1 && ngts!=2 ) { if ( args->verbosity && (!multiploid_warned || args->verbosity > 1) ) { @@ -3691,7 +3699,7 @@ int test_cds(args_t *args, bcf1_t *rec, vbuf_t *vbuf) fprintf(stderr," This message is printed only once, the verbosity can be increased with `--verbose 2`\n"); multiploid_warned = 1; } - if ( args->out ) + if ( args->out ) fprintf(args->out,"LOG\tWarning: Skipping site with non-diploid/non-haploid genotypes at %s:%"PRId64"\t%s>%s\n", chr,(int64_t) rec->pos+1,rec->d.allele[0],rec->d.allele[1]); continue; } @@ -3766,7 +3774,7 @@ int test_cds(args_t *args, bcf1_t *rec, vbuf_t *vbuf) } if ( child->type==HAP_SSS ) { - csq_t csq; + csq_t csq; memset(&csq, 0, sizeof(csq_t)); csq.pos = rec->pos; csq.type.biotype = tr->type; @@ -3890,7 +3898,7 @@ int test_utr(args_t *args, bcf1_t *rec) splice.csq = 0; int splice_ret = splice_csq(args, &splice, utr->beg, utr->end); if ( splice_ret!=SPLICE_INSIDE && splice_ret!=SPLICE_OVERLAP ) continue; - csq_t csq; + csq_t csq; memset(&csq, 0, sizeof(csq_t)); csq.pos = rec->pos; csq.type.type = utr->which==prime5 ? CSQ_UTR5 : CSQ_UTR3; @@ -3958,7 +3966,7 @@ int test_tscript(args_t *args, bcf1_t *rec) splice.csq = 0; int splice_ret = splice_csq(args, &splice, tr->beg, tr->end); if ( splice_ret!=SPLICE_INSIDE && splice_ret!=SPLICE_OVERLAP ) continue; // SPLICE_OUTSIDE or SPLICE_REF - csq_t csq; + csq_t csq; memset(&csq, 0, sizeof(csq_t)); csq.pos = rec->pos; csq.type.type = GF_is_coding(tr->type) ? CSQ_INTRON : CSQ_NON_CODING; @@ -3996,7 +4004,7 @@ void test_symbolic_alt(args_t *args, bcf1_t *rec) { while ( regitr_overlap(args->itr) ) { - csq_t csq; + csq_t csq; memset(&csq, 0, sizeof(csq_t)); gf_cds_t *cds = regitr_payload(args->itr,gf_cds_t*); tscript_t *tr = cds->tr; @@ -4014,7 +4022,7 @@ void test_symbolic_alt(args_t *args, bcf1_t *rec) { while ( regitr_overlap(args->itr) ) { - csq_t csq; + csq_t csq; memset(&csq, 0, sizeof(csq_t)); gf_utr_t *utr = regitr_payload(args->itr, gf_utr_t*); tscript_t *tr = utr->tr; @@ -4054,7 +4062,7 @@ void test_symbolic_alt(args_t *args, bcf1_t *rec) while ( regitr_overlap(args->itr) ) { - csq_t csq; + csq_t csq; memset(&csq, 0, sizeof(csq_t)); tscript_t *tr = splice.tr = regitr_payload(args->itr, tscript_t*); splice.vcf.alt = rec->d.allele[1]; @@ -4143,7 +4151,7 @@ static void process(args_t *args, bcf1_t **rec_ptr) return; } - if ( args->rid != rec->rid ) + if ( args->rid != rec->rid ) { hap_flush(args, REGIDX_MAX); vbuf_flush(args, REGIDX_MAX); @@ -4172,7 +4180,7 @@ static void process(args_t *args, bcf1_t **rec_ptr) static const char *usage(void) { - return + return "\n" "About: Haplotype-aware consequence caller.\n" "Usage: bcftools csq [OPTIONS] in.vcf\n" @@ -4182,7 +4190,7 @@ static const char *usage(void) " -g, --gff-annot FILE GFF3 annotation file\n" "\n" "CSQ options:\n" - " -B, --trim-protein-seq INT Abbreviate protein-changing predictions to max INT aminoacids\n" + " -B, --trim-protein-seq INT Abbreviate protein-changing predictions to max INT aminoacids\n" " -c, --custom-tag STRING Use this tag instead of the default BCSQ\n" " -l, --local-csq Localized predictions, consider only one VCF record at a time\n" " -n, --ncsq INT Maximum number of per-haplotype consequences to consider for each site [15]\n" @@ -4261,13 +4269,13 @@ int main_csq(int argc, char *argv[]) {"no-version",no_argument,NULL,3}, {0,0,0,0} }; - int c, targets_is_file = 0, regions_is_file = 0; + int c, targets_is_file = 0, regions_is_file = 0; int regions_overlap = 1; int targets_overlap = 0; char *targets_list = NULL, *regions_list = NULL, *tmp; while ((c = getopt_long(argc, argv, "?hr:R:t:T:i:e:f:o:O:g:s:S:p:qc:ln:bB:v:",loptions,NULL)) >= 0) { - switch (c) + switch (c) { case 1 : args->force = 1; break; case 2 : @@ -4279,19 +4287,19 @@ int main_csq(int argc, char *argv[]) args->brief_predictions = 1; fprintf(stderr,"Warning: the -b option will be removed in future versions. Please use -B 1 instead.\n"); break; - case 'B': + case 'B': args->brief_predictions = strtol(optarg,&tmp,10); if ( *tmp || args->brief_predictions<1 ) error("Could not parse argument: --trim-protein-seq %s\n", optarg); break; case 'l': args->local_csq = 1; break; case 'c': args->bcsq_tag = optarg; break; case 'q': error("Error: the -q option has been deprecated, use -v, --verbose instead.\n"); break; - case 'v': + case 'v': args->verbosity = atoi(optarg); if ( args->verbosity<0 || args->verbosity>2 ) error("Error: expected integer 0-2 with -v, --verbose\n"); break; case 'p': - switch (optarg[0]) + switch (optarg[0]) { case 'a': args->phase = PHASE_AS_IS; break; case 'm': args->phase = PHASE_MERGE; break; @@ -4303,7 +4311,7 @@ int main_csq(int argc, char *argv[]) break; case 'f': args->fa_fname = optarg; break; case 'g': args->gff_fname = optarg; break; - case 'n': + case 'n': args->ncsq2_max = 2 * atoi(optarg); if ( args->ncsq2_max <= 0 ) error("Expected positive integer with -n, got %s\n", optarg); break; diff --git a/test/csq/ENST00000360372/ENST00000360372.fa b/test/csq/ENST00000360372/ENST00000360372.fa new file mode 100644 index 000000000..9b8189141 --- /dev/null +++ b/test/csq/ENST00000360372/ENST00000360372.fa @@ -0,0 +1,240 @@ +>chr1 chr1:201358989-201373274 +GAAGGGGACGTGACAGAAATGCCAGTCAGTGTGTGGTGGCTTTTTATTACTGGTGTGGAG +TGGGTGTGGGGGCAGGCAGGAGTGGTGGCTCCCACCTAGGCCAGCTCCCCATTTCCAAAC +AGGAGCTGCCTGGGGTGCCCAGGAGGGCCCGGGAACTGGGGGAGTGCAGGCCGGAGGCAG +GTGCGAGCGAGGAGCAGATCTTTGGTGAAGGAGGCCAGGCTCTATTTCCAGCGCCCGGTG +ACTTTAGCCTTCCCGCGGGTCTTGGAGCTGCAGGGGAAGCAGGACGCAGTGACATGGAGA +CACAGGCAGGGTAGTAGGTCACCATGCGGCTGGGGTAGGACTGGGGTGCCAAAGGGGAGA +GGAGCAGGCTGGAGCTGCCTCCAGGGGCAGAATAGGACAGCAGCCTGAGGCTGGAGGGAA +GCTTCTCCGCCCCACATTTCACCCCCACCAGCAAGCAGAGGCCACAGGGAGAGAAGCACG +AGGCCCCGGAGGAGCCAGAGAAGGAAACCTGTGGGCTGAAGCAGAGGAGGAAGGGCTGGG +AGCCTGGGGCCCTCCAAGGAGGAATGGGATAGCTGGAAGGTAGGGAAGGAGGGGGCAGGG +GGAGGGCTAGGCGAGAATGACCTCAGACACTTACACTTTCTGGTTATCGTTGATCCTGTT +TCGGAGAACATTGATCTGCAAGAAAAGTGGGAAGGACAAAGAGCAACGCTGGAGCTGACT +GGCTCAGGTCCCAGGTGGCCTGGGGATGGGGAGAAGGGGGCTGAGTGCAGCAGTGCAGGA +GGAGAAGGAGGAGCATGGAAGAGTAGGAGGGGTTAGGATAGTTAAGGGTCAGGAGGGGCC +CGTGTACCACAGGCAGAAGCCAAGGAGAAGCTTCCAGGATGCCTCATGGGCCTCCCACTG +TGGGGTCCCAGGGCCATAATAGGTTCAGGATATGAGAGTCCCATAAGAAGGGCCTCTGAG +AGCTGGGCACAAAGCTGGAGGCTGTGTCATGGAGCCCTCCTAGCAGCCCAGCCCCAGACC +CCTCTGGGGCACCCCTGCCCAGCTGCCCACCATCCCGGAAGCTGTGCCCTTTGAGCAGTA +GCATCCCCATGCACCACCCCTGCAGGGTGCTGCCCCAAAGTTTGGCAAATCTGTGTCCTG +TTGGCCGGTGCAGAGTTCAGTGTGGAACCAAAAAAAGAGAAAAAAGTGGAAGGCACAGGA +CTAGAGAGGCCATAACAATGGCTGACACCTGCTGAGCATTTAGTGGGTGCCAGGCTCTGT +CCTGAGCACCTTCCCAGATATGAACCCATAGGGCTGCTATGAGGGCATAGTAAGTTAATA +CATGGGACATGCTTGGAACAGTGGTTGGAACACTATAGCAATAATAACAATTAGTATTAT +CTCTGTAACCCTCACAATCACCCTCTGAAGTATATTGTAGTGTTACCTGTGGAAATGGAG +GCAAGGAACAGTGGACTAACTCACCCAATGTCACACAGCCAGTGAGGGGCACAGGTAGAA +ATTCAACCCAGGCATTATGGCTCCAAAGTCCATGCCACTGTCACCAGGCAATACAGCCTC +TCTCCGTATTGGGAGGTGGGAGTACCCTGTAGCCACTGCAGCCTGAGCCTGCCCAGCGAG +GGGCTTCTTGCCCAGGGAGGAGTGGTTTGGCAGGAGCAGCAAAGGAGACCTTCCAGGGGA +AGCTGAATTCTTCCCTTAGGTAGCAAAGAGGCCCTGGGACCGGGGCTCGGGGGTGGTGGG +TAAGGAAGGACTGGCGCCCAGGTCTAAGCTCCGGTATGCAGCATCAGTGTCCTCTAAGCC +ATTTCCTTGCCTGGTGTCTGTTCACCTAAGACCCTCATTAGTGCACATAGGACTCCGAAA +GACTGTGAGCTTGAGGCTCAGCCTAATTGTGCCCACACCAGGACCTTGGGTGTATGTGGG +GAGAAGCACCTCTCTGTTGGCAGCACTCCCCTTCCACTGGGGGTCCTGGCTTGGTGCATC +CTGGTCCTTGTAACCAGCTCAGATCACTGAGCTGCTGCCTCAACGTGTTGGAGACCCCCA +GGGTTGGAACACCAGGAAAGTGTCTCTGCTCAGCCCCAGCGAGCTCTCAGACACTTCCAG +CAAGCAGTCGTCAATGCGGTGGACATGGAACACTGCTGAAGGCCAGGCAGCAGGGGCAGA +TGCAGGAGCTGAAGGGGGCTGTTGGGGAATAGGGACAGGGACCCAGGGACCTGCAGCAGT +ATTACCGGACCCAGTGAACCAGGAGGAGTGTGAGATGGAGATGCTGGGCGGGGACAGCAT +GGCGGCCCACCTCATATTTCTGCTGCTTGAACTTCTCCTGCAGGTCGAACTTCTCTGCCT +CCAAGTTATAGATGCTCTGCCACAGCTCCTTGGCCTTCTCCCTGCACGGGCAAGGGTGAG +AATGGGGAGGTCCAGTAAGAAAGGGCCCTCCTGGGCCTCCGTCCTGGTCCCGGCCCAGCC +CCCAGCATCCCAGCCCTCCTTCCCACCTCCAGGCCTGCCAAGGGTACCCCAGCCCACCCC +CTGGGCCTGACCCAGCCTGGGGACCAGACGGCAGCACCCAGTGCTCAGGAACGGACACCA +GGGACTGCCAGGGCAAAGTTCCAAGAACAAGCGGGGAGCAGGAGAAGCCCTTCTGGCGCA +GGAGAGCATCTAGTTCAATCCCCTGTCCTGACACCCGTGTGCAGGTGGGTAGGTGAAGCT +CAGAGGGGTGGGGCACCTGCTCAGTTCTCTTTCCCCATCAGCAAAGCCCAGAAAGGAGTT +GGCCCGACCTGCTGGGGCCCAGCTCTGGTCCCACCAAACTTGCCATGGGAAAATATGTGA +GGCAGTCCTGCCCTCTGGTGGCTCACAGCAAGAAGTGCCCTTGGCCCGACCCCTCCCAGA +GCAGATGCGGGCAGTGCCCCAGGACCATTCCTCCCAGCCCCCACCTCAGCTGATCTTCAT +TCAGGTGGTCAATGGCCAGCACCTTCCTCCTCTCAGCCAGAATCTTCTTCTTCTTTTCCC +GCTCAGTCTGCCTCTTCCCACTTTTCCGCTCTGTCTGGAGGGTGTGGGAAGCAGAGTAAA +CTGGCCAGATTGCCCCCTCCCTGTCCCCTAACCCTCCCCAAACCCCCTGGGGGTGGAGCA +AGGCCTGCAGGAGGGCCAGGTTCTTATGCTCTTCTTCCTGCCACACCCCCCAACTACCAA +CTACATGTATTCCCTAGGGAAACTGAGGTAGGGGCAAGAAGGATCACGTCAGTCTCTTCC +TTCTTTGCCTAACTAATCTCTTTCACCTCTCACCAGCTTCCCCCCTCCCCAGCCAGCCCA +ATCTCTTCACTCCTCCCCTCCAGCAAGGCGCCTTCCCCTCCCAGGGAGCTCTCCAAAACT +ATGGGGAGGAAGAAGGCTTGAGGTTTTTGGTACCCACCTGGGCCTGCTAAACCGGGAAAC +CATGAGAGAGAGGCCCATAGAAAAAGACCAAGACGGCAACAGAGACACAGAGAGAAGGCA +GGAAGACAAAGGCAAGGAGAGACATGGAAGAGAAGATTCAGATACTCGCTGTAGTCAGCC +GGGTTTACTAGGACGTGGGTCTGAGGGTTACAGCAGGGGCTGTTCGGTAGCATGAAGACT +TTGATGCCAAAGTCTTGGCTGGTGTGGTCACCATGGGGGCAGAGGCAGGGGGTGGCCTAG +TCCTGAGCTAGGGACTAAGCTGGAAATCTAAGAAAATGTTTTGATTCCTTCACTACCTAG +AGAAAATCAATTTCACATATCCCTCCTCCCTCGAGAATGGAGGACCTAGGAGGAATGGGG +CACAAAAGTTAGGGATCGAGAGTGAGTTTCCAGGAACAAACAACCTCACATCTGTGTGGC +ACATAGACACTTTCCATGGTAGCTCATTTGAGCTTCTCAAAGCATCAAGGCAGGCAATAT +GAGTGCCAGTTGAGGAAACCGAGGCTCAGAGGTTGCAAAAGGTCACACAACTGTATGTGG +CAGAGCTGGGTCTCCAACTAGAGCTCTGACTCTAGGCACAAGGCTCTTCCAGCTGCACCC +AGCCTCCTTGGGGGCTCCTGAGCACTGCTGGAGCCAGGCATGGGGGGCACCATTGGTGCC +CCAGGCTCTGCCTGTAGCCCCCTACCCCAGCAAGCCCCTCCTAGTGCAAGCCGCGGTCAG +GCTGAAAACCAGCTCAGGGCTGGGCATGAGGAGACCTCAGTCTTCCACCCACAGCAGCTG +GGAATCTCTTCCTGGGACCTGACCTAAAGTCTACCTGCTGCAGTGGACACCTCATTCCTC +AGGGCTATACTAGGATCTCCTGGCAACCCCTGCTGCTCCCTACCTACCTTCTGGATGTAA +CCCCCAAAATGCATCATGTTGGACAAAGCCTTCTTCTTCCGGGCCTCATCCTCAGCCTTC +CTCCTGTTCTCCTCCTCCTCTCGTCGAGCCCTCTCTTCCTGATTTACAGCAGGGAGGAAG +AAAGCAAATTAGGGGAAAGGATTGGAAACCCTGATTCTGGGCTGAAGCTTGTGGTCTTTA +TGGGTGAGTTCAGCTTTCTCTCCGCTCAGCAAGGAGCTTTCTGAGAGGGTAGCTCCCAGC +ACAGTGCTGGCCCACAGGAGTCCACTGACTGAGAAATGACTGCGTGATTGAATGAGGTCC +TGATTCCCAAATGTGAGGTCTCGTCATCCCCTTAAGCTGGGAGTGCCCCTGGAAGACCTG +TTGCTCTGGAAATGCCTTCAGCAGCTGCACAGGAAGAGAGCTACGGGGCCTTCGGTTCCC +ACGAAGTCTGCACTGGGGAAGGGATGAGGGCTGGAGAGTCTTATAAAATAACACGTTCAT +AAGGACGCAGGCATTTCTGTCTTGTTTGCTGATGTATTATCAGAGCCAAGACAATGCCCA +GCACTTCCTAGGTTGATATTGATATTGTCTCTTTTTTTTCCTTTTTTTTTTTTTTTGAGT +TGGAGTTTCACTCTTGTTGCCCAGGCTAGAGTGCAATGGCATGACCTCGGCTCACTGCAA +CCTTGCCTCCTGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTAGGATGACC +GGCATGTGCCACCACGCCTGGCTAATTTTGTATTTTTAGTAGAGACAGGGTTTCTCCGTT +GGTCAGGATGGTCTCGAACTCCCAACCTCAAGTGATCTACCCGCCTTGGCCTCCCAAAGT +GCTGGGATTACAGGCGTGAGCCACCGCACCCGGCCAATATTGTCTCTTGACTGATTTCAT +TCATGTTGATGAATAGAGAGGGGCCTGGGGGCCCAGCAGGAGCTGGGAGCATGGGGGGCC +TCCATGGGCCTGGGCTAGGGGTCACTCACAGCCAGGCGGTTCTGCCGCTCCTTCTCCCGC +TCATTCCGGATGCGCTGCTGCTCGGCCCGCTCTGCCCGACGTCTCTCCTAAGGAGAAGAG +GCAAAGCCCACCCAGGTGTGCATAGGGAGAAGGTGACATCGCAGGTACAGAAACCTGCAT +GGGGTGGCAAGGGAATTCCTGGGGGAGGGTTCCTTCCAGAGTCTTGAAGCAATGGTGCCC +GGCCTCCAAGGGCCTCCACTTTCAACCAGCTCCACGGACGTGCACACCAGGGTACCTGCA +GTGACCCACCTCCAACATTCCTCATGGTGAGACTGCCCTCCACAACTGGGAGACATCAGG +CAGGCTCCTTCTGGGCTCTGCCCCCACCTCCATCCCACCCTGCCCTGGCAGCTGCTCTGT +GCCATATGCTTGGATAGATGGCCAAGTCATTGCTCCAGCCAGAGCAGCATGTCTGTGGGA +AGGCAAGTTTGATGGGGAGAAACAAAAGCAATCAAAGCAGCCTCCACGCTCTGCAGGAGA +AGGATGTGGGATTCTGCAGGTCACACTCCCCTTCATCTGCGGGGGAAGAGGAGGCAAGGG +CAGGGGTGGCGCAGCAGGCCTGTGACCAATCAGTCCACAGCCCGGGCCTGAATTAGGCCC +TGGGGGAGGCCTGAAACAGATCAGACTCAGCTCTGGCAGTCAAGGAGCATCCAGTAGGAT +GGGGAGGGAAGGCAGGGACCCGAGAAACCAGTCAGGGCTGCAGGAGCTGTGCAGAATGCT +GGAGGGCCTCTGAAGGAGACCTCACACCTAGCTGGGTTTGAGGCGCCGAGGAAGGCTGTC +TGGAGGAGGTGGGGCCTCACAAAAGGGATGGAGGACAGACTGGGCCATCAGAGAATGTTA +GGTGGGCAGACTGGACACCTACGATCCTGTCTTTGAGAGAAACGAGCTCCTCCTCCTCTT +TCTTCCTGTTCTCAAAGTGAGCCTCGATCAGCGCCTGCAACTCATTCAGGTCCTTCTCCA +TGCGCTTCCGGTGGATGTCCTGTGGGTGGACCGCTGCGGCTCAGAGGCTGCCACTCCAAA +GAGTCCAGAGGAGAGATGGGTGGGCTAGACACCCCCCAACGCAGTGCAAAAGACCTCTGG +CAGGGCCTGGCGCCTGGCCAGGGAAGGGGTAACTGTGGCCTGAACCCAGGACCACGCTCA +TGGATGGGCACCCAGCCTGGCTGGTGCTGCACCCCATCCCACCTATGCTCTACCCCAGCC +CAAGGTCACAAAATCTCTGTCACTGAGGGCCCTTGGGACTATCCCCAGCCCAGGCCTACT +CAACCCACAGCCACCGCTTACATCAAAGTCCACTCTCTCTCCATCGGGGATCTTGGGAGG +CACCAAGTTGGGCATGAACGACCTGTTGGAGAGAGGAATAGTCAGCATCAGCCCCATTCT +GGACCCAGGGACTGAGGGTGTCCAGGACAGGCAGGGCCCTGATCCTTCCTAGAGAATCTT +CCAGCACTGCCCCGACCAACCACAGCAATGATAGTAACACTGACGTCAACAATGGCAGTC +CTCAGCCTTGCTCAGCACCTGGGAATACACAAAGCTCTTTCACATATGCTATTTCACTTC +ATGCTCATGATATGCCCATGAAGTGGGTACCGTTAATCTCACTTAGGAGAACTGAGGCTC +AGGGAGGTAGAATGACTTGCTCAAAGCCACACAACTTGGAATCAAAGAAGCTGTGACAAG +ATGCCATGCTTCTTGGACTTCAAATCCCCTGGTGGACCCCGCAGAAACTGGCCATGAACC +TGGGAGTCTTGCAGTTTGGTCCTGGTCCCAACACATACTGAGACCCAGGGGGTTCTCTGA +TTCTTCATGTCCCCATCTGCCCTCAGGTGTGTGGAGCTGAAATGAGATACCGCAGTGCAC +AAGAGGCCAGGAAGGGGGAAGGCACTGGGCAAATAAATGGATCTGGGATGTCTTGGGCTG +GTTTCAGAAGGCCCCACTGAAATGGGAAGAGCCTGTGAGTGGGCAGAGGTGCCATGGGTC +AACCTCTGCTGGCAGGGTTGGCATCATAAAAAGGGAAATGCTCCCTATCCCCCAGCCCCC +CCCAGCACACACCACCTTCAGGTGGGCTTCACGTGTGTGGCACCAAGCCGTCCTGCCCTC +TCTCAGCTCTCTGAAGCCGCCATGCCTATGCTGGCACGGTTTCATTGTTTGGCTCCCCAC +AATTTGCTTCCCTTAATCCCAAGGTCCCACCTCGGCCATGGAGGAGGGTGTTCTGGCCAT +ACTGTGAGAGAGGAGAGTGTCCGTTCAGGGCCCTTCCTCTAGAAGAACATAGCCCCATCC +CTGCTAGGGTGCACGATTGGTGATGGAGTGTTGGGTGGAATTCAGCCCTCACTCACTCCC +TTAGGAAGAGACGCTTGTGCAGTACACAACTTGTACAACTGTACTGTGGTGCTCTGTGCC +CACCAAACCCCCAGCCCGTGTCCACTGCACCATACTGCACCCCGTTCCATCATCATCCTC +TCTCCCTGAGCCTCTGCTCCCGGCTCTACCCAGGTGCCTCCCCACTCACCTGGGCTTTGG +TTTGGACTCCTCCATTGGGCCATCTGGAGGAGATAGAAGCACACAGCCATGGGTCAGGGG +GCCCCAGAAGTGGTCCCAACTCCGCCCTCGATGAGCTAGATCCCTGTGGATTTCCATTTC +CCCATCTGCACAGTGAGTCCCTCCCGGCACTGGGGAGCCCTGATTCCAGAAGCATCCAGG +AGAATGAAGGCAGCGGGGGCTGCAGATGCCACACTCCCCCTCCCATAGAGTTCTGCAGGG +CACACACTCACGCAGTGTGGAACTTCACACAAAGCCTTCTCTCACTCACCAGTTCTGGGC +AAAGCAATTTTGCTTCTCTTGTGCTTCACAGTGACAAGGCCTTTGGAAAGGTCCCCAAGG +GTCCTGGCCCTAGAATCCCCTCCCAGGTCTTTGCCTTCTTTGTTACCCCTTGGACTTCCC +GGTGGCCACAGGGCAGAAGCTGATGACATGATTCCAAGCCCCAGCTGGTTGTCCCCTCCC +CTTTGGAGAAGTGACTGGGACCACTTAGAACCCTGGTGAAGGCTGCAGCATGACGATGAC +TGCAGCAATGACCCACCATGACCATCTATGCATTGGGATTTCATCCTACGGACACCACAT +CCTACAAGTGATTTCACCTAAGCTCTAGGAGCTTCATGTGTGGATATGACTTCTGGGTCC +CATTGCTCTGTCCAGACCAGGGGGCTGGACAATGGTCCCCTCTCCCACTGGGTGCCACCA +ATGCAACTTCTCTGGGAGAAGGGGCAAAGTTGAAAGCTCAACATCTAAAACTTTGGAAGT +GCCACCAAGTTCTGTCCTCTCCTCTCCCAAACCCTCTCAGTGCACATCCACTTCCCTGGA +AAGAGCACTGTGGGCATTCTCCTCCAAAGCTGCTGTGAGGGGTTCCTTTGCCTCCCTTGT +ACCTCTCTCCTGATATCCTTACCTTCAGCCTCCTTTGCTTCCTCTTCTTCTTCATCTTCT +AAATGAAACACGAGAAATCAATCAAGGTCCTTGTTCTGAGCTCAAGTCCCCCCCTCCGCC +ACCAGCAAGAGCCTTCCCCACAGATAAGCCCTAGCCAAGATGCACTCTGTTGGTTTTTGG +GGTTACAGAGCTGTCTCTCACACACACATTCCCCTGGACCCAAGACTGCCTGACACAAGA +GAAGCGCTGGGTCAACGTTTGTTGATTGGGCAATCAATGGTTGAATCTTAGTCAATAGGA +GAGTCAGGTGCACATGGGAAAGCCTGTTCTGGGGGGTTTCTTACTGCCTCAGGAATGGCT +CCAGGGGCTCTCGCCACCCCCTGAGGCCCCTGCACCCTCAACCAGAGACTTACCTTCTGC +CCTGGTCTCCTCGGTCTCAGCCTCTGCTTCAGCATCCTCTTCCGCTGCCTCCTCCTGCTC +TGGAGAAGTGAAGCAGACAGAGTGAAGAAGCAGGCCCCACTCATGCTATCAGGCAGAACC +CAGAGCAGAGAATGGGCAGCGGGGAGTGGGGATGGGGGTCAAGACGTCTAGGTCCAGATG +AATTTGGGGGCAACCAACGTGCTGGGGGGCTGCCATTCTTGGTTTTGACTGTCGGCTACC +TCCCGCCACCCAGCTTAGCCCCACTCATCCCGGCAACCTCCCTGATGATGGGACTCCACC +TCATTCCCCAACTTTCCAGCCCAGAAGTTCCACCCCGTGTCTGGCACCACAGAACATGCT +CTGCTTAAGCCGAGGTGTCCAGAAGCTCCTGTCCTGAACCTAGTGACTCTAGACACCCTC +AATCCACATCTCAAAGAAACCAAAAGAGTACGACTGTGTGGCTGGATGGCACACTCAATA +TCTGGATCTTCGTACTATCCAGAAAGTGGGCAGGATTTTTCTATTTTCATCTATTTGTTT +GGCAGGATGTGGCCCCCATCTCACTCAGGCACTTGGTGTAGACAGACAGACAAACAGATA +AGGGAGACAGGATGCCGCCTGGCCTGGGCTGTGCCTGTAGGAAGTGTTCTGTGATGCCTG +TTCACTGATGCACTGGGAAGTGGGTGCCTCTTGGCAGAGGGAGAAGAAAAACCTCAGACA +GGAGGAAGACACCATCGTGGGAGAAGGGTTGGCCTTCATTCCCTCTGTCCTCCCTTCCCA +GGTCTGAGTCCTCTCTGAAGCCTGGAGATGCCTTTTATTTGATCCCTGCAGGAGTCTTAC +CTCAAAATGATCCTTCTAGAAAGTGTGAAAGCAGAGGGCTAGCGAGGAAGGACATGGCCA +TTGTGGGGTCTACCTTTAGGCCATCTTGTTCACACCTCTGCCACCTCATCTGACGTGTCA +TTTCTCTATATAATATACCCCAGCCCACCCAGTGGCCATGCAACATCCCAAGGATGGGGA +GCTTACTGCCTCCCCAACCCACCTACTGCATCTTGAGATATAGCTGTCAGAACGCACTTT +CTAAAATTAAGCCCTGGTCTCACTCCCTTGCCTTGGTCCTGTGCTCCCCATCAGCAGGGC +GCATCTGAAGGCTGACGTCATGTCCTTCCTGCTCTGGCTATTTCCAGTCTCCCTGGCTGC +TCTCCAGAGGACTCTGTCCCCAGACCCCCCAACCAACACCTGGCCACCCTGCTTGGTGCT +GTCCAGCTCCTAAGGAGGGCCCAGCATGGAACACTGGGGTGTGCGCGGGGGCAGGGTGGC +GCTGCTGTCTTCCAGGTGCCAGGTCCCCTCTATGGCCACATTTGGAGCAGCTTGGGAGAC +CAGCTAGCCTTGGTCCCTCCCACCACCCAACCCAGGGGAAGGATCCAGGAACCAGGAAGA +GGAGCCAGTGGCCCTGAAGTTCAGGCATGATGATCAGCTTGGAACTGTGATCCTGGCCCC +TGGGAGGCAGGGGAGGAAACGACTGACCCACTCCGTCCCTGCCGCCTACTCACACCCCCC +AGCCCCCAGAACAGGGCCCCTGGACAAGGAGGCTGCACTTGGGACAGCAGGCAGCAGAAA +GCACCACAGAAGGAAAGGCTGTACTACCGTCTTCGTCCTCTCTCCAGTCCTCCTCTTCTG +AGGTTCAGGGAGTGGCCGCAGCGGAGGGGAAAAGCGAGACAGGTTAGTCTGGGAGCAGAG +AGCCCGCGGCAGGAGCAGCCACCCAGCGCAGTGGTTTTAAGAGTGTGGGCTTTGGAGTTA +GGCCGGCATTCCAATTCCCAAGCCACTACTTTCCAGCAACAGGGGCAACTCTCAGTTACT +TCCCTGAGCCTCAGGTGCCTCATCAGTAAAATGGGAATCATTCTACTCACTTCTCAGCCG +TGGTGAGGACTGAATGACCTAGCGTGCATAGAGCGCCCAGCAGGTGCCTGGCACAAGAGG +AGCATGCGATCTGTGGTAACTGCAATGCCTCTAGACGACAGAGCCTTGGCCTCCTTCTTA +CTAAGACAGAGGCCCCTAAAGAGCAGAGAGTGGGGGACAATTCTCTTCCATCAAATTTCC +TGCCCTCAACGAGCCTGCCCATGTTCCTGCTCTGAATGAGGCTCTTGGGTATCCTGCAAA +CTATGTCCAGTTTCCAGGAGTCACACTTTAGAAAGCCTCATTGGAGAGCCTGGCCCCAGG +GGAGATTTGCCCGGCCTGTTGGGAGGATGCTGCCCCATCTAAGAAGGGTCCAGCATTATA +AATCTAAGGAAAGAGGCTGCATCTACAACAGTTGTTCTACGTACAAATATCTGCCCAAAA +AAACAGTTCCAGCAAGTGGAACAATTCCTCTCCTGGAAGAAGGACACCTGGCATTATCTA +TCCTGCAGGCTTAGTGGACACCCATCTAGACGTTGCTCTCTCTTGATCATTTGCAGCCAG +ATCCTCAACTGTGTGGGAGGCAAGTCTCGTCTATTCATGGCAAGCAAGGCAGATGCTACA +CGGCTCAGGCCCCAGCACAGTGGAGAATGACTCTGCTAACTCACAGCCAAATTCTACTGT +GTGTGGCAGGCAGATTGGTCCCAAATCCAGAGATCTATGTCTCAAACTCCACCACCCTAA +ACCTGTTATAAGGAAGTGGAAAATCCTCCAAAACAAAGGAAGGGATATCATATCAAGAGT +CTGTTCAGGGAACACAGCAGAATTTGGAGCCAGTTAGATTTTTTATTCAAAAATATATTT +CTGATAGCTTCTGAAGTATCTGGTGTTCCTTAAAAACCAAAAAAGACGCCTGTGGCCTCT +TTCAGTTTCTCCTGTGAATTTCTCTTCTGTCTCCTCTTTGGCCAGACAGCCCTGGAACAG +CCCTAAATGTGCAGGAGGGTCCCCATTTTCCCTAGGAGCCATGGGGAGCAAGGGCGGGGC +CACCTGGGCTCCCCCCTTGGACCTTCATAGAGACCCTTCTCCTAATATCTACATGCCACA +TGCTGAAGTGATACCTGAGCCACTAAAAGGCAGGGTCCACCTGCCTGGGGTGCAGGGGGA +GGACTGGAGTGAAGCCTCTGAGTCATTTCCATGTGCCAAGCTCTCAGGAAGAAGGGAAGG +TGAGGGCGTTCTTTCAGGGAGATGTGGGACCCACAGCTGAGGAGGGCGATGGGTTAACCG +ATCAGCATAGGAGCAGCAAGAGGGGCCTCTGCAAGCTCAGAATCATGACAAATCTTCATG +CCGAGATAAGACGTCTCAGATCACTGAGCAATTTCATACTCACAATCGCATTTGAGAAAT +TACTAAATGGAATCTTTTGGGGCATATCATGGCATTGTGGTTATGGTTTTTAAGTAGTGC +TTATCTCTTAGAGATACGGTGTAGCGAAATCTTGAAGCGTGAACTGACATGGTGCCTGGG +AACAATTTTGGATGTCTGCTCCAAAATAACTGGTGGAAGGTGGAGTATAGAGGAAAGAAG +ACTGGCCCTAAGATGATGATTGTTGAAGCTGGTAATGGGTACCTTGGGCAGGGGGGGCCA +TTATTATTATTATTGCTACCTTTATGTGCATTTAAAATTTCCCATGATAAAAGGGAGAAG +AAGCAAAAAAAATTGGGAAAAGTGATCAGTGTGTTTGAAGCAAATGGCAGACAGAAGAGA +CAGGTTTAAATCGTTTGCCTCAAGACCCGAGCAACCCAGGTAGGACTGATTCCCATTTTA +GAAGGCACTGTTGTTGGAGGATCTTGCTCAGCTGAGAGTGAGGAGCAGGGACAGATGAGC +TGCTTTCCCAGGGCTCCCAGGATTTCCACATTGCTGAGCCTGCCCCTTTCTGGCTCTCCA +CCTGCCTGAGGCACATACCTTCAACAGCTGCTTCTGCTCAGAAGAGAAGTCCAGGCAGCA +AGAGAAGAGAGAAGAGGTGGGTCAGTTTCGAACCAGGCTGTCTTTGATCCAAATGAGTAC +ACACGTTTACGCTTACCTTCCTGCTCCCTGAGAGCAACAGGAAACACTGTCAGTAGCTCG +CACACAAGCACATGCAAACACACACGCCTGCACACACATGCACACACTGGCCTTTCCCCA +AAGATAATCCCCCTTTCTTTTCCCTTGTTGCCTAGTGGAGTCCACGCTGCCCTGCCCACC +TTGCAATGACACCCACTAGCCTGGCCTGCCGTTCTCATGCAGGGCTGCCTCCTACCATCC +TCCGCAAGCCTCCGCCCCAGCCAGCTTGGTCTCACCAGCGTTCTGCTCACTTACTCTTTC +CATCTTTGCCCAAGCTGTACCCCTTTCTAGAAAGTCCTGCCCTCTCCCAAATCTCTTATC +TTTCCAAATTCTACACAGGTAAGACCTGCCTTCTCCACACAGCCCCCTGACTATTCCAGC +CCCTGATCTCCCTCTCCTCAGAACTCCTACACTACCAACAGCCCGCCCTCCACACCAGGC +CCCCAGTTGCTAATTTCTTCTCCCAGTTTATGTCTTAACATCTCAACAAGAGTAAGTTCT +GTGAGGGCAGTAGCCGTGCCTATACCTCTGTCTCCTCCCTGGTGACCACTATCCTCTGTA +GTTATTGGATTGGCTGTGTCCCACCCCCTGGTTTCCCTCTGGGATAGGACTGTGGGCAGG +GCACTGTCATGAGAGAGTAGGGATCCAAGACAGGGTGATAACACTGGGTTCTGAGCTGGG +GTTTGGGGGGCATAATCAGCTCTGTGCCTCTGGAGAGTCACTGAACCTTCCTCAGTCAGT +TTCAGGAGACCCAACATCTCAGCTTCTCTGTTCATGGCCCCTAGCCAAGACTGGCCAAGG +ACACTGATGACCCTGGAGCTGAACCTCTGTGCTTCCCGAAGTCTCTCGGCCTGTGCTCTG +CCTGGGATCTACAACCCAGGGGTACAGGAGTGGAAAGGAAATGGCTATATCTCTCCTCGG +GGTGCCCAAAACACACACAGCTACTTCTACCCAGAATCCGAGGGACAGCTGGGAGGCTCC +TGGACCAGGTGTCAGGGCAGCGGCGGGAGAGGACCCCACTCAGGCAAGATGCTCCAGATA +CTCACTCCTCCTCGTACTCTTCCACCACCTCTTCTATGTCAGACATGGTCTCTGCTCTCC +CTCCAA diff --git a/test/csq/ENST00000360372/ENST00000360372.gff b/test/csq/ENST00000360372/ENST00000360372.gff new file mode 100644 index 000000000..d8d930b28 --- /dev/null +++ b/test/csq/ENST00000360372/ENST00000360372.gff @@ -0,0 +1,30 @@ +chr1 ensembl_havana gene 20 18776 . - . ID=gene:ENSG00000118194;Name=TNNT2;biotype=protein_coding;description=troponin T2%2C cardiac type [Source:HGNC Symbol%3BAcc:HGNC:11949];gene_id=ENSG00000118194;logic_name=ensembl_havana_gene_homo_sapiens;version=20 +chr1 ensembl mRNA 21 14266 . - . ID=transcript:ENST00000360372;Parent=gene:ENSG00000118194;Name=TNNT2-202;biotype=protein_coding;ccdsid=CCDS60390.1;tag=basic;transcript_id=ENST00000360372;transcript_support_level=5;version=8 +chr1 ensembl exon 21 267 . - . Parent=transcript:ENST00000360372;Name=ENSE00003722768;constitutive=0;ensembl_end_phase=-1;ensembl_phase=2;exon_id=ENSE00003722768;rank=14;version=1 +chr1 ensembl CDS 222 267 . - 1 ID=CDS:ENSP00000353535;Parent=transcript:ENST00000360372;protein_id=ENSP00000353535 +chr1 ensembl exon 635 675 . - . Parent=transcript:ENST00000360372;Name=ENSE00003490622;constitutive=0;ensembl_end_phase=2;ensembl_phase=0;exon_id=ENSE00003490622;rank=13;version=1 +chr1 ensembl CDS 635 675 . - 0 ID=CDS:ENSP00000353535;Parent=transcript:ENST00000360372;protein_id=ENSP00000353535 +chr1 ensembl exon 2291 2381 . - . Parent=transcript:ENST00000360372;Name=ENSE00003488921;constitutive=0;ensembl_end_phase=0;ensembl_phase=2;exon_id=ENSE00003488921;rank=12;version=1 +chr1 ensembl CDS 2291 2381 . - 1 ID=CDS:ENSP00000353535;Parent=transcript:ENST00000360372;protein_id=ENSP00000353535 +chr1 ensembl exon 2925 3034 . - . Parent=transcript:ENST00000360372;Name=ENSE00003666033;constitutive=0;ensembl_end_phase=2;ensembl_phase=0;exon_id=ENSE00003666033;rank=11;version=1 +chr1 ensembl CDS 2925 3034 . - 0 ID=CDS:ENSP00000353535;Parent=transcript:ENST00000360372;protein_id=ENSP00000353535 +chr1 ensembl exon 4308 4418 . - . Parent=transcript:ENST00000360372;Name=ENSE00003523427;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=ENSE00003523427;rank=10;version=1 +chr1 ensembl CDS 4308 4418 . - 0 ID=CDS:ENSP00000353535;Parent=transcript:ENST00000360372;protein_id=ENSP00000353535 +chr1 ensembl exon 5310 5387 . - . Parent=transcript:ENST00000360372;Name=ENSE00003686160;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=ENSE00003686160;rank=9;version=1 +chr1 ensembl CDS 5310 5387 . - 0 ID=CDS:ENSP00000353535;Parent=transcript:ENST00000360372;protein_id=ENSP00000353535 +chr1 ensembl exon 6622 6682 . - . Parent=transcript:ENST00000360372;Name=ENSE00003514510;constitutive=0;ensembl_end_phase=0;ensembl_phase=2;exon_id=ENSE00003514510;rank=8;version=1 +chr1 ensembl CDS 6622 6682 . - 1 ID=CDS:ENSP00000353535;Parent=transcript:ENST00000360372;protein_id=ENSP00000353535 +chr1 ensembl exon 7850 7883 . - . Parent=transcript:ENST00000360372;Name=ENSE00003718704;constitutive=0;ensembl_end_phase=2;ensembl_phase=1;exon_id=ENSE00003718704;rank=7;version=1 +chr1 ensembl CDS 7850 7883 . - 2 ID=CDS:ENSP00000353535;Parent=transcript:ENST00000360372;protein_id=ENSP00000353535 +chr1 ensembl exon 8783 8815 . - . Parent=transcript:ENST00000360372;Name=ENSE00003646496;constitutive=0;ensembl_end_phase=1;ensembl_phase=1;exon_id=ENSE00003646496;rank=6;version=1 +chr1 ensembl CDS 8783 8815 . - 2 ID=CDS:ENSP00000353535;Parent=transcript:ENST00000360372;protein_id=ENSP00000353535 +chr1 ensembl exon 9174 9239 . - . Parent=transcript:ENST00000360372;Name=ENSE00003520322;constitutive=0;ensembl_end_phase=1;ensembl_phase=1;exon_id=ENSE00003520322;rank=5;version=1 +chr1 ensembl CDS 9174 9239 . - 2 ID=CDS:ENSP00000353535;Parent=transcript:ENST00000360372;protein_id=ENSP00000353535 +chr1 ensembl exon 10828 10857 . - . Parent=transcript:ENST00000360372;Name=ENSE00001444197;constitutive=0;ensembl_end_phase=1;ensembl_phase=1;exon_id=ENSE00001444197;rank=4;version=1 +chr1 ensembl CDS 10828 10857 . - 2 ID=CDS:ENSP00000353535;Parent=transcript:ENST00000360372;protein_id=ENSP00000353535 +chr1 ensembl exon 13039 13053 . - . Parent=transcript:ENST00000360372;Name=ENSE00003554410;constitutive=0;ensembl_end_phase=1;ensembl_phase=1;exon_id=ENSE00003554410;rank=3;version=1 +chr1 ensembl CDS 13039 13053 . - 2 ID=CDS:ENSP00000353535;Parent=transcript:ENST00000360372;protein_id=ENSP00000353535 +chr1 ensembl exon 13157 13167 . - . Parent=transcript:ENST00000360372;Name=ENSE00003661906;constitutive=0;ensembl_end_phase=1;ensembl_phase=2;exon_id=ENSE00003661906;rank=2;version=1 +chr1 ensembl CDS 13157 13167 . - 1 ID=CDS:ENSP00000353535;Parent=transcript:ENST00000360372;protein_id=ENSP00000353535 +chr1 ensembl exon 14226 14266 . - . Parent=transcript:ENST00000360372;Name=ENSE00001315772;constitutive=0;ensembl_end_phase=2;ensembl_phase=0;exon_id=ENSE00001315772;rank=1;version=4 +chr1 ensembl CDS 14226 14266 . - 0 ID=CDS:ENSP00000353535;Parent=transcript:ENST00000360372;protein_id=ENSP00000353535 diff --git a/test/csq/ENST00000360372/mnp.txt b/test/csq/ENST00000360372/mnp.txt new file mode 100644 index 000000000..7b01be0d1 --- /dev/null +++ b/test/csq/ENST00000360372/mnp.txt @@ -0,0 +1,3 @@ +4391 CC AA stop_gained|TNNT2|ENST00000360372|protein_coding|-|132EE>132D*|4391CC>AA +4391 CC AA stop_gained|TNNT2|ENST00000360372|protein_coding|-|132EE>132D*|4391CC>AA + diff --git a/test/csq/ENST00000360372/mnp.vcf b/test/csq/ENST00000360372/mnp.vcf new file mode 100644 index 000000000..169a95789 --- /dev/null +++ b/test/csq/ENST00000360372/mnp.vcf @@ -0,0 +1,7 @@ +##fileformat=VCFv4.2 +##contig= +##INFO= +##INFO= +##INFO= +#CHROM POS ID REF ALT QUAL FILTER INFO +chr1 4391 . CC AA . . type=ENST00000360372:201363379-CC-AA;EXP=stop_gained|TNNT2|ENST00000360372|protein_coding|-|132EE>132D*|4391CC>AA From 846fc41c8285e720adeda1b04ff8f8b81ab383ec Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Wed, 2 Nov 2022 08:40:43 +0000 Subject: [PATCH 46/84] Restore functionality of the --pair-logic option. Fixes #1808 --- NEWS | 4 +++- test/annotate.id.2.1.out | 8 ++++++++ test/annotate.id.2.2.out | 8 ++++++++ test/annotate.id.2.vcf | 7 +++++++ test/annots.id.2.vcf | 9 +++++++++ test/test.pl | 2 ++ vcfannotate.c | 1 + 7 files changed, 38 insertions(+), 1 deletion(-) create mode 100644 test/annotate.id.2.1.out create mode 100644 test/annotate.id.2.2.out create mode 100644 test/annotate.id.2.vcf create mode 100644 test/annots.id.2.vcf diff --git a/NEWS b/NEWS index e7806cb39..e57b9069d 100644 --- a/NEWS +++ b/NEWS @@ -4,7 +4,9 @@ Changes affecting specific commands: * bcftools annotate - - Support sample reordering of annotation file ( #1785) + - Support sample reordering of annotation file (#1785) + + - Restore lost functionality of the --pair-logic option (#1808) * bcftools call diff --git a/test/annotate.id.2.1.out b/test/annotate.id.2.1.out new file mode 100644 index 000000000..76cadaf69 --- /dev/null +++ b/test/annotate.id.2.1.out @@ -0,0 +1,8 @@ +##fileformat=VCFv4.2 +##FILTER= +##contig= +##reference=hg38.fa +#CHROM POS ID REF ALT QUAL FILTER INFO +chrM 10 . T . . . . +chrM 73 existingID A T . . . +chrM 146 rs370482130 T C . . . diff --git a/test/annotate.id.2.2.out b/test/annotate.id.2.2.out new file mode 100644 index 000000000..87191b615 --- /dev/null +++ b/test/annotate.id.2.2.out @@ -0,0 +1,8 @@ +##fileformat=VCFv4.2 +##FILTER= +##contig= +##reference=hg38.fa +#CHROM POS ID REF ALT QUAL FILTER INFO +chrM 10 rs879233578 T . . . . +chrM 73 existingID A T . . . +chrM 146 rs370482130 T C . . . diff --git a/test/annotate.id.2.vcf b/test/annotate.id.2.vcf new file mode 100644 index 000000000..ecd06cd73 --- /dev/null +++ b/test/annotate.id.2.vcf @@ -0,0 +1,7 @@ +##fileformat=VCFv4.2 +##contig= +##reference=hg38.fa +#CHROM POS ID REF ALT QUAL FILTER INFO +chrM 10 . T . . . . +chrM 73 existingID A T . . . +chrM 146 rs370482130 T C . . . diff --git a/test/annots.id.2.vcf b/test/annots.id.2.vcf new file mode 100644 index 000000000..399ecba7a --- /dev/null +++ b/test/annots.id.2.vcf @@ -0,0 +1,9 @@ +##fileformat=VCFv4.2 +##reference=GRCh38.p13 +##contig= +#CHROM POS ID REF ALT QUAL FILTER INFO +chrM 10 rs879233578 T C . . . +chrM 73 rs869183622 A C . . . +chrM 73 rs869183622 A G . . . +chrM 146 rs370482130 T A . . . +chrM 146 rs370482130 T C . . . diff --git a/test/test.pl b/test/test.pl index 17e1df3da..929bc70fd 100755 --- a/test/test.pl +++ b/test/test.pl @@ -495,6 +495,8 @@ run_test(\&test_vcf_annotate,$opts,in=>'annotate.olap',tab=>'annots.olap',out=>'annotate.olap.2.out',args=>'-c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5'); run_test(\&test_vcf_annotate,$opts,in=>'annotate.id',vcf=>'annots.id',out=>'annotate.id.1.out',args=>'-c ALT'); run_test(\&test_vcf_annotate,$opts,in=>'annotate.id',vcf=>'annots.id',out=>'annotate.id.2.out',args=>'-c +ALT'); +run_test(\&test_vcf_annotate,$opts,in=>'annotate.id.2',vcf=>'annots.id.2',out=>'annotate.id.2.1.out',args=>'--pair-logic some -c +ID'); +run_test(\&test_vcf_annotate,$opts,in=>'annotate.id.2',vcf=>'annots.id.2',out=>'annotate.id.2.2.out',args=>'--pair-logic any -c +ID'); run_test(\&test_vcf_annotate,$opts,in=>'annotate27',tab=>'annotate27',out=>'annotate.32.out',args=>'-c CHROM,POS,REF,ALT,EVIDENCE'); run_test(\&test_vcf_annotate,$opts,in=>'annotate28',tab=>'annots28',out=>'annotate28.1.out',args=>'-c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2'); run_test(\&test_vcf_annotate,$opts,in=>'annotate28',tab=>'annots28',out=>'annotate28.2.out',args=>'-c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1'); diff --git a/vcfannotate.c b/vcfannotate.c index 0cbf400bb..495d2b5a3 100644 --- a/vcfannotate.c +++ b/vcfannotate.c @@ -3427,6 +3427,7 @@ int main_vcfannotate(int argc, char *argv[]) case 'H': args->header_lines = dbuf_push(args->header_lines,strdup(optarg)); break; case 1 : args->rename_chrs = optarg; break; case 2 : + if ( args->pair_logic==-1 ) args->pair_logic = 0; if ( !strcmp(optarg,"snps") ) args->pair_logic |= BCF_SR_PAIR_SNP_REF; else if ( !strcmp(optarg,"indels") ) args->pair_logic |= BCF_SR_PAIR_INDEL_REF; else if ( !strcmp(optarg,"both") ) args->pair_logic |= BCF_SR_PAIR_BOTH_REF; From cd491e198546fd733ccab841bd28b10ca152d1ac Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Wed, 2 Nov 2022 10:00:32 +0000 Subject: [PATCH 47/84] Add more tags with -t all. See also #916 --- plugins/fill-tags.c | 17 ++++++++++------- test/fill-tags-AN0.out | 2 ++ test/fill-tags-hemi.1.out | 2 ++ test/fill-tags-hemi.2.out | 2 ++ test/fill-tags-hwe.out | 2 ++ 5 files changed, 18 insertions(+), 7 deletions(-) diff --git a/plugins/fill-tags.c b/plugins/fill-tags.c index eecf1bd72..79aeebdd6 100644 --- a/plugins/fill-tags.c +++ b/plugins/fill-tags.c @@ -90,7 +90,8 @@ struct _pop_t struct _args_t { bcf_hdr_t *in_hdr, *out_hdr; - int npop, tags, drop_missing, gt_id; + uint32_t tags, warned; + int npop, drop_missing, gt_id; pop_t *pop, **smpl2pop; float *farr; int32_t *iarr, niarr, miarr, nfarr, mfarr, unpack; @@ -459,17 +460,20 @@ int parse_func(args_t *args, char *tag_expr, char *expr) ret |= parse_func_pop(args,&args->pop[i],tag_expr,expr); return ret; } -int parse_tags(args_t *args, const char *str) +uint32_t parse_tags(args_t *args, const char *str) { if ( !args->in_hdr ) error("%s", usage()); - int i,j, flag = 0, n_tags; + args->warned = 0; + uint32_t flag = 0; + int i, n_tags; char **tags = hts_readlist(str, 0, &n_tags), *ptr; for(i=0; iwarned = ~(SET_END|SET_TYPE); args->unpack |= BCF_UN_FMT; } else if ( !strcasecmp(tags[i],"AN") ) { flag |= SET_AN; args->unpack |= BCF_UN_FMT; } @@ -977,11 +981,10 @@ static void process_vaf_vaf1(bcf1_t *rec) args->niarr = bcf_get_format_int32(args->in_hdr, rec, "AD", &args->iarr, &args->miarr); if ( args->niarr <= 0 ) { - static int missing_ad_warned = 0; - if ( !missing_ad_warned ) + if ( !(args->warned&(SET_VAF|SET_VAF1)) ) fprintf(stderr,"Warning: cannot add the VAF/VAF1 annotations, the required FORMAT/AD tag is missing at %s:%"PRIhts_pos".\n" " (This warning is printed only once.)\n",bcf_seqname(args->in_hdr,rec),rec->pos+1); - missing_ad_warned = 1; + args->warned |= SET_VAF|SET_VAF1; return; } diff --git a/test/fill-tags-AN0.out b/test/fill-tags-AN0.out index 0b7898354..38efb93a9 100644 --- a/test/fill-tags-AN0.out +++ b/test/fill-tags-AN0.out @@ -15,6 +15,8 @@ ##INFO= ##INFO= ##INFO= +##FORMAT= +##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMP_A SAMP_B SAMP_C SAMP_E chr1 10146 . AC A . PASS NS=2;AN=4;AF=0.5;AC=2;F_MISSING=0.5;MAF=0.5;AC_Het=2;AC_Hom=0;AC_Hemi=0;HWE=1;ExcHet=0.666667;END=10147;TYPE=INDEL GT ./. 0/1 ./. 0/1 chr1 10153 . A C . PASS NS=0;AN=0;AF=.;AC=0;F_MISSING=1;MAF=.;AC_Het=0;AC_Hom=0;AC_Hemi=0;HWE=1;ExcHet=1;END=10153;TYPE=SNP GT ./. ./. ./. ./. diff --git a/test/fill-tags-hemi.1.out b/test/fill-tags-hemi.1.out index c037bc1e6..10d4ddca3 100644 --- a/test/fill-tags-hemi.1.out +++ b/test/fill-tags-hemi.1.out @@ -13,6 +13,8 @@ ##INFO= ##INFO= ##INFO= +##FORMAT= +##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B 1 3177144 . G T,A 45 PASS NS=2;AN=2;AF=0.5,0.5;MAF=0.5;AC=1,1;AC_Het=0,0;AC_Hom=0,0;AC_Hemi=1,1;HWE=1,1;ExcHet=1,1 GT 1 2 1 3177144 . G T 45 PASS NS=2;AN=2;AF=0.5;MAF=0.5;AC=1;AC_Het=0;AC_Hom=0;AC_Hemi=1;HWE=1;ExcHet=1 GT 0/. 1/. diff --git a/test/fill-tags-hemi.2.out b/test/fill-tags-hemi.2.out index 4797a7451..e746d6c6a 100644 --- a/test/fill-tags-hemi.2.out +++ b/test/fill-tags-hemi.2.out @@ -13,6 +13,8 @@ ##INFO= ##INFO= ##INFO= +##FORMAT= +##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B 1 3177144 . G T,A 45 PASS NS=2;AN=2;AF=0.5,0.5;MAF=0.5;AC=1,1;AC_Het=0,0;AC_Hom=0,0;AC_Hemi=1,1;HWE=1,1;ExcHet=1,1 GT 1 2 1 3177144 . G T 45 PASS NS=2;AN=2;AF=0.5;MAF=0.5;AC=1;AC_Het=0;AC_Hom=0;AC_Hemi=0;HWE=1;ExcHet=1 GT 0/. 1/. diff --git a/test/fill-tags-hwe.out b/test/fill-tags-hwe.out index 6c0e990e8..45f0ae0e8 100644 --- a/test/fill-tags-hwe.out +++ b/test/fill-tags-hwe.out @@ -13,6 +13,8 @@ ##INFO= ##INFO= ##INFO= +##FORMAT= +##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1 S2 S3 S4 S5 S6 S7 S8 S9 S10 1 3177144 . G T 45 PASS NS=10;AN=20;AF=0;MAF=0;AC=0;AC_Het=0;AC_Hom=0;AC_Hemi=0;HWE=1;ExcHet=1 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1 3177144 . G T 45 PASS NS=10;AN=20;AF=0.1;MAF=0.1;AC=2;AC_Het=2;AC_Hom=0;AC_Hemi=0;HWE=1;ExcHet=0.947368 GT 1/0 1/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 From 815fd54e261ee400010082129ff860ff7023c5d0 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Mon, 7 Nov 2022 09:15:51 +0000 Subject: [PATCH 48/84] Fix a bug where indels constrained with `-C alleles -T` would sometimes be missed. Fixes #1706 --- NEWS | 2 ++ test/mpileup.cAls.6.out | 2 +- test/mpileup.cAls.7.out | 2 +- test/mpileup.cals.8.out | 2 +- test/mpileup.cals.9.out | 2 +- vcfcall.c | 2 +- 6 files changed, 7 insertions(+), 5 deletions(-) diff --git a/NEWS b/NEWS index e57b9069d..ad95180e0 100644 --- a/NEWS +++ b/NEWS @@ -13,6 +13,8 @@ Changes affecting specific commands: - Fix a bug where too many alleles passed to `-C alleles` via `-T` caused memory corruption (#1790) + - Fix a bug where indels constrained with `-C alleles -T` would sometimes be missed (#1706) + * bcftools convert - Make variantkey conversion work for sites without an ALT allele (#1806) diff --git a/test/mpileup.cAls.6.out b/test/mpileup.cAls.6.out index 1a507325b..0e8e4fb51 100644 --- a/test/mpileup.cAls.6.out +++ b/test/mpileup.cAls.6.out @@ -17,8 +17,8 @@ ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample 1 1368828 . GT G 61.5766 . DP=1;MQ0F=0;AC=0;AN=2;DP4=1,0,0,0;MQ=60 GT:PL 0/0:0,3,35 -1 1368833 . T C 39.5768 . DP=1;MQ0F=0;AC=0;AN=2;DP4=0,1,0,0;MQ=60 GT:PL 0/0:0,3,13 1 1368833 . TAAAAAAAAAAAAAAAA TAAAAAAAAAAAAAA 24.1741 . DP=2;AC=0;AN=2;DP4=0,1,1,0;MQ=60 GT:PL 0/0:6,0,6 +1 1368833 . T C 39.5768 . DP=1;MQ0F=0;AC=0;AN=2;DP4=0,1,0,0;MQ=60 GT:PL 0/0:0,3,13 1 1368833 . T G . . . GT . 1 1368834 . A T 59.5765 . DP=1;MQ0F=0;AC=0;AN=2;DP4=1,0,0,0;MQ=60 GT:PL 0/0:0,3,33 16 60288 . C A . . . GT . diff --git a/test/mpileup.cAls.7.out b/test/mpileup.cAls.7.out index 7168edf56..56a87b2a4 100644 --- a/test/mpileup.cAls.7.out +++ b/test/mpileup.cAls.7.out @@ -44,7 +44,7 @@ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A 1 790667 . C T . . . GT . 1 116844268 . GA G 58.5765 . DP=1;MQ0F=0;AC=0;AN=2;DP4=1,0,0,0;MQ=60 GT:PL 0/0:0,3,32 -1 116844279 . GAA G 39.5768 . DP=1;MQ0F=0;AC=0;AN=2;DP4=0,1,0,0;MQ=60 GT:PL 0/0:0,3,13 +1 116844279 . GAAAAAAAAAAAAAAAA GAAAAAAAAAAAAAA 24.1741 . INDEL;IDV=1;IMF=0.5;DP=2;VDB=0.5;SGB=-0.379885;MQSB=1;MQ0F=0;AC=0;AN=2;DP4=0,1,1,0;MQ=60 GT:PL 0/0:6,0,6 1 116844450 . T A . . . GT . 20 68799 . T C . . . GT . 20 68810 . G A . . . GT . diff --git a/test/mpileup.cals.8.out b/test/mpileup.cals.8.out index e07af78b9..150c45a44 100644 --- a/test/mpileup.cals.8.out +++ b/test/mpileup.cals.8.out @@ -26,4 +26,4 @@ ##INFO= ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 -6 263708 . CTT C,CT 279.818 . DP=211;MQSB=0.901445;MQ0F=0;AC=0,0;AN=2;DP4=117,27,0,0;MQ=57 GT:PL:DP:SP:ADF:ADR:AD 0/0:0,255,255,255,255,255:144:0:117,0,0:27,0,0:144,0,0 +6 263708 . CTT C,CT 27.0816 . INDEL;IDV=27;IMF=0.127358;DP=212;VDB=0.0105186;SGB=-0.693079;MQSB=0.971475;MQ0F=0;AC=0,0;AN=2;DP4=100,83,20,9;MQ=56 GT:PL:DP:SP:ADF:ADR:AD 0/0:0,255,39,255,74,39:212:8:100,1,12:83,1,5:183,2,17 diff --git a/test/mpileup.cals.9.out b/test/mpileup.cals.9.out index 886817f46..61bba3dfb 100644 --- a/test/mpileup.cals.9.out +++ b/test/mpileup.cals.9.out @@ -16,6 +16,6 @@ ##INFO= ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample -1 1368833 . T C 39.5768 . DP=1;MQ0F=0;AC=0;AN=2;DP4=0,1,0,0;MQ=60 GT:PL 0/0:0,3,13 1 1368833 . TAAAAAAAAAAAAAAAA TAAAAAAAAAAAAAA 24.1741 . DP=2;AC=0;AN=2;DP4=0,1,1,0;MQ=60 GT:PL 0/0:6,0,6 +1 1368833 . T C 39.5768 . DP=1;MQ0F=0;AC=0;AN=2;DP4=0,1,0,0;MQ=60 GT:PL 0/0:0,3,13 1 1370000 . C CT . . DP=11;MQ0F=0;AC=0;AN=0;DP4=11,0,0,0;MQ=29 GT:PL ./.:0,0,0 diff --git a/vcfcall.c b/vcfcall.c index 4c9e88c68..1cd6f504c 100644 --- a/vcfcall.c +++ b/vcfcall.c @@ -568,9 +568,9 @@ bcf1_t *next_line(args_t *args) memset(&rec_tgt,0,sizeof(rec_tgt)); regidx_overlap(args->tgt_idx, bcf_seqname(args->aux.hdr,rec0),rec0->pos,rec0->pos,args->tgt_itr); regitr_t *tmp_itr = regitr_init(args->tgt_idx); - regitr_copy(tmp_itr, args->tgt_itr); for (i=0; itgt_itr); rec = vcfbuf_peek(args->vcfbuf, i); int rec_indel = is_indel(rec->n_allele, rec->d.allele) ? 1 : -1; while ( regitr_overlap(tmp_itr) ) From 1829ad20c77c530cce5839306d9ca1ddf875db7a Mon Sep 17 00:00:00 2001 From: Andrew Whitwham Date: Fri, 11 Nov 2022 14:12:04 +0000 Subject: [PATCH 49/84] Another error message alteration. --- misc/plot-roh.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/misc/plot-roh.py b/misc/plot-roh.py index 9c6bb02f0..58db5adce 100755 --- a/misc/plot-roh.py +++ b/misc/plot-roh.py @@ -361,7 +361,10 @@ def parse_samples(fname,highlight): dat_rg1 = {} if not chrs: - usage("No GT lines found in input file. Was it generated using the run-roh.pl script?") + usage("\nNo GT lines found in input file. Was it generated using the run-roh.pl script?\n" + "This script is unable to process the raw output of \"bcftools roh\",\n" + "the output of the following query may need to be added to the roh result.\n\n" + "bcftools query -f'GT\\t%CHROM\\t%POS[\\t%SAMPLE\\t%GT]\\n' in.bcf\n") for chr in chrs: if chr in dat_rg: From b5cbcd5d047a8478ac892d8fec4a5c4ffc4e0a48 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Wed, 16 Nov 2022 15:49:24 +0100 Subject: [PATCH 50/84] Fix a bug of not filling in missing FORMAT value and using the present vector_end instead. Fixes #1818 --- test/norm.m-any.1.out | 10 ++++++++++ test/norm.m-any.vcf | 8 ++++++++ test/test.pl | 1 + vcfnorm.c | 32 ++++++++++++++++++++++++-------- 4 files changed, 43 insertions(+), 8 deletions(-) create mode 100644 test/norm.m-any.1.out create mode 100644 test/norm.m-any.vcf diff --git a/test/norm.m-any.1.out b/test/norm.m-any.1.out new file mode 100644 index 000000000..f95353133 --- /dev/null +++ b/test/norm.m-any.1.out @@ -0,0 +1,10 @@ +##fileformat=VCFv4.2 +##FILTER= +##contig= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Samp1 Samp2 +chr1 98 . GCCT G . . . IR:FR:IA:FA 1,2:.,.:.:. .,.:1,2:1:1 +chr1 98 . GCCT GC . . . IR:FR:IA:FA 1,3:.,.:.:. .,.:1,3:2:2 diff --git a/test/norm.m-any.vcf b/test/norm.m-any.vcf new file mode 100644 index 000000000..c63c07cb6 --- /dev/null +++ b/test/norm.m-any.vcf @@ -0,0 +1,8 @@ +##fileformat=VCFv4.2 +##contig= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Samp1 Samp2 +chr1 98 . GCCT G,GC . . . IR:FR:IA:FA 1,2,3 .:1,2,3:1,2:1,2 diff --git a/test/test.pl b/test/test.pl index 929bc70fd..dfb5c4db2 100755 --- a/test/test.pl +++ b/test/test.pl @@ -266,6 +266,7 @@ run_test(\&test_vcf_norm,$opts,in=>'norm.4',out=>'norm.4.2.out',args=>'-m +any'); run_test(\&test_vcf_norm,$opts,in=>'norm.5',out=>'norm.5.1.out',args=>'-m - --multi-overlaps 0'); run_test(\&test_vcf_norm,$opts,in=>'norm.5',out=>'norm.5.2.out',args=>'-m - --multi-overlaps .'); +run_test(\&test_vcf_norm,$opts,in=>'norm.m-any',out=>'norm.m-any.1.out',args=>'-m -any'); run_test(\&test_vcf_view,$opts,in=>'view',out=>'view.1.out',args=>'-aUc1 -C1 -s NA00002 -v snps',reg=>''); run_test(\&test_vcf_view,$opts,in=>'view',out=>'view.2.out',args=>'-f PASS -Xks NA00003',reg=>'-r20,Y'); run_test(\&test_vcf_view,$opts,in=>'view',out=>'view.3.out',args=>'-xs NA00003',reg=>''); diff --git a/vcfnorm.c b/vcfnorm.c index 73ef2071d..9538f8d01 100644 --- a/vcfnorm.c +++ b/vcfnorm.c @@ -726,7 +726,7 @@ static void split_format_genotype(args_t *args, bcf1_t *src, bcf_fmt_t *fmt, int } static void split_format_numeric(args_t *args, bcf1_t *src, bcf_fmt_t *fmt, int ialt, bcf1_t *dst) { - #define BRANCH_NUMERIC(type,type_t,is_vector_end,is_missing,set_vector_end) \ + #define BRANCH_NUMERIC(type,type_t,is_vector_end,is_missing,set_vector_end,set_missing) \ { \ const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,fmt->id); \ int ntmp = args->ntmp_arr1 / sizeof(type_t); \ @@ -765,7 +765,10 @@ static void split_format_numeric(args_t *args, bcf1_t *src, bcf_fmt_t *fmt, int type_t *src_vals = vals, *dst_vals = vals; \ for (i=0; ihdr,BCF_HL_FMT,fmt->id)) { - case BCF_HT_INT: BRANCH_NUMERIC(int32, int32_t, src_vals[j]==bcf_int32_vector_end, src_vals[j]==bcf_int32_missing, dst_vals[2]=bcf_int32_vector_end); break; - case BCF_HT_REAL: BRANCH_NUMERIC(float, float, bcf_float_is_vector_end(src_vals[j]), bcf_float_is_missing(src_vals[j]), bcf_float_set_vector_end(dst_vals[2])); break; + case BCF_HT_INT: BRANCH_NUMERIC(int32, int32_t, src_vals[isrc]==bcf_int32_vector_end, src_vals[isrc]==bcf_int32_missing, dst_vals[idst]=bcf_int32_vector_end, dst_vals[idst]=bcf_int32_missing); break; + case BCF_HT_REAL: BRANCH_NUMERIC(float, float, bcf_float_is_vector_end(src_vals[isrc]), bcf_float_is_missing(src_vals[isrc]), bcf_float_set_vector_end(dst_vals[idst]), bcf_float_set_missing(src_vals[idst])); break; } #undef BRANCH_NUMERIC } From 9b5be4be800772dfe318608f1a3b15a89086630f Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Mon, 14 Nov 2022 07:17:38 +0000 Subject: [PATCH 51/84] Make most of the mpileup -a output tags optional --- bam2bcf.c | 129 ++++++++------------ bam2bcf.h | 23 ++-- mpileup.c | 195 ++++++++++++++++++------------ test/mpileup/annot-NMBZ.1.1.out | 4 +- test/mpileup/annot-NMBZ.2.1.out | 4 +- test/mpileup/annot-NMBZ.3.1.out | 6 +- test/mpileup/indel-AD.1.out | 12 +- test/mpileup/indel-AD.2.out | 6 +- test/mpileup/indel-AD.3.out | 6 +- test/mpileup/indel-AD.4.out | 6 +- test/mpileup/mpileup-SCR.out | 4 +- test/mpileup/mpileup-filter.1.out | 4 +- test/mpileup/mpileup-filter.2.out | 4 +- test/mpileup/mpileup.1.out | 4 +- test/mpileup/mpileup.10.out | 4 +- test/mpileup/mpileup.11.out | 4 +- test/mpileup/mpileup.2.out | 4 +- test/mpileup/mpileup.3.out | 4 +- test/mpileup/mpileup.4.out | 4 +- test/mpileup/mpileup.5.out | 4 +- test/mpileup/mpileup.6.out | 4 +- test/mpileup/mpileup.7.out | 4 +- test/mpileup/mpileup.8.out | 4 +- test/mpileup/mpileup.9.out | 4 +- 24 files changed, 234 insertions(+), 213 deletions(-) diff --git a/bam2bcf.c b/bam2bcf.c index b4e0c4a86..7e949dcde 100644 --- a/bam2bcf.c +++ b/bam2bcf.c @@ -388,7 +388,7 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t if ( baseQ > 59 ) baseQ = 59; if ( mapQ > 59 ) mapQ = 59; int len, epos = 0, sc_len = 0, sc_dist = 0; - if ( bca->fmt_flag & (B2B_INFO_RPB|B2B_INFO_VDB|B2B_INFO_SCB) ) + if ( bca->fmt_flag & (B2B_INFO_RPBZ|B2B_INFO_VDB|B2B_INFO_SCBZ) ) { int pos = get_position(p, &len, &sc_len, &sc_dist); epos = (double)pos/(len+1) * bca->npos; @@ -1017,56 +1017,42 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, bcf_callaux_t *bca, int // No need to calculate MWU tests when there is no ALT allele, this should speed up things slightly if ( !has_alt ) return 0; - calc_SegBias(calls, call); + if ( bca->fmt_flag & B2B_INFO_SGB ) calc_SegBias(calls, call); // calc_chisq_bias("XPOS", call->bcf_hdr->id[BCF_DT_CTG][call->tid].key, call->pos, bca->ref_pos, bca->alt_pos, bca->npos); // calc_chisq_bias("XMQ", call->bcf_hdr->id[BCF_DT_CTG][call->tid].key, call->pos, bca->ref_mq, bca->alt_mq, bca->nqual); // calc_chisq_bias("XBQ", call->bcf_hdr->id[BCF_DT_CTG][call->tid].key, call->pos, bca->ref_bq, bca->alt_bq, bca->nqual); - if (bca->fmt_flag & B2B_INFO_ZSCORE) { - // U z-normalised as +/- number of standard deviations from mean. - if (call->ori_ref < 0) { // indel - if (bca->fmt_flag & B2B_INFO_RPB) - call->mwu_pos = calc_mwu_biasZ(bca->iref_pos, bca->ialt_pos, bca->npos, 0, 1); + // U z-normalised as +/- number of standard deviations from mean. + if (call->ori_ref < 0) { // indel + if ( bca->fmt_flag & B2B_INFO_RPBZ ) + call->mwu_pos = calc_mwu_biasZ(bca->iref_pos, bca->ialt_pos, bca->npos, 0, 1); + if ( bca->fmt_flag & B2B_INFO_MQBZ ) call->mwu_mq = calc_mwu_biasZ(bca->iref_mq, bca->ialt_mq, bca->nqual,1,1); - if ( bca->fmt_flag & B2B_INFO_SCB ) - call->mwu_sc = calc_mwu_biasZ(bca->iref_scl, bca->ialt_scl, 100, 0,1); - } else { - if (bca->fmt_flag & B2B_INFO_RPB) - call->mwu_pos = calc_mwu_biasZ(bca->ref_pos, bca->alt_pos, bca->npos, 0, 1); + if ( bca->fmt_flag & B2B_INFO_SCBZ ) + call->mwu_sc = calc_mwu_biasZ(bca->iref_scl, bca->ialt_scl, 100, 0,1); + } else { + if ( bca->fmt_flag & B2B_INFO_RPBZ ) + call->mwu_pos = calc_mwu_biasZ(bca->ref_pos, bca->alt_pos, bca->npos, 0, 1); + if ( bca->fmt_flag & B2B_INFO_MQBZ ) call->mwu_mq = calc_mwu_biasZ(bca->ref_mq, bca->alt_mq, bca->nqual,1,1); + if ( bca->fmt_flag & B2B_INFO_BQBZ ) call->mwu_bq = calc_mwu_biasZ(bca->ref_bq, bca->alt_bq, bca->nqual,0,1); + if ( bca->fmt_flag & B2B_INFO_MQSBZ ) call->mwu_mqs = calc_mwu_biasZ(bca->fwd_mqs, bca->rev_mqs, bca->nqual,0,1); - if ( bca->fmt_flag & B2B_INFO_SCB ) - call->mwu_sc = calc_mwu_biasZ(bca->ref_scl, bca->alt_scl, 100, 0,1); - } + if ( bca->fmt_flag & B2B_INFO_SCBZ ) + call->mwu_sc = calc_mwu_biasZ(bca->ref_scl, bca->alt_scl, 100, 0,1); + } + if ( bca->fmt_flag & B2B_INFO_NMBZ ) call->mwu_nm[0] = calc_mwu_biasZ(bca->ref_nm, bca->alt_nm, B2B_N_NM,0,1); - if ( bca->fmt_flag & B2B_FMT_NMBZ ) + if ( bca->fmt_flag & B2B_FMT_NMBZ ) + { + for (i=0; imwu_nm[i+1] = val!=HUGE_VAL ? val : 0; - } + float val = calc_mwu_biasZ(calls[i].ref_nm, calls[i].alt_nm, B2B_N_NM,0,1); + call->mwu_nm[i+1] = val!=HUGE_VAL ? val : 0; } - } else { - // Old method; U as probability between 0 and 1 - if ( bca->fmt_flag & B2B_INFO_RPB ) - call->mwu_pos = calc_mwu_biasZ(bca->ref_pos, bca->alt_pos, bca->npos, 0, 0); - call->mwu_mq = calc_mwu_biasZ(bca->ref_mq, bca->alt_mq, bca->nqual, 1, 0); - call->mwu_bq = calc_mwu_biasZ(bca->ref_bq, bca->alt_bq, bca->nqual, 0, 0); - call->mwu_mqs = calc_mwu_biasZ(bca->fwd_mqs, bca->rev_mqs, bca->nqual, 0, 0); } - -#if CDF_MWU_TESTS - // CDF version of MWU tests is not calculated by default - if ( bca->fmt_flag & B2B_INFO_RPB ) - call->mwu_pos_cdf = calc_mwu_bias_cdf(bca->ref_pos, bca->alt_pos, bca->npos); - call->mwu_mq_cdf = calc_mwu_bias_cdf(bca->ref_mq, bca->alt_mq, bca->nqual); - call->mwu_bq_cdf = calc_mwu_bias_cdf(bca->ref_bq, bca->alt_bq, bca->nqual); - call->mwu_mqs_cdf = calc_mwu_bias_cdf(bca->fwd_mqs, bca->rev_mqs, bca->nqual); -#endif - if ( bca->fmt_flag & B2B_INFO_VDB ) call->vdb = calc_vdb(bca->alt_pos, bca->npos); @@ -1130,11 +1116,13 @@ int bcf_call2bcf(bcf_call_t *bc, bcf1_t *rec, bcf_callret1_t *bcr, int fmt_flag, bc->tmp.l = 0; // INFO - if (bc->ori_ref < 0) + if ( bc->ori_ref < 0 ) { bcf_update_info_flag(hdr, rec, "INDEL", NULL, 1); - bcf_update_info_int32(hdr, rec, "IDV", &bca->max_support, 1); - bcf_update_info_float(hdr, rec, "IMF", &bca->max_frac, 1); + if ( fmt_flag&B2B_INFO_IDV ) + bcf_update_info_int32(hdr, rec, "IDV", &bca->max_support, 1); + if ( fmt_flag&B2B_INFO_IMF ) + bcf_update_info_float(hdr, rec, "IMF", &bca->max_frac, 1); } bcf_update_info_int32(hdr, rec, "DP", &bc->ori_depth, 1); if ( fmt_flag&B2B_INFO_ADF ) @@ -1156,55 +1144,40 @@ int bcf_call2bcf(bcf_call_t *bc, bcf1_t *rec, bcf_callret1_t *bcr, int fmt_flag, for (i=0; i<16; i++) tmpf[i] = bc->anno[i]; bcf_update_info_float(hdr, rec, "I16", tmpf, 16); bcf_update_info_float(hdr, rec, "QS", bc->qsum, nals); - bcf_update_info_int32(hdr, rec, "MIN_PL_SUM", &bc->shift, 1); if ( has_alt ) { - if ( bc->vdb != HUGE_VAL ) bcf_update_info_float(hdr, rec, "VDB", &bc->vdb, 1); - if ( bc->seg_bias != HUGE_VAL ) bcf_update_info_float(hdr, rec, "SGB", &bc->seg_bias, 1); - if ( bca->nnm[0] || bca->nnm[1] ) + if ( fmt_flag&B2B_INFO_MIN_PL_SUM ) + bcf_update_info_int32(hdr, rec, "MIN_PL_SUM", &bc->shift, 1); + if ( fmt_flag&B2B_INFO_VDB && bc->vdb != HUGE_VAL ) + bcf_update_info_float(hdr, rec, "VDB", &bc->vdb, 1); + if ( fmt_flag&B2B_INFO_SGB && bc->seg_bias != HUGE_VAL ) + bcf_update_info_float(hdr, rec, "SGB", &bc->seg_bias, 1); + if ( fmt_flag&B2B_INFO_NM && (bca->nnm[0] || bca->nnm[1]) ) { for (i=0; i<2; i++) bc->nm[i] = bca->nnm[i] ? bca->nm[i]/bca->nnm[i] : 0; bcf_update_info_float(hdr, rec, "NM", bc->nm, 2); } - if (bca->fmt_flag & B2B_INFO_ZSCORE) { - if ( bc->mwu_pos != HUGE_VAL ) - bcf_update_info_float(hdr, rec, "RPBZ", &bc->mwu_pos, 1); - if ( bc->mwu_mq != HUGE_VAL ) - bcf_update_info_float(hdr, rec, "MQBZ", &bc->mwu_mq, 1); - if ( bc->mwu_mqs != HUGE_VAL ) - bcf_update_info_float(hdr, rec, "MQSBZ", &bc->mwu_mqs, 1); - if ( bc->mwu_bq != HUGE_VAL ) - bcf_update_info_float(hdr, rec, "BQBZ", &bc->mwu_bq, 1); - if ( bc->mwu_nm[0] != HUGE_VAL ) - bcf_update_info_float(hdr, rec, "NMBZ", bc->mwu_nm, 1); - if ( bc->mwu_sc != HUGE_VAL ) - bcf_update_info_float(hdr, rec, "SCBZ", &bc->mwu_sc, 1); - } else { - if ( bc->mwu_pos != HUGE_VAL ) - bcf_update_info_float(hdr, rec, "RPB", &bc->mwu_pos, 1); - if ( bc->mwu_mq != HUGE_VAL ) - bcf_update_info_float(hdr, rec, "MQB", &bc->mwu_mq, 1); - if ( bc->mwu_mqs != HUGE_VAL ) - bcf_update_info_float(hdr, rec, "MQSB", &bc->mwu_mqs, 1); - if ( bc->mwu_bq != HUGE_VAL ) - bcf_update_info_float(hdr, rec, "BQB", &bc->mwu_bq, 1); - } - - if ( bc->strand_bias != HUGE_VAL ) + if ( fmt_flag&B2B_INFO_RPBZ && bc->mwu_pos != HUGE_VAL ) + bcf_update_info_float(hdr, rec, "RPBZ", &bc->mwu_pos, 1); + if ( fmt_flag&B2B_INFO_MQBZ && bc->mwu_mq != HUGE_VAL ) + bcf_update_info_float(hdr, rec, "MQBZ", &bc->mwu_mq, 1); + if ( fmt_flag&B2B_INFO_MQSBZ && bc->mwu_mqs != HUGE_VAL ) + bcf_update_info_float(hdr, rec, "MQSBZ", &bc->mwu_mqs, 1); + if ( fmt_flag&B2B_INFO_BQBZ && bc->mwu_bq != HUGE_VAL ) + bcf_update_info_float(hdr, rec, "BQBZ", &bc->mwu_bq, 1); + if ( fmt_flag&B2B_INFO_NMBZ && bc->mwu_nm[0] != HUGE_VAL ) + bcf_update_info_float(hdr, rec, "NMBZ", bc->mwu_nm, 1); + if ( fmt_flag&B2B_INFO_SCBZ && bc->mwu_sc != HUGE_VAL ) + bcf_update_info_float(hdr, rec, "SCBZ", &bc->mwu_sc, 1); + if ( fmt_flag&B2B_INFO_FS && bc->strand_bias != HUGE_VAL ) bcf_update_info_float(hdr, rec, "FS", &bc->strand_bias, 1); - -#if CDF_MWU_TESTS - if ( bc->mwu_pos_cdf != HUGE_VAL ) bcf_update_info_float(hdr, rec, "RPB2", &bc->mwu_pos_cdf, 1); - if ( bc->mwu_mq_cdf != HUGE_VAL ) bcf_update_info_float(hdr, rec, "MQB2", &bc->mwu_mq_cdf, 1); - if ( bc->mwu_mqs_cdf != HUGE_VAL ) bcf_update_info_float(hdr, rec, "MQSB2", &bc->mwu_mqs_cdf, 1); - if ( bc->mwu_bq_cdf != HUGE_VAL ) bcf_update_info_float(hdr, rec, "BQB2", &bc->mwu_bq_cdf, 1); -#endif } tmpf[0] = bc->ori_depth ? (float)bc->mq0/bc->ori_depth : 0; - bcf_update_info_float(hdr, rec, "MQ0F", tmpf, 1); + if ( fmt_flag&B2B_INFO_MQ0F ) + bcf_update_info_float(hdr, rec, "MQ0F", tmpf, 1); // FORMAT rec->n_sample = bc->n; diff --git a/bam2bcf.h b/bam2bcf.h index 67bda58b3..3ab43059a 100644 --- a/bam2bcf.h +++ b/bam2bcf.h @@ -58,11 +58,21 @@ DEALINGS IN THE SOFTWARE. */ #define B2B_INFO_SCR (1<<12) #define B2B_FMT_SCR (1<<13) #define B2B_INFO_VDB (1<<14) -#define B2B_INFO_RPB (1<<15) -#define B2B_FMT_QS (1<<16) -#define B2B_INFO_SCB (1<<17) -#define B2B_FMT_NMBZ (1<<18) // per-sample NMBZ -#define B2B_INFO_ZSCORE (1<<30) // MWU as-is or Z-normalised +#define B2B_FMT_QS (1<<15) +#define B2B_FMT_NMBZ (1<<16) // per-sample NMBZ +#define B2B_INFO_NMBZ (1<<17) +#define B2B_INFO_BQBZ (1<<18) +#define B2B_INFO_MQBZ (1<<19) +#define B2B_INFO_MQSBZ (1<<20) +#define B2B_INFO_RPBZ (1<<21) +#define B2B_INFO_SCBZ (1<<22) +#define B2B_INFO_SGB (1<<23) +#define B2B_INFO_MIN_PL_SUM (1<<24) +#define B2B_INFO_NM (1<<25) +#define B2B_INFO_MQ0F (1<<26) +#define B2B_INFO_IDV (1<<27) +#define B2B_INFO_IMF (1<<28) +#define B2B_INFO_FS (1<<29) #define B2B_MAX_ALLELES 5 #define B2B_N_NM 32 // number of NMBZ bins, i.e. max number of mismatches @@ -159,9 +169,6 @@ typedef struct { uint8_t *fmt_arr; float vdb; // variant distance bias float mwu_pos, mwu_mq, mwu_bq, mwu_mqs, mwu_sc, *mwu_nm, nm[2]; -#if CDF_MWU_TESTS - float mwu_pos_cdf, mwu_mq_cdf, mwu_bq_cdf, mwu_mqs_cdf; -#endif float seg_bias; float strand_bias; // phred-scaled fisher-exact test kstring_t tmp; diff --git a/mpileup.c b/mpileup.c index 3fe0a16e5..6bb44e17c 100644 --- a/mpileup.c +++ b/mpileup.c @@ -68,7 +68,8 @@ typedef struct _mplp_pileup_t mplp_pileup_t; // Data shared by all bam files typedef struct { int min_mq, flag, min_baseQ, max_baseQ, delta_baseQ, capQ_thres, max_depth, - max_indel_depth, max_read_len, fmt_flag, ambig_reads; + max_indel_depth, max_read_len, ambig_reads; + uint32_t fmt_flag; int rflag_skip_any_unset, rflag_skip_all_unset, rflag_skip_any_set, rflag_skip_all_set, output_type; int openQ, extQ, tandemQ, min_support, indel_win_size; // for indels double min_frac; // for indels @@ -776,42 +777,38 @@ static int mpileup(mplp_conf_t *conf) bcf_hdr_append(conf->bcf_hdr,"##ALT="); bcf_hdr_append(conf->bcf_hdr,"##INFO="); - bcf_hdr_append(conf->bcf_hdr,"##INFO="); - bcf_hdr_append(conf->bcf_hdr,"##INFO="); + if ( conf->fmt_flag&B2B_INFO_IDV ) + bcf_hdr_append(conf->bcf_hdr,"##INFO="); + if ( conf->fmt_flag&B2B_INFO_IMF ) + bcf_hdr_append(conf->bcf_hdr,"##INFO="); bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_VDB ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); - if (conf->fmt_flag & B2B_INFO_ZSCORE) { - if ( conf->fmt_flag&B2B_INFO_RPB ) - bcf_hdr_append(conf->bcf_hdr,"##INFO="); + if ( conf->fmt_flag&B2B_INFO_RPBZ ) + bcf_hdr_append(conf->bcf_hdr,"##INFO="); + if ( conf->fmt_flag&B2B_INFO_MQBZ ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); + if ( conf->fmt_flag&B2B_INFO_BQBZ ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); + if ( conf->fmt_flag&B2B_INFO_MQSBZ ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); + if ( conf->fmt_flag&B2B_INFO_MIN_PL_SUM ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); + if ( conf->fmt_flag&B2B_INFO_NM ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); + if ( conf->fmt_flag&B2B_INFO_NMBZ ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); - if ( conf->fmt_flag&B2B_FMT_NMBZ ) - bcf_hdr_append(conf->bcf_hdr,"##FORMAT="); - if ( conf->fmt_flag&B2B_INFO_SCB ) - bcf_hdr_append(conf->bcf_hdr,"##INFO="); - } else { - if ( conf->fmt_flag&B2B_INFO_RPB ) - bcf_hdr_append(conf->bcf_hdr,"##INFO="); - bcf_hdr_append(conf->bcf_hdr,"##INFO="); - bcf_hdr_append(conf->bcf_hdr,"##INFO="); - bcf_hdr_append(conf->bcf_hdr,"##INFO="); - } - - bcf_hdr_append(conf->bcf_hdr,"##INFO="); -#if CDF_MWU_TESTS - bcf_hdr_append(conf->bcf_hdr,"##INFO="); - bcf_hdr_append(conf->bcf_hdr,"##INFO="); - bcf_hdr_append(conf->bcf_hdr,"##INFO="); - bcf_hdr_append(conf->bcf_hdr,"##INFO="); -#endif - bcf_hdr_append(conf->bcf_hdr,"##INFO="); - bcf_hdr_append(conf->bcf_hdr,"##INFO="); + if ( conf->fmt_flag&B2B_FMT_NMBZ ) + bcf_hdr_append(conf->bcf_hdr,"##FORMAT="); + if ( conf->fmt_flag&B2B_INFO_SCBZ ) + bcf_hdr_append(conf->bcf_hdr,"##INFO="); + if ( conf->fmt_flag&B2B_INFO_FS ) + bcf_hdr_append(conf->bcf_hdr,"##INFO="); + if ( conf->fmt_flag&B2B_INFO_SGB ) + bcf_hdr_append(conf->bcf_hdr,"##INFO="); + if ( conf->fmt_flag&B2B_INFO_MQ0F ) + bcf_hdr_append(conf->bcf_hdr,"##INFO="); bcf_hdr_append(conf->bcf_hdr,"##INFO="); bcf_hdr_append(conf->bcf_hdr,"##INFO="); bcf_hdr_append(conf->bcf_hdr,"##FORMAT="); @@ -1061,38 +1058,68 @@ int read_file_list(const char *file_list,int *n,char **argv[]) } #undef MAX_PATH_LEN -int parse_format_flag(const char *str) +#define SET_FMT_FLAG(str,bit,msg) \ + if (!strcasecmp(tag,str) || !strcasecmp(tag,"FMT/"str) || !strcasecmp(tag,"FORMAT/"str)) \ + { \ + if ( *msg ) fprintf(stderr,"%s",msg); \ + if ( exclude ) \ + *flag &= ~bit; \ + else \ + *flag |= bit; \ + free(tags[i]); \ + continue; \ + } +#define SET_INFO_FLAG(str,bit,msg) if (!strcasecmp(tag,"INFO/"str)) \ + { \ + if ( exclude ) \ + *flag &= ~bit; \ + else \ + *flag |= bit; \ + free(tags[i]); \ + continue; \ + } + +void parse_format_flag(uint32_t *flag, const char *str) { - int i, flag = 0, n_tags; + int i, n_tags; char **tags = hts_readlist(str, 0, &n_tags); for(i=0; i ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= ##INFO= diff --git a/test/mpileup/annot-NMBZ.2.1.out b/test/mpileup/annot-NMBZ.2.1.out index 6f626ae5e..d28f68e73 100644 --- a/test/mpileup/annot-NMBZ.2.1.out +++ b/test/mpileup/annot-NMBZ.2.1.out @@ -11,10 +11,10 @@ ##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= ##INFO= diff --git a/test/mpileup/annot-NMBZ.3.1.out b/test/mpileup/annot-NMBZ.3.1.out index 26b95fb87..27d5dec32 100644 --- a/test/mpileup/annot-NMBZ.3.1.out +++ b/test/mpileup/annot-NMBZ.3.1.out @@ -11,14 +11,14 @@ ##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= ##INFO= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample sample2 chr16 75 . C T,<*> 0 . DP=246;I16=114,125,1,0,8929,339403,8,64,14340,860400,40,1600,3901,80155,11,121;QS=1.99845,0.00154859,0;SGB=-0.516033;RPBZ=-1.13322;MQBZ=-15.4596;MQSBZ=1.04257;BQBZ=-1.74564;NMBZ=7.74597;SCBZ=10.8628;FS=0;MQ0F=0 PL 0,255,255,255,255,255 0,255,255,255,255,255 -chr16 75 . CTTTTTTTT CTTTTTTTTT,CTTTTTTTTTT 0 . INDEL;IDV=38;IMF=0.368932;DP=246;I16=78,96,23,16,6960,278400,1580,64400,10440,626400,2340,140400,3155,66991,675,13499;QS=1.40527,0.576876,0.0178571;VDB=0.543627;SGB=-13.9289;RPBZ=-1.68678;MQBZ=0.434057;MQSBZ=1.04257;BQBZ=-1.74564;NMBZ=-0.823886;SCBZ=-0.615101;FS=0;MQ0F=0 PL 255,0,128,255,206,255 0,255,201,255,204,214 +chr16 75 . CTTTTTTTT CTTTTTTTTT,CTTTTTTTTTT 0 . INDEL;IDV=38;IMF=0.368932;DP=246;I16=92,109,23,16,8040,321600,1580,64400,12040,721600,2340,140400,3237,66777,675,13499;QS=1.43466,0.548367,0.0169779;VDB=0.543627;SGB=-13.9289;RPBZ=-1.68678;MQBZ=0.434057;MQSBZ=1.04257;BQBZ=-1.74564;NMBZ=-0.886523;SCBZ=-0.615101;FS=0;MQ0F=0 PL 255,0,116,255,195,255 0,255,198,255,201,210 diff --git a/test/mpileup/indel-AD.1.out b/test/mpileup/indel-AD.1.out index d852bd8f9..695c2aa00 100644 --- a/test/mpileup/indel-AD.1.out +++ b/test/mpileup/indel-AD.1.out @@ -11,10 +11,10 @@ ##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= ##INFO= @@ -167,9 +167,9 @@ 000000F 535 . G A,<*> 0 . DP=125;I16=65,52,0,1,4309,171791,12,144,7020,421200,60,3600,2679,64385,25,625;QS=0.997223,0.00277713,0;SGB=-0.379885;RPBZ=-1.14518;MQBZ=0;MQSBZ=0;BQBZ=-1.74874;NMBZ=-0.250141;SCBZ=0.0762539;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:117,1,0 000000F 536 . T G,A,<*> 0 . DP=125;I16=65,51,0,2,4274,171298,24,288,6960,417600,120,7200,2661,64041,48,1154;QS=0.994416,0.002792,0.002792,0;VDB=0.1;SGB=-0.453602;RPBZ=-1.69957;MQBZ=0;MQSBZ=0;BQBZ=-2.39373;NMBZ=-0.292578;SCBZ=-0.714873;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:116,1,1,0 000000F 537 . A <*> 0 . DP=125;I16=65,53,0,0,4390,175290,0,0,7080,424800,0,0,2713,65375,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:118,0 -000000F 537 . AC A 0 . INDEL;IDV=60;IMF=0.48;DP=125;I16=37,25,30,27,2480,99200,2280,91200,3720,223200,3420,205200,1399,33485,1298,31150;QS=0.260049,0.739951;VDB=0.455511;SGB=-0.693147;RPBZ=-0.543708;MQBZ=0;MQSBZ=0;BQBZ=-2.39373;NMBZ=0.469542;SCBZ=0.641853;FS=0;MQ0F=0 PL:AD 255,0,27:62,57 +000000F 537 . AC A 0 . INDEL;IDV=60;IMF=0.48;DP=125;I16=36,26,30,27,2480,99200,2280,91200,3720,223200,3420,205200,1433,34549,1298,31150;QS=0.263673,0.736327;VDB=0.455511;SGB=-0.693147;RPBZ=-0.543708;MQBZ=0;MQSBZ=0;BQBZ=-2.39373;NMBZ=0.25078;SCBZ=0.641853;FS=0;MQ0F=0 PL:AD 255,0,28:62,57 000000F 538 . C <*> 0 . DP=65;I16=36,26,0,0,2195,86349,0,0,3720,223200,0,0,1432,34600,0,0;QS=1,0;MQ0F=0 PL:AD 0,187,255:62,0 -000000F 538 . CT C 0 . INDEL;IDV=64;IMF=0.512;DP=125;I16=30,26,36,25,2240,89600,2440,97600,3360,201600,3660,219600,1279,30735,1380,33214;QS=0.218762,0.781238;VDB=0.0040309;SGB=-0.693147;RPBZ=0.242079;MQBZ=0;MQSBZ=0;BQBZ=-2.39373;NMBZ=-2.10156;SCBZ=-0.994262;FS=0;MQ0F=0 PL:AD 255,0,27:56,61 +000000F 538 . CT C 0 . INDEL;IDV=64;IMF=0.512;DP=125;I16=30,26,36,25,2240,89600,2440,97600,3360,201600,3660,219600,1277,30663,1380,33214;QS=0.22136,0.77864;VDB=0.0040309;SGB=-0.693147;RPBZ=0.242079;MQBZ=0;MQSBZ=0;BQBZ=-2.39373;NMBZ=-2.25501;SCBZ=-0.994262;FS=0;MQ0F=0 PL:AD 255,0,28:56,61 000000F 539 . T <*> 0 . DP=60;I16=29,26,0,0,2120,86238,0,0,3300,198000,0,0,1260,30374,0,0;QS=1,0;MQ0F=0 PL:AD 0,166,255:55,0 000000F 540 . G <*> 0 . DP=124;I16=64,53,0,0,4130,161310,0,0,7020,421200,0,0,2703,65511,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:117,0 000000F 541 . G <*> 0 . DP=124;I16=64,53,0,0,4143,160525,0,0,7020,421200,0,0,2705,65703,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:117,0 @@ -287,11 +287,11 @@ 000000F 653 . A <*> 0 . DP=21;I16=9,12,0,0,804,31130,0,0,1260,75600,0,0,303,5555,0,0;QS=1,0;MQ0F=0 PL:AD 0,63,255:21,0 000000F 654 . A <*> 0 . DP=21;I16=9,12,0,0,659,22061,0,0,1260,75600,0,0,285,5117,0,0;QS=1,0;MQ0F=0 PL:AD 0,63,255:21,0 000000F 655 . C <*> 0 . DP=21;I16=9,12,0,0,664,22342,0,0,1260,75600,0,0,266,4666,0,0;QS=1,0;MQ0F=0 PL:AD 0,63,255:21,0 -000000F 655 . CACAATACAA CACAA 0 . INDEL;IDV=6;IMF=0.285714;DP=21;I16=0,2,5,1,240,28800,720,86400,120,7200,360,21600,46,1060,100,1788;QS=0.0977444,0.902256;VDB=0.00211394;SGB=-0.616816;RPBZ=-2.81289;MQBZ=0;MQSBZ=0;BQBZ=-1.67266;NMBZ=-2.1454;SCBZ=-2.52262;FS=0;MQ0F=0 PL:AD 159,0,2:2,6 +000000F 655 . CACAATACAA CACAA 0 . INDEL;IDV=6;IMF=0.285714;DP=21;I16=4,11,5,1,1800,216000,720,86400,900,54000,360,21600,166,2878,100,1788;QS=0.371728,0.628272;VDB=0.00211394;SGB=-0.616816;RPBZ=-2.81289;MQBZ=0;MQSBZ=0;BQBZ=-1.67266;NMBZ=-2.79934;SCBZ=-2.52262;FS=0;MQ0F=0 PL:AD 129,0,28:15,6 000000F 656 . A <*> 0 . DP=11;I16=4,7,0,0,404,15690,0,0,660,39600,0,0,141,2411,0,0;QS=1,0;MQ0F=0 PL:AD 0,33,255:11,0 000000F 657 . C <*> 0 . DP=11;I16=4,7,0,0,413,15607,0,0,660,39600,0,0,131,2189,0,0;QS=1,0;MQ0F=0 PL:AD 0,33,255:11,0 000000F 658 . A <*> 0 . DP=10;I16=3,7,0,0,121,1651,0,0,600,36000,0,0,122,1986,0,0;QS=1,0;MQ0F=0 PL:AD 0,30,79:10,0 -000000F 658 . AA AAATTA 0 . INDEL;IDV=2;IMF=0.125;DP=16;I16=2,1,1,2,300,30000,300,30000,180,10800,180,10800,59,1205,50,902;QS=0.31694,0.68306;VDB=0.045681;SGB=-0.511536;RPBZ=-1.70026;MQBZ=0;MQSBZ=0;BQBZ=-1.67266;NMBZ=2.23607;SCBZ=-1.35678;FS=0;MQ0F=0 PL:AD 99,0,38:3,3 +000000F 658 . AA AAATTA 0 . INDEL;IDV=2;IMF=0.125;DP=16;I16=5,6,1,2,1100,110000,300,30000,660,39600,180,10800,141,2389,50,902;QS=0.418605,0.581395;VDB=0.045681;SGB=-0.511536;RPBZ=-1.70026;MQBZ=0;MQSBZ=0;BQBZ=-1.67266;NMBZ=-1.17947;SCBZ=-1.35678;FS=0;MQ0F=0 PL:AD 76,0,29:11,3 000000F 659 . A <*> 0 . DP=10;I16=3,5,0,0,86,1088,0,0,480,28800,0,0,75,1077,0,0;QS=1,0;MQ0F=0 PL:AD 0,24,63:8,0 000000F 660 . T <*> 0 . DP=2;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;QS=0,0;MQ0F=0 PL:AD 0,0,0:0,0 000000F 661 . A <*> 0 . DP=8;I16=0,2,0,0,8,32,0,0,120,7200,0,0,26,340,0,0;QS=1,0;MQ0F=0 PL:AD 0,6,7:2,0 diff --git a/test/mpileup/indel-AD.2.out b/test/mpileup/indel-AD.2.out index 649c3db6e..138ace728 100644 --- a/test/mpileup/indel-AD.2.out +++ b/test/mpileup/indel-AD.2.out @@ -11,10 +11,10 @@ ##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= ##INFO= @@ -22,4 +22,4 @@ ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample 11 75 . G <*> 0 . DP=68;I16=6,62,0,0,2437,87909,0,0,3770,217210,0,0,838,15940,0,0;QS=1,0;MQ0F=0 PL:AD 0,205,255:68,0 -11 75 . GTAAAATAAAATAAAATAAAATAAA GTAAAATAAAATAAAATAAAATAAAATAAA 0 . INDEL;IDV=6;IMF=0.0882353;DP=68;I16=5,9,1,5,1680,201600,720,86400,840,50400,174,5046,244,5778,147,3609;QS=0.730233,0.269767;VDB=0.00476095;SGB=-0.616816;RPBZ=-3.24592;MQBZ=-6.13241;MQSBZ=0;BQBZ=0;NMBZ=0;SCBZ=-0.546919;FS=0;MQ0F=0 PL:AD 83,0,244:14,6 +11 75 . GTAAAATAAAATAAAATAAAATAAA GTAAAATAAAATAAAATAAAATAAAATAAA 0 . INDEL;IDV=6;IMF=0.0882353;DP=68;I16=5,57,1,5,7440,892800,720,86400,3596,212164,174,5046,691,12331,147,3609;QS=0.834915,0.165085;VDB=0.00476095;SGB=-0.616816;RPBZ=-3.24592;MQBZ=-6.13241;MQSBZ=0;BQBZ=0;NMBZ=-0.546919;SCBZ=-0.546919;FS=0;MQ0F=0 PL:AD 0,54,150:62,6 diff --git a/test/mpileup/indel-AD.3.out b/test/mpileup/indel-AD.3.out index 3d4e60257..138ace728 100644 --- a/test/mpileup/indel-AD.3.out +++ b/test/mpileup/indel-AD.3.out @@ -11,10 +11,10 @@ ##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= ##INFO= @@ -22,4 +22,4 @@ ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample 11 75 . G <*> 0 . DP=68;I16=6,62,0,0,2437,87909,0,0,3770,217210,0,0,838,15940,0,0;QS=1,0;MQ0F=0 PL:AD 0,205,255:68,0 -11 75 . GTAAAATAAAATAAAATAAAATAAA GTAAAATAAAATAAAATAAAATAAAATAAA 0 . INDEL;IDV=6;IMF=0.0882353;DP=68;I16=5,9,1,5,1680,201600,720,86400,840,50400,174,5046,244,5778,147,3609;QS=0.730233,0.269767;VDB=0.00476095;SGB=-0.616816;RPBZ=-3.24592;MQBZ=-6.13241;MQSBZ=0;BQBZ=0;NMBZ=0;SCBZ=-0.546919;FS=0;MQ0F=0 PL:AD 83,0,244:45,23 +11 75 . GTAAAATAAAATAAAATAAAATAAA GTAAAATAAAATAAAATAAAATAAAATAAA 0 . INDEL;IDV=6;IMF=0.0882353;DP=68;I16=5,57,1,5,7440,892800,720,86400,3596,212164,174,5046,691,12331,147,3609;QS=0.834915,0.165085;VDB=0.00476095;SGB=-0.616816;RPBZ=-3.24592;MQBZ=-6.13241;MQSBZ=0;BQBZ=0;NMBZ=-0.546919;SCBZ=-0.546919;FS=0;MQ0F=0 PL:AD 0,54,150:62,6 diff --git a/test/mpileup/indel-AD.4.out b/test/mpileup/indel-AD.4.out index 7d2afac71..138ace728 100644 --- a/test/mpileup/indel-AD.4.out +++ b/test/mpileup/indel-AD.4.out @@ -11,10 +11,10 @@ ##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= ##INFO= @@ -22,4 +22,4 @@ ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample 11 75 . G <*> 0 . DP=68;I16=6,62,0,0,2437,87909,0,0,3770,217210,0,0,838,15940,0,0;QS=1,0;MQ0F=0 PL:AD 0,205,255:68,0 -11 75 . GTAAAATAAAATAAAATAAAATAAA GTAAAATAAAATAAAATAAAATAAAATAAA 0 . INDEL;IDV=6;IMF=0.0882353;DP=68;I16=5,9,1,5,1680,201600,720,86400,840,50400,174,5046,244,5778,147,3609;QS=0.730233,0.269767;VDB=0.00476095;SGB=-0.616816;RPBZ=-3.24592;MQBZ=-6.13241;MQSBZ=0;BQBZ=0;NMBZ=0;SCBZ=-0.546919;FS=0;MQ0F=0 PL:AD 83,0,244:62,6 +11 75 . GTAAAATAAAATAAAATAAAATAAA GTAAAATAAAATAAAATAAAATAAAATAAA 0 . INDEL;IDV=6;IMF=0.0882353;DP=68;I16=5,57,1,5,7440,892800,720,86400,3596,212164,174,5046,691,12331,147,3609;QS=0.834915,0.165085;VDB=0.00476095;SGB=-0.616816;RPBZ=-3.24592;MQBZ=-6.13241;MQSBZ=0;BQBZ=0;NMBZ=-0.546919;SCBZ=-0.546919;FS=0;MQ0F=0 PL:AD 0,54,150:62,6 diff --git a/test/mpileup/mpileup-SCR.out b/test/mpileup/mpileup-SCR.out index 26af1fbb0..35e805380 100644 --- a/test/mpileup/mpileup-SCR.out +++ b/test/mpileup/mpileup-SCR.out @@ -11,10 +11,10 @@ ##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= ##INFO= diff --git a/test/mpileup/mpileup-filter.1.out b/test/mpileup/mpileup-filter.1.out index c9540d542..b3aacdc87 100644 --- a/test/mpileup/mpileup-filter.1.out +++ b/test/mpileup/mpileup-filter.1.out @@ -11,10 +11,10 @@ ##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= ##INFO= diff --git a/test/mpileup/mpileup-filter.2.out b/test/mpileup/mpileup-filter.2.out index 661594560..6e8064a6e 100644 --- a/test/mpileup/mpileup-filter.2.out +++ b/test/mpileup/mpileup-filter.2.out @@ -11,10 +11,10 @@ ##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= ##INFO= diff --git a/test/mpileup/mpileup.1.out b/test/mpileup/mpileup.1.out index 48bea5ab5..1efd2af29 100644 --- a/test/mpileup/mpileup.1.out +++ b/test/mpileup/mpileup.1.out @@ -11,10 +11,10 @@ ##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= ##INFO= diff --git a/test/mpileup/mpileup.10.out b/test/mpileup/mpileup.10.out index 585e06ffb..425c47eb7 100644 --- a/test/mpileup/mpileup.10.out +++ b/test/mpileup/mpileup.10.out @@ -11,10 +11,10 @@ ##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= ##INFO= diff --git a/test/mpileup/mpileup.11.out b/test/mpileup/mpileup.11.out index 36d61d4ae..b83755dde 100644 --- a/test/mpileup/mpileup.11.out +++ b/test/mpileup/mpileup.11.out @@ -11,10 +11,10 @@ ##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= ##INFO= diff --git a/test/mpileup/mpileup.2.out b/test/mpileup/mpileup.2.out index 45cdd502e..8e4335abe 100644 --- a/test/mpileup/mpileup.2.out +++ b/test/mpileup/mpileup.2.out @@ -11,10 +11,10 @@ ##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= ##INFO= diff --git a/test/mpileup/mpileup.3.out b/test/mpileup/mpileup.3.out index 596a1d3b5..a3c30a6f4 100644 --- a/test/mpileup/mpileup.3.out +++ b/test/mpileup/mpileup.3.out @@ -11,10 +11,10 @@ ##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= ##INFO= diff --git a/test/mpileup/mpileup.4.out b/test/mpileup/mpileup.4.out index a2a6c1272..4cb2620bc 100644 --- a/test/mpileup/mpileup.4.out +++ b/test/mpileup/mpileup.4.out @@ -11,10 +11,10 @@ ##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= ##INFO= diff --git a/test/mpileup/mpileup.5.out b/test/mpileup/mpileup.5.out index b25f199e5..a0ed55e00 100644 --- a/test/mpileup/mpileup.5.out +++ b/test/mpileup/mpileup.5.out @@ -11,10 +11,10 @@ ##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= ##INFO= diff --git a/test/mpileup/mpileup.6.out b/test/mpileup/mpileup.6.out index 9b4cef2dc..0eb18fd41 100644 --- a/test/mpileup/mpileup.6.out +++ b/test/mpileup/mpileup.6.out @@ -11,10 +11,10 @@ ##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= ##INFO= diff --git a/test/mpileup/mpileup.7.out b/test/mpileup/mpileup.7.out index 59e1f4c0d..256c98a55 100644 --- a/test/mpileup/mpileup.7.out +++ b/test/mpileup/mpileup.7.out @@ -11,10 +11,10 @@ ##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= ##INFO= diff --git a/test/mpileup/mpileup.8.out b/test/mpileup/mpileup.8.out index 1f3f6ff7f..82046fcbd 100644 --- a/test/mpileup/mpileup.8.out +++ b/test/mpileup/mpileup.8.out @@ -11,10 +11,10 @@ ##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= ##INFO= diff --git a/test/mpileup/mpileup.9.out b/test/mpileup/mpileup.9.out index 06b6ab4c5..1031ac34c 100644 --- a/test/mpileup/mpileup.9.out +++ b/test/mpileup/mpileup.9.out @@ -11,10 +11,10 @@ ##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##INFO= ##INFO= From 47fe5b819fc907c2da733b9836b992a0b8fc5011 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Tue, 22 Nov 2022 14:19:43 +0000 Subject: [PATCH 52/84] Remember read's realn status in a clean way, not by misusing bam->core.flag --- bam2bcf.h | 6 ++++-- mpileup.c | 7 ++----- 2 files changed, 6 insertions(+), 7 deletions(-) diff --git a/bam2bcf.h b/bam2bcf.h index 3ab43059a..139aeb491 100644 --- a/bam2bcf.h +++ b/bam2bcf.h @@ -87,12 +87,14 @@ DEALINGS IN THE SOFTWARE. */ #define PLP_CD(x) ((plp_cd_t*)((x)->p)) #define PLP_HAS_SOFT_CLIP(cd) (PLP_CD(cd)->i & 1) #define PLP_HAS_INDEL(cd) (PLP_CD(cd)->i & 2) -#define PLP_SAMPLE_ID(cd) (PLP_CD(cd)->i >> 2) +#define PLP_IS_REALN(cd) (PLP_CD(cd)->i & 4) +#define PLP_SAMPLE_ID(cd) (PLP_CD(cd)->i >> 3) #define PLP_QLEN(cd) (PLP_CD(cd)->qlen) #define PLP_SET_SOFT_CLIP(cd) (PLP_CD(cd)->i |= 1) #define PLP_SET_INDEL(cd) (PLP_CD(cd)->i |= 2) -#define PLP_SET_SAMPLE_ID(cd,n) (PLP_CD(cd)->i |= (n)<<2) +#define PLP_SET_REALN(cd) (PLP_CD(cd)->i |= 4) +#define PLP_SET_SAMPLE_ID(cd,n) (PLP_CD(cd)->i |= (n)<<3) typedef struct { diff --git a/mpileup.c b/mpileup.c index 6bb44e17c..5102b30af 100644 --- a/mpileup.c +++ b/mpileup.c @@ -441,8 +441,6 @@ static void mplp_realn(int n, int *n_plp, const bam_pileup1_t **plp, return; } -static int reminded = 0; -if ( !reminded ) { fprintf(stderr,"todo: use plp_cd_t to avoid the read-only limitation of p->cd.i\n"); reminded = 1; } // Realign for (i = 0; i < n; i++) { // iterate over bams for (j = 0; j < n_plp[i]; j++) { // iterate over reads @@ -459,9 +457,8 @@ if ( !reminded ) { fprintf(stderr,"todo: use plp_cd_t to avoid the read-only lim // We could use our own structure (p->cd.p), allocated during // the constructor, but for simplicity we play dirty and // abuse an unused flag bit instead. - if (b->core.flag & 32768) - continue; - b->core.flag |= 32768; + if ( PLP_IS_REALN(&(p->cd)) ) continue; + PLP_SET_REALN(&(p->cd)); if (b->core.l_qseq > max_read_len) continue; From 321c0d01ab051735be7c53ab218a9a02cfcbd27c Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Tue, 22 Nov 2022 14:47:21 +0000 Subject: [PATCH 53/84] Declare inline functions as static in the hope it fixes a compiler error in the -std=gnu99 test --- cigar_state.h | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/cigar_state.h b/cigar_state.h index 5822d1cea..a12a70995 100644 --- a/cigar_state.h +++ b/cigar_state.h @@ -42,7 +42,7 @@ typedef struct } cigar_state_t; -inline void cstate_init(cigar_state_t *cs, bam1_t *bam) +static inline void cstate_init(cigar_state_t *cs, bam1_t *bam) { cs->bam = bam; cs->cigar = bam_get_cigar(bam); @@ -67,7 +67,7 @@ inline void cstate_init(cigar_state_t *cs, bam1_t *bam) * - pos inside a deletion && trim_left=1 .. returns position after the deletion * - pos inside a deletion && trim_left=0 .. returns position before the deletion */ -inline int cstate_seek_fwd(cigar_state_t *cs, hts_pos_t *pos_ptr, int trim_left) +static inline int cstate_seek_fwd(cigar_state_t *cs, hts_pos_t *pos_ptr, int trim_left) { hts_pos_t pos = *pos_ptr; while ( cs->ref_pos <= pos ) @@ -131,7 +131,7 @@ inline int cstate_seek_fwd(cigar_state_t *cs, hts_pos_t *pos_ptr, int trim_left) * is still not entirely consumed (e.g. a deletion or a soft-clip); -2 * when there is no overlap (i.e. the read ends before the position). */ -inline int cstate_seek_op_fwd(cigar_state_t *cs, hts_pos_t pos, int seek_op, int *oplen) +static inline int cstate_seek_op_fwd(cigar_state_t *cs, hts_pos_t pos, int seek_op, int *oplen) { while ( cs->ref_pos <= pos ) { From 2b6f05d3e4cf4d73aca9971a58329b8b76313ba2 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Wed, 23 Nov 2022 12:20:41 +0000 Subject: [PATCH 54/84] Update documentation and NEWS --- NEWS | 28 ++++++++++++++++++++++++++++ doc/bcftools.txt | 6 ++++++ mpileup.c | 2 +- 3 files changed, 35 insertions(+), 1 deletion(-) diff --git a/NEWS b/NEWS index ad95180e0..88ac48870 100644 --- a/NEWS +++ b/NEWS @@ -24,17 +24,40 @@ Changes affecting specific commands: - Fix a bug where a MNV with multiple consequences (e.g. missense + stop_gained) would report only the less severe one (#1810) +* bcftools + + - More of the available annotations are now added by the `-t all` option + +* bcftools fixref + + - New INFO/FIXREF annotation + + - New -m swap mode + * bcftools +mendelian - The +mendelian plugin has been deprecated and replaced with +mendelian2. The function of the plugin is the same but the command line options and the output format has changed, and for this was introduced as a new plugin. +* mpileup + + - Most of the annotations generated by mpileup are now optional via the + `-a, --annotate` option and add several new (mostly experimental) annotations. + + - New option `--indels-2.0` for an EXPERIMENTAL indel calling model. This model aims + to address some known deficiencies of the current indel calling algorithm, specifically, + it uses diploid reference consensus sequence. Note that in the current version it + has the potential to increase sensitivity but at the cost of decreased specificity. + * bcftools norm - New --multi-overlaps option allows to set overlapping alleles either to the ref allele (the current default) or to a missing allele (#1764 and #1802) + - Fixed a bug in `-m -` which does not split missing FORMAT values correctly and + could lead to empty FORMAT fields such as `::` instead of the correct `:.:` (#1818) + * bcftools query - Fix a rare bug where the printing of SAMPLE field with `query` was incorrectly @@ -50,11 +73,16 @@ Changes affecting specific commands: - New options `-g, --gene-list` and `--gene-list-fields` which allow to prioritize consequences from a list of genes, or restrict output to the listed genes + - New `-H, --print-header` option to print the header with `-f` + * bcftools +trio-dnm2 - New -n, --strictly-novel option to downplay alleles which violate Mendelian inheritance but are not novel + - Allow to set the `--pn` and `--pns` options separately for SNVs and indels and make + the indel settings more strict by default + ## Release 1.16 (18th August 2022) diff --git a/doc/bcftools.txt b/doc/bcftools.txt index 47222bed9..a147792cb 100644 --- a/doc/bcftools.txt +++ b/doc/bcftools.txt @@ -2054,6 +2054,12 @@ those scenarios. ? FILE_3.bam SAMPLE_D ---- +*--indels-2.0*:: + A new EXPERIMENTAL indel calling model which aims to address some known deficiencies of + the current indel calling algorithm. Specifically, it uses diploid reference consensus + sequence. Note that in the current version it has the potential to increase sensitivity + but at the cost of decreased specificity + *-q, -min-MQ* 'INT':: Minimum mapping quality for an alignment to be used [0] diff --git a/mpileup.c b/mpileup.c index 5102b30af..5327af6f0 100644 --- a/mpileup.c +++ b/mpileup.c @@ -1251,7 +1251,7 @@ static void print_usage(FILE *fp, const mplp_conf_t *mplp) fprintf(fp, " --indel-size INT Approximate maximum indel size considered [%d]\n", mplp->indel_win_size); fprintf(fp, - " --indels-2.0 New indel calling model (diploid reference consensus)\n"); + " --indels-2.0 New EXPERIMENTAL indel calling model (diploid reference consensus)\n"); fprintf(fp,"\n"); fprintf(fp, "Configuration profiles activated with -X, --config:\n" From b044ef88a56443ee767060a5180c3086f0de0988 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Fri, 25 Nov 2022 12:44:07 +0000 Subject: [PATCH 55/84] Add missing cigar case (hard clip) and remove a debugging warning --- read_consensus.c | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/read_consensus.c b/read_consensus.c index 2408aec73..5c8133f28 100644 --- a/read_consensus.c +++ b/read_consensus.c @@ -185,8 +185,7 @@ static void add_ins(read_cns_t *rcns, int ref_pos, int seq_pos, uint8_t *raw_seq for (i=0; int16_seq[i]; i++) if ( ifrq->len[i]==len && !memcmp(ifrq->nt16_seq[i],str,len) ) break; -if ( i>=NI ) fprintf(stderr,"xxx: many ins types at pos=%d\n",(int)rcns->pos); // how frequent is it to have too many insertion types? - if ( i>=NI ) return; // too many choices; discard + if ( i>=NI ) return; // too many choices, typically homopolymers in long reads; discard if ( !ifrq->nt16_seq[i] ) // new insertion { @@ -208,8 +207,7 @@ static void add_del(read_cns_t *rcns, int ref_pos, int len) for (i=0; ilen[i]; i++) if ( dfrq->len[i]==len ) break; -if ( i>=NI ) fprintf(stderr,"xxx: many del types at pos=%d\n",(int)rcns->pos); // how frequent is it to have too many insertion types? - if ( i>=NI ) return; // too many choices; discard + if ( i>=NI ) return; // too many choices, typically homopolymers in long reads; discard if ( !dfrq->len[i] ) dfrq->len[i] = len; // new deletion dfrq->freq[i]++; @@ -286,6 +284,7 @@ int rcns_set_reads(read_cns_t *rcns, bam_pileup1_t *plp, int nplp) } x += len; } + else if ( op==BAM_CHARD_CLIP ) continue; else error("rcns_set_reads todo: unknown cigar operator %d\n",op); if ( local_band_max < local_band ) local_band_max = local_band; } From cad9340305534b21a1a9808fea465b9b3c841404 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Fri, 25 Nov 2022 13:53:57 +0000 Subject: [PATCH 56/84] Cache NM values, for speed. See #1826 --- bam2bcf.c | 68 ++++++++++++++++++++++++++++++++++++------------------- bam2bcf.h | 3 +++ mpileup.c | 2 ++ 3 files changed, 50 insertions(+), 23 deletions(-) diff --git a/bam2bcf.c b/bam2bcf.c index 48aa815c0..08fb5cdd4 100644 --- a/bam2bcf.c +++ b/bam2bcf.c @@ -91,28 +91,44 @@ void bcf_call_destroy(bcf_callaux_t *bca) free(bca->bases); free(bca->inscns); free(bca); } -static int get_aux_nm(bam1_t *rec, int32_t qpos, int is_ref) +static int get_aux_nm(const bam_pileup1_t *p, int32_t qpos, int is_ref) { - uint8_t *nm_tag = bam_aux_get(rec, "NM"); - if ( !nm_tag ) return -1; - int64_t nm = bam_aux2i(nm_tag); + int64_t nm; + const bam_pileup_cd *cd = &p->cd; - // Count indels as single events, not as the number of inserted/deleted - // bases (which is what NM does). Add soft clips as mismatches. - int i; - for (i=0; i < rec->core.n_cigar; i++) + if ( PLP_NM(cd) == -1 ) return -1; + if ( PLP_NM(cd) == PLP_NM_UNSET ) { - int val = bam_get_cigar(rec)[i] & BAM_CIGAR_MASK; - if ( val==BAM_CSOFT_CLIP ) + // todo: make this localized to be useful for long reads as well + bam1_t *rec = p->b; + uint8_t *nm_tag = bam_aux_get(rec, "NM"); + if ( !nm_tag ) { - nm += bam_get_cigar(rec)[i] >> BAM_CIGAR_SHIFT; + PLP_NM(cd) = -1; + return -1; } - else if ( val==BAM_CINS || val==BAM_CDEL ) + nm = bam_aux2i(nm_tag); + + // Count indels as single events, not as the number of inserted/deleted + // bases (which is what NM does). Add soft clips as mismatches. + int i; + for (i=0; i < rec->core.n_cigar; i++) { - val = bam_get_cigar(rec)[i] >> BAM_CIGAR_SHIFT; - if ( val > 1 ) nm -= val - 1; + int val = bam_get_cigar(rec)[i] & BAM_CIGAR_MASK; + if ( val==BAM_CSOFT_CLIP ) + { + nm += bam_get_cigar(rec)[i] >> BAM_CIGAR_SHIFT; + } + else if ( val==BAM_CINS || val==BAM_CDEL ) + { + val = bam_get_cigar(rec)[i] >> BAM_CIGAR_SHIFT; + if ( val > 1 ) nm -= val - 1; + } } + PLP_NM(cd) = nm; } + else + nm = PLP_NM(cd); // Take into account MNPs, 2% of de novo SNVs appear within 20bp of another de novo SNV // http://www.genome.org/cgi/doi/10.1101/gr.239756.118 @@ -274,7 +290,7 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t // p->indel .. is there an indel starting after this position (i.e. does this read have the tested indel) if (p->is_del && !is_indel) continue; // not testing an indel and the read has a spanning deletion - int inm; + int inm = -1; ++ori_depth; if (is_indel) // testing an indel position @@ -304,11 +320,14 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t } is_diff = b ? 1 : 0; - inm = get_aux_nm(p->b,p->qpos,is_diff?0:1); - if ( inm>=0 ) + if ( bca->fmt_flag&(B2B_FMT_NMBZ|B2B_INFO_NMBZ|B2B_INFO_NM) ) { - bca->nnm[is_diff]++; - bca->nm[is_diff] += inm; + inm = get_aux_nm(p,p->qpos,is_diff?0:1); + if ( inm>=0 ) + { + bca->nnm[is_diff]++; + bca->nm[is_diff] += inm; + } } if (q < bca->min_baseQ) @@ -344,11 +363,14 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t baseQ = q; seqQ = 99; is_diff = (ref4 < 4 && b == ref4)? 0 : 1; - inm = get_aux_nm(p->b,p->qpos,is_diff?0:1); - if ( inm>=0 ) + if ( bca->fmt_flag&(B2B_FMT_NMBZ|B2B_INFO_NMBZ|B2B_INFO_NM) ) { - bca->nnm[is_diff]++; - bca->nm[is_diff] += inm; + inm = get_aux_nm(p,p->qpos,is_diff?0:1); + if ( inm>=0 ) + { + bca->nnm[is_diff]++; + bca->nm[is_diff] += inm; + } } } mapQ = p->b->core.qual < 255? p->b->core.qual : DEF_MAPQ; // special case for mapQ==255 diff --git a/bam2bcf.h b/bam2bcf.h index 139aeb491..955c022bf 100644 --- a/bam2bcf.h +++ b/bam2bcf.h @@ -90,6 +90,8 @@ DEALINGS IN THE SOFTWARE. */ #define PLP_IS_REALN(cd) (PLP_CD(cd)->i & 4) #define PLP_SAMPLE_ID(cd) (PLP_CD(cd)->i >> 3) #define PLP_QLEN(cd) (PLP_CD(cd)->qlen) +#define PLP_NM(cd) (PLP_CD(cd)->nm) +#define PLP_NM_UNSET -2 #define PLP_SET_SOFT_CLIP(cd) (PLP_CD(cd)->i |= 1) #define PLP_SET_INDEL(cd) (PLP_CD(cd)->i |= 2) @@ -100,6 +102,7 @@ typedef struct { int64_t i; // used to store sample id and flags for presence of soft-clip and indel uint32_t qlen; // cached output of bam_cigar2qlen(), 0 if unset + int nm; // -2 PLP_NM_UNSET; -1 not available; >=0 NM value computed by get_aux_nm() } plp_cd_t; diff --git a/mpileup.c b/mpileup.c index 5327af6f0..523fac5b9 100644 --- a/mpileup.c +++ b/mpileup.c @@ -300,6 +300,8 @@ static int pileup_constructor(void *data, const bam1_t *b, bam_pileup_cd *cd) { cd->p = calloc(1,sizeof(plp_cd_t)); + PLP_NM(cd) = PLP_NM_UNSET; + mplp_aux_t *ma = (mplp_aux_t *)data; int n = bam_smpl_get_sample_id(ma->conf->bsmpl, ma->bam_id, (bam1_t *)b); PLP_SET_SAMPLE_ID(cd, n); From c021478c1354b638c925b26dc7c162b5ac2ff391 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Fri, 25 Nov 2022 14:48:12 +0000 Subject: [PATCH 57/84] Remove NMBZ from default annotations, for perfomrance reasons. See #1826 --- mpileup.c | 4 +- test/mpileup/indel-AD.1.out | 225 +++++++++++++++--------------- test/mpileup/indel-AD.2.out | 3 +- test/mpileup/indel-AD.3.out | 3 +- test/mpileup/indel-AD.4.out | 3 +- test/mpileup/mpileup-SCR.out | 3 +- test/mpileup/mpileup-filter.1.out | 1 - test/mpileup/mpileup-filter.2.out | 1 - test/mpileup/mpileup.1.out | 19 ++- test/mpileup/mpileup.10.out | 19 ++- test/mpileup/mpileup.11.out | 159 +++++++++++---------- test/mpileup/mpileup.2.out | 97 +++++++------ test/mpileup/mpileup.3.out | 1 - test/mpileup/mpileup.4.out | 97 +++++++------ test/mpileup/mpileup.5.out | 97 +++++++------ test/mpileup/mpileup.6.out | 97 +++++++------ test/mpileup/mpileup.7.out | 3 +- test/mpileup/mpileup.8.out | 17 ++- test/mpileup/mpileup.9.out | 3 +- test/test.pl | 6 +- 20 files changed, 420 insertions(+), 438 deletions(-) diff --git a/mpileup.c b/mpileup.c index 523fac5b9..e06ecd2d8 100644 --- a/mpileup.c +++ b/mpileup.c @@ -1156,7 +1156,7 @@ static void list_annotations(FILE *fp) "* INFO/MQBZ .. Mann-Whitney U test of Mapping Quality Bias (Number=1,Type=Float)\n" "* INFO/MQSBZ .. Mann-Whitney U-z test of Mapping Quality vs Strand Bias (Number=1,Type=Float)\n" " INFO/NM .. Approximate average number of mismatches in ref and alt reads, experimental (Number=2,Type=Float)\n" - "* INFO/NMBZ .. Mann-Whitney U-z test of Number of Mismatches within supporting reads (Number=1,Type=Float)\n" + " INFO/NMBZ .. Mann-Whitney U-z test of Number of Mismatches within supporting reads (Number=1,Type=Float)\n" "* INFO/RPBZ .. Mann-Whitney U test of Read Position Bias (Number=1,Type=Float)\n" "* INFO/SCBZ .. Mann-Whitney U-z test of Soft-Clip Length Bias (Number=1,Type=Float)\n" " INFO/SCR .. Number of soft-clipped reads (Number=1,Type=Integer)\n" @@ -1300,7 +1300,7 @@ int main_mpileup(int argc, char *argv[]) mplp.n_threads = 0; mplp.bsmpl = bam_smpl_init(); // the default to be changed in future, see also parse_format_flag() - mplp.fmt_flag = B2B_INFO_BQBZ|B2B_INFO_FS|B2B_INFO_IDV|B2B_INFO_IMF|B2B_INFO_MQ0F|B2B_INFO_MQBZ|B2B_INFO_MQSBZ|B2B_INFO_NMBZ|B2B_INFO_RPBZ|B2B_INFO_SCBZ|B2B_INFO_SGB|B2B_INFO_VDB; + mplp.fmt_flag = B2B_INFO_BQBZ|B2B_INFO_FS|B2B_INFO_IDV|B2B_INFO_IMF|B2B_INFO_MQ0F|B2B_INFO_MQBZ|B2B_INFO_MQSBZ|B2B_INFO_RPBZ|B2B_INFO_SCBZ|B2B_INFO_SGB|B2B_INFO_VDB; mplp.max_read_len = 500; mplp.ambig_reads = B2B_DROP; mplp.indel_win_size = 110; diff --git a/test/mpileup/indel-AD.1.out b/test/mpileup/indel-AD.1.out index 865765aef..196bad1eb 100644 --- a/test/mpileup/indel-AD.1.out +++ b/test/mpileup/indel-AD.1.out @@ -11,7 +11,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -29,47 +28,47 @@ 000000F 397 . A <*> 0 . 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DP=9;I16=5,4,0,0,288,10546,0,0,540,32400,0,0,131,2363,0,0;QS=1,0;MQ0F=0 PL:AD 0,27,214:9,0 000000F 414 . G <*> 0 . DP=9;I16=5,4,0,0,317,12083,0,0,540,32400,0,0,140,2634,0,0;QS=1,0;MQ0F=0 PL:AD 0,27,236:9,0 -000000F 415 . T G,<*> 0 . DP=9;I16=5,3,0,1,291,10937,22,484,480,28800,60,3600,136,2754,13,169;QS=0.929712,0.0702875,0;SGB=-0.379885;RPBZ=0.195283;MQBZ=0;MQSBZ=0;BQBZ=-1.5;NMBZ=0.388922;SCBZ=-0.690269;FS=0;MQ0F=0 PL:AD 0,5,202,24,205,214:8,1,0 -000000F 416 . G C,<*> 0 . DP=10;I16=6,3,0,1,324,11944,12,144,540,32400,60,3600,144,3034,14,196;QS=0.964286,0.0357143,0;SGB=-0.379885;RPBZ=0.350285;MQBZ=0;MQSBZ=0;BQBZ=-1.62698;NMBZ=0.525427;SCBZ=-0.642529;FS=0;MQ0F=0 PL:AD 0,17,225,27,228,228:9,1,0 +000000F 415 . T G,<*> 0 . DP=9;I16=5,3,0,1,291,10937,22,484,480,28800,60,3600,136,2754,13,169;QS=0.929712,0.0702875,0;SGB=-0.379885;RPBZ=0.195283;MQBZ=0;MQSBZ=0;BQBZ=-1.5;SCBZ=-0.690269;FS=0;MQ0F=0 PL:AD 0,5,202,24,205,214:8,1,0 +000000F 416 . G C,<*> 0 . DP=10;I16=6,3,0,1,324,11944,12,144,540,32400,60,3600,144,3034,14,196;QS=0.964286,0.0357143,0;SGB=-0.379885;RPBZ=0.350285;MQBZ=0;MQSBZ=0;BQBZ=-1.62698;SCBZ=-0.642529;FS=0;MQ0F=0 PL:AD 0,17,225,27,228,228:9,1,0 000000F 417 . T <*> 0 . DP=10;I16=6,4,0,0,364,13992,0,0,600,36000,0,0,166,3454,0,0;QS=1,0;MQ0F=0 PL:AD 0,30,255:10,0 000000F 418 . A <*> 0 . DP=10;I16=6,4,0,0,360,13680,0,0,600,36000,0,0,173,3643,0,0;QS=1,0;MQ0F=0 PL:AD 0,30,254:10,0 000000F 419 . A <*> 0 . DP=10;I16=6,4,0,0,344,13112,0,0,600,36000,0,0,180,3846,0,0;QS=1,0;MQ0F=0 PL:AD 0,30,242:10,0 -000000F 420 . A C,<*> 0 . DP=11;I16=7,3,0,1,306,11440,12,144,600,36000,60,3600,190,4180,18,324;QS=0.962382,0.0376176,0;SGB=-0.379885;RPBZ=0.476513;MQBZ=0;MQSBZ=0;BQBZ=-1.00766;NMBZ=0.317675;SCBZ=-0.73252;FS=0;MQ0F=0 PL:AD 0,20,212,30,215,215:10,1,0 +000000F 420 . A C,<*> 0 . DP=11;I16=7,3,0,1,306,11440,12,144,600,36000,60,3600,190,4180,18,324;QS=0.962382,0.0376176,0;SGB=-0.379885;RPBZ=0.476513;MQBZ=0;MQSBZ=0;BQBZ=-1.00766;SCBZ=-0.73252;FS=0;MQ0F=0 PL:AD 0,20,212,30,215,215:10,1,0 000000F 421 . A <*> 0 . DP=12;I16=8,4,0,0,388,13950,0,0,720,43200,0,0,236,5160,0,0;QS=1,0;MQ0F=0 PL:AD 0,36,255:12,0 000000F 422 . C <*> 0 . DP=13;I16=8,5,0,0,484,18266,0,0,780,46800,0,0,243,5389,0,0;QS=1,0;MQ0F=0 PL:AD 0,39,255:13,0 000000F 423 . A <*> 0 . DP=15;I16=9,6,0,0,509,18579,0,0,900,54000,0,0,266,5858,0,0;QS=1,0;MQ0F=0 PL:AD 0,45,255:15,0 000000F 424 . G <*> 0 . DP=15;I16=9,6,0,0,516,19368,0,0,900,54000,0,0,276,6150,0,0;QS=1,0;MQ0F=0 PL:AD 0,45,255:15,0 000000F 425 . A <*> 0 . DP=15;I16=9,6,0,0,516,19668,0,0,900,54000,0,0,284,6360,0,0;QS=1,0;MQ0F=0 PL:AD 0,45,255:15,0 -000000F 426 . G T,<*> 0 . DP=15;I16=9,5,0,1,519,20109,12,144,840,50400,60,3600,288,6570,4,16;QS=0.977401,0.0225989,0;SGB=-0.379885;RPBZ=-1.28103;MQBZ=0;MQSBZ=0;BQBZ=-1.70698;NMBZ=-0.582288;SCBZ=-0.879593;FS=0;MQ0F=0 PL:AD 0,31,255,42,255,255:14,1,0 +000000F 426 . G T,<*> 0 . DP=15;I16=9,5,0,1,519,20109,12,144,840,50400,60,3600,288,6570,4,16;QS=0.977401,0.0225989,0;SGB=-0.379885;RPBZ=-1.28103;MQBZ=0;MQSBZ=0;BQBZ=-1.70698;SCBZ=-0.879593;FS=0;MQ0F=0 PL:AD 0,31,255,42,255,255:14,1,0 000000F 427 . C <*> 0 . DP=15;I16=9,6,0,0,550,21100,0,0,900,54000,0,0,300,6828,0,0;QS=1,0;MQ0F=0 PL:AD 0,45,255:15,0 000000F 428 . T <*> 0 . DP=15;I16=9,6,0,0,521,19363,0,0,900,54000,0,0,306,6984,0,0;QS=1,0;MQ0F=0 PL:AD 0,45,255:15,0 -000000F 429 . C A,<*> 0 . DP=17;I16=10,6,0,1,533,19507,12,144,960,57600,60,3600,287,6527,25,625;QS=0.977982,0.0220183,0;SGB=-0.379885;RPBZ=1.33584;MQBZ=0;MQSBZ=0;BQBZ=-1.55274;NMBZ=-0.307698;SCBZ=-0.887279;FS=0;MQ0F=0 PL:AD 0,37,255,48,255,255:16,1,0 +000000F 429 . C A,<*> 0 . DP=17;I16=10,6,0,1,533,19507,12,144,960,57600,60,3600,287,6527,25,625;QS=0.977982,0.0220183,0;SGB=-0.379885;RPBZ=1.33584;MQBZ=0;MQSBZ=0;BQBZ=-1.55274;SCBZ=-0.887279;FS=0;MQ0F=0 PL:AD 0,37,255,48,255,255:16,1,0 000000F 430 . A <*> 0 . DP=18;I16=10,8,0,0,583,20803,0,0,1080,64800,0,0,320,7334,0,0;QS=1,0;MQ0F=0 PL:AD 0,54,255:18,0 000000F 431 . A <*> 0 . DP=19;I16=10,8,0,0,616,23012,0,0,1080,64800,0,0,328,7482,0,0;QS=1,0;MQ0F=0 PL:AD 0,54,255:18,0 000000F 432 . T <*> 0 . DP=19;I16=11,8,0,0,682,26264,0,0,1140,68400,0,0,337,7647,0,0;QS=1,0;MQ0F=0 PL:AD 0,57,255:19,0 000000F 433 . T <*> 0 . DP=19;I16=11,8,0,0,696,26452,0,0,1140,68400,0,0,346,7830,0,0;QS=1,0;MQ0F=0 PL:AD 0,57,255:19,0 000000F 434 . T <*> 0 . DP=19;I16=11,8,0,0,678,25728,0,0,1140,68400,0,0,354,7980,0,0;QS=1,0;MQ0F=0 PL:AD 0,57,255:19,0 000000F 435 . T <*> 0 . DP=20;I16=11,9,0,0,717,26931,0,0,1200,72000,0,0,362,8146,0,0;QS=1,0;MQ0F=0 PL:AD 0,60,255:20,0 -000000F 436 . A C,<*> 0 . DP=21;I16=11,9,0,1,728,28034,12,144,1200,72000,60,3600,346,7704,25,625;QS=0.983784,0.0162162,0;SGB=-0.379885;RPBZ=0.909477;MQBZ=0;MQSBZ=0;BQBZ=-1.66309;NMBZ=0.165792;SCBZ=-0.82685;FS=0;MQ0F=0 PL:AD 0,49,255,60,255,255:20,1,0 +000000F 436 . A C,<*> 0 . DP=21;I16=11,9,0,1,728,28034,12,144,1200,72000,60,3600,346,7704,25,625;QS=0.983784,0.0162162,0;SGB=-0.379885;RPBZ=0.909477;MQBZ=0;MQSBZ=0;BQBZ=-1.66309;SCBZ=-0.82685;FS=0;MQ0F=0 PL:AD 0,49,255,60,255,255:20,1,0 000000F 437 . T <*> 0 . DP=21;I16=11,10,0,0,770,29698,0,0,1260,75600,0,0,381,8531,0,0;QS=1,0;MQ0F=0 PL:AD 0,63,255:21,0 000000F 438 . T <*> 0 . DP=22;I16=11,10,0,0,726,26976,0,0,1260,75600,0,0,391,8753,0,0;QS=1,0;MQ0F=0 PL:AD 0,63,255:21,0 000000F 439 . T <*> 0 . DP=25;I16=14,10,0,0,804,30038,0,0,1440,86400,0,0,444,9912,0,0;QS=1,0;MQ0F=0 PL:AD 0,72,255:24,0 -000000F 440 . T A,<*> 0 . DP=27;I16=15,11,1,0,896,33856,12,144,1560,93600,60,3600,455,10163,25,625;QS=0.986784,0.0132159,0;SGB=-0.379885;RPBZ=1.28585;MQBZ=0;MQSBZ=0;BQBZ=-1.41134;NMBZ=0.643909;SCBZ=0.48519;FS=0;MQ0F=0 PL:AD 0,66,255,78,255,255:26,1,0 +000000F 440 . T A,<*> 0 . DP=27;I16=15,11,1,0,896,33856,12,144,1560,93600,60,3600,455,10163,25,625;QS=0.986784,0.0132159,0;SGB=-0.379885;RPBZ=1.28585;MQBZ=0;MQSBZ=0;BQBZ=-1.41134;SCBZ=0.48519;FS=0;MQ0F=0 PL:AD 0,66,255,78,255,255:26,1,0 000000F 441 . G <*> 0 . DP=29;I16=17,11,0,0,1033,39137,0,0,1680,100800,0,0,495,11163,0,0;QS=1,0;MQ0F=0 PL:AD 0,84,255:28,0 000000F 442 . T <*> 0 . DP=29;I16=18,11,0,0,1067,41223,0,0,1740,104400,0,0,531,11951,0,0;QS=1,0;MQ0F=0 PL:AD 0,87,255:29,0 000000F 443 . A <*> 0 . DP=31;I16=20,11,0,0,1078,40562,0,0,1860,111600,0,0,544,12226,0,0;QS=1,0;MQ0F=0 PL:AD 0,93,255:31,0 @@ -80,45 +79,45 @@ 000000F 448 . T <*> 0 . DP=35;I16=23,12,0,0,1220,45736,0,0,2100,126000,0,0,667,15037,0,0;QS=1,0;MQ0F=0 PL:AD 0,105,255:35,0 000000F 449 . T <*> 0 . DP=35;I16=23,12,0,0,1249,47703,0,0,2100,126000,0,0,679,15245,0,0;QS=1,0;MQ0F=0 PL:AD 0,105,255:35,0 000000F 450 . G <*> 0 . DP=38;I16=25,13,0,0,1449,56453,0,0,2280,136800,0,0,715,16059,0,0;QS=1,0;MQ0F=0 PL:AD 0,114,255:38,0 -000000F 451 . T A,<*> 0 . DP=43;I16=24,16,0,1,1485,57079,12,144,2400,144000,60,3600,708,15882,0,0;QS=0.991984,0.00801603,0;SGB=-0.379885;RPBZ=-1.56545;MQBZ=0;MQSBZ=0;BQBZ=-1.91213;NMBZ=-0.383201;SCBZ=-0.839032;FS=0;MQ0F=0 PL:AD 0,107,255,120,255,255:40,1,0 -000000F 452 . G T,<*> 0 . DP=45;I16=24,18,0,1,1541,58723,12,144,2520,151200,60,3600,707,15841,23,529;QS=0.992273,0.00772698,0;SGB=-0.379885;RPBZ=0.645561;MQBZ=0;MQSBZ=0;BQBZ=-1.75577;NMBZ=0.933309;SCBZ=0.629801;FS=0;MQ0F=0 PL:AD 0,113,255,126,255,255:42,1,0 +000000F 451 . T A,<*> 0 . DP=43;I16=24,16,0,1,1485,57079,12,144,2400,144000,60,3600,708,15882,0,0;QS=0.991984,0.00801603,0;SGB=-0.379885;RPBZ=-1.56545;MQBZ=0;MQSBZ=0;BQBZ=-1.91213;SCBZ=-0.839032;FS=0;MQ0F=0 PL:AD 0,107,255,120,255,255:40,1,0 +000000F 452 . G T,<*> 0 . DP=45;I16=24,18,0,1,1541,58723,12,144,2520,151200,60,3600,707,15841,23,529;QS=0.992273,0.00772698,0;SGB=-0.379885;RPBZ=0.645561;MQBZ=0;MQSBZ=0;BQBZ=-1.75577;SCBZ=0.629801;FS=0;MQ0F=0 PL:AD 0,113,255,126,255,255:42,1,0 000000F 453 . C <*> 0 . DP=45;I16=24,19,0,0,1623,65335,0,0,2580,154800,0,0,753,16853,0,0;QS=1,0;MQ0F=0 PL:AD 0,129,255:43,0 -000000F 454 . A C,<*> 0 . DP=47;I16=24,20,1,0,1699,68295,12,144,2640,158400,60,3600,774,17286,25,625;QS=0.992987,0.00701344,0;SGB=-0.379885;RPBZ=1.46482;MQBZ=0;MQSBZ=0;BQBZ=-1.87433;NMBZ=0.5422;SCBZ=0.550575;FS=0;MQ0F=0 PL:AD 0,119,255,132,255,255:44,1,0 +000000F 454 . A C,<*> 0 . DP=47;I16=24,20,1,0,1699,68295,12,144,2640,158400,60,3600,774,17286,25,625;QS=0.992987,0.00701344,0;SGB=-0.379885;RPBZ=1.46482;MQBZ=0;MQSBZ=0;BQBZ=-1.87433;SCBZ=0.550575;FS=0;MQ0F=0 PL:AD 0,119,255,132,255,255:44,1,0 000000F 455 . G <*> 0 . DP=48;I16=26,20,0,0,1807,74553,0,0,2760,165600,0,0,823,18385,0,0;QS=1,0;MQ0F=0 PL:AD 0,138,255:46,0 000000F 456 . T <*> 0 . DP=49;I16=26,21,0,0,1757,69583,0,0,2820,169200,0,0,845,18853,0,0;QS=1,0;MQ0F=0 PL:AD 0,141,255:47,0 000000F 457 . T <*> 0 . DP=49;I16=26,21,0,0,1836,73528,0,0,2820,169200,0,0,866,19264,0,0;QS=1,0;MQ0F=0 PL:AD 0,141,255:47,0 000000F 458 . A <*> 0 . DP=50;I16=26,22,0,0,1817,72337,0,0,2880,172800,0,0,887,19717,0,0;QS=1,0;MQ0F=0 PL:AD 0,144,255:48,0 000000F 459 . G <*> 0 . DP=50;I16=26,22,0,0,1791,70171,0,0,2880,172800,0,0,909,20213,0,0;QS=1,0;MQ0F=0 PL:AD 0,144,255:48,0 000000F 460 . A <*> 0 . DP=49;I16=26,22,0,0,1675,63873,0,0,2880,172800,0,0,923,20689,0,0;QS=1,0;MQ0F=0 PL:AD 0,144,255:48,0 -000000F 461 . A T,C,<*> 0 . DP=52;I16=25,22,1,1,1650,63298,24,288,2820,169200,120,7200,927,21061,17,145;QS=0.985663,0.00716846,0.00716846,0;VDB=0.06;SGB=-0.453602;RPBZ=-1.92231;MQBZ=0;MQSBZ=0;BQBZ=-2.2578;NMBZ=0.127077;SCBZ=-0.055422;FS=0;MQ0F=0 PL:AD 0,128,255,128,255,255,141,255,255,255:47,1,1,0 -000000F 462 . A T,<*> 0 . DP=52;I16=26,22,0,1,1705,65163,12,144,2880,172800,60,3600,955,21615,10,100;QS=0.993011,0.00698893,0;SGB=-0.379885;RPBZ=-1.09702;MQBZ=0;MQSBZ=0;BQBZ=-1.74927;NMBZ=0.0355665;SCBZ=-0.853241;FS=0;MQ0F=0 PL:AD 0,130,255,144,255,255:48,1,0 +000000F 461 . A T,C,<*> 0 . DP=52;I16=25,22,1,1,1650,63298,24,288,2820,169200,120,7200,927,21061,17,145;QS=0.985663,0.00716846,0.00716846,0;VDB=0.06;SGB=-0.453602;RPBZ=-1.92231;MQBZ=0;MQSBZ=0;BQBZ=-2.2578;SCBZ=-0.055422;FS=0;MQ0F=0 PL:AD 0,128,255,128,255,255,141,255,255,255:47,1,1,0 +000000F 462 . A T,<*> 0 . DP=52;I16=26,22,0,1,1705,65163,12,144,2880,172800,60,3600,955,21615,10,100;QS=0.993011,0.00698893,0;SGB=-0.379885;RPBZ=-1.09702;MQBZ=0;MQSBZ=0;BQBZ=-1.74927;SCBZ=-0.853241;FS=0;MQ0F=0 PL:AD 0,130,255,144,255,255:48,1,0 000000F 463 . A <*> 0 . DP=52;I16=26,24,0,0,1836,71956,0,0,3000,180000,0,0,996,22366,0,0;QS=1,0;MQ0F=0 PL:AD 0,151,255:50,0 -000000F 464 . T G,<*> 0 . DP=52;I16=26,23,0,1,1873,73813,12,144,2940,176400,60,3600,993,22355,25,625;QS=0.993634,0.00636605,0;SGB=-0.379885;RPBZ=0.173386;MQBZ=0;MQSBZ=0;BQBZ=-1.93908;NMBZ=-0.453085;SCBZ=-0.840331;FS=0;MQ0F=0 PL:AD 0,133,255,148,255,255:49,1,0 +000000F 464 . T G,<*> 0 . DP=52;I16=26,23,0,1,1873,73813,12,144,2940,176400,60,3600,993,22355,25,625;QS=0.993634,0.00636605,0;SGB=-0.379885;RPBZ=0.173386;MQBZ=0;MQSBZ=0;BQBZ=-1.93908;SCBZ=-0.840331;FS=0;MQ0F=0 PL:AD 0,133,255,148,255,255:49,1,0 000000F 465 . A <*> 0 . DP=52;I16=26,24,0,0,1950,78232,0,0,3000,180000,0,0,1039,23587,0,0;QS=1,0;MQ0F=0 PL:AD 0,151,255:50,0 -000000F 466 . A C,<*> 0 . DP=52;I16=25,24,1,0,1858,74740,12,144,2940,176400,60,3600,1033,23509,25,625;QS=0.993583,0.00641711,0;SGB=-0.379885;RPBZ=-1.24865;MQBZ=0;MQSBZ=0;BQBZ=-1.79438;NMBZ=1.18468;SCBZ=1.87165;FS=0;MQ0F=0 PL:AD 0,133,255,148,255,255:49,1,0 +000000F 466 . A C,<*> 0 . DP=52;I16=25,24,1,0,1858,74740,12,144,2940,176400,60,3600,1033,23509,25,625;QS=0.993583,0.00641711,0;SGB=-0.379885;RPBZ=-1.24865;MQBZ=0;MQSBZ=0;BQBZ=-1.79438;SCBZ=1.87165;FS=0;MQ0F=0 PL:AD 0,133,255,148,255,255:49,1,0 000000F 467 . T <*> 0 . DP=53;I16=26,25,0,0,1890,74962,0,0,3060,183600,0,0,1076,24668,0,0;QS=1,0;MQ0F=0 PL:AD 0,154,255:51,0 000000F 468 . A <*> 0 . DP=54;I16=27,25,0,0,1967,78281,0,0,3120,187200,0,0,1095,25239,0,0;QS=1,0;MQ0F=0 PL:AD 0,157,255:52,0 000000F 469 . T <*> 0 . DP=54;I16=27,25,0,0,2046,83348,0,0,3120,187200,0,0,1113,25747,0,0;QS=1,0;MQ0F=0 PL:AD 0,157,255:52,0 000000F 470 . G <*> 0 . DP=55;I16=28,25,0,0,2047,81939,0,0,3180,190800,0,0,1131,26291,0,0;QS=1,0;MQ0F=0 PL:AD 0,160,255:53,0 000000F 471 . A <*> 0 . DP=56;I16=28,26,0,0,2028,80100,0,0,3240,194400,0,0,1150,26872,0,0;QS=1,0;MQ0F=0 PL:AD 0,163,255:54,0 000000F 472 . T <*> 0 . DP=59;I16=29,28,0,0,2122,83726,0,0,3420,205200,0,0,1191,27925,0,0;QS=1,0;MQ0F=0 PL:AD 0,172,255:57,0 -000000F 473 . C A,G,<*> 0 . DP=63;I16=19,15,12,13,1263,49285,963,39221,2040,122400,1500,90000,705,16449,548,12960;QS=0.567385,0.427224,0.00539084,0;VDB=1.64281e-06;SGB=-0.692914;RPBZ=1.05908;MQBZ=0;MQSBZ=0;BQBZ=1.40915;NMBZ=1.4735;SCBZ=0.597801;FS=0;MQ0F=0 PL:AD 255,0,255,255,255,255,255,255,255,255:34,24,1,0 +000000F 473 . C A,G,<*> 0 . DP=63;I16=19,15,12,13,1263,49285,963,39221,2040,122400,1500,90000,705,16449,548,12960;QS=0.567385,0.427224,0.00539084,0;VDB=1.64281e-06;SGB=-0.692914;RPBZ=1.05908;MQBZ=0;MQSBZ=0;BQBZ=1.40915;SCBZ=0.597801;FS=0;MQ0F=0 PL:AD 255,0,255,255,255,255,255,255,255,255:34,24,1,0 000000F 474 . A <*> 0 . DP=64;I16=33,28,0,0,2172,84276,0,0,3660,219600,0,0,1296,30488,0,0;QS=1,0;MQ0F=0 PL:AD 0,184,255:61,0 000000F 475 . A <*> 0 . DP=64;I16=34,28,0,0,2092,79478,0,0,3720,223200,0,0,1322,31258,0,0;QS=1,0;MQ0F=0 PL:AD 0,187,255:62,0 -000000F 476 . A G,<*> 0 . DP=65;I16=34,28,0,1,2176,83678,12,144,3720,223200,60,3600,1319,31299,25,625;QS=0.994516,0.00548446,0;SGB=-0.379885;RPBZ=1.04564;MQBZ=0;MQSBZ=0;BQBZ=-1.59705;NMBZ=0.856031;SCBZ=0.713967;FS=0;MQ0F=0 PL:AD 0,172,255,187,255,255:62,1,0 -000000F 477 . T G,<*> 0 . DP=65;I16=34,28,0,1,2352,93436,12,144,3720,223200,60,3600,1338,31806,25,625;QS=0.994924,0.00507614,0;SGB=-0.379885;RPBZ=-0.687896;MQBZ=0;MQSBZ=0;BQBZ=-1.84472;NMBZ=-0.0276069;SCBZ=-0.892396;FS=0;MQ0F=0 PL:AD 0,172,255,187,255,255:62,1,0 +000000F 476 . A G,<*> 0 . DP=65;I16=34,28,0,1,2176,83678,12,144,3720,223200,60,3600,1319,31299,25,625;QS=0.994516,0.00548446,0;SGB=-0.379885;RPBZ=1.04564;MQBZ=0;MQSBZ=0;BQBZ=-1.59705;SCBZ=0.713967;FS=0;MQ0F=0 PL:AD 0,172,255,187,255,255:62,1,0 +000000F 477 . T G,<*> 0 . DP=65;I16=34,28,0,1,2352,93436,12,144,3720,223200,60,3600,1338,31806,25,625;QS=0.994924,0.00507614,0;SGB=-0.379885;RPBZ=-0.687896;MQBZ=0;MQSBZ=0;BQBZ=-1.84472;SCBZ=-0.892396;FS=0;MQ0F=0 PL:AD 0,172,255,187,255,255:62,1,0 000000F 478 . C <*> 0 . DP=65;I16=34,29,0,0,2376,94566,0,0,3780,226800,0,0,1381,32925,0,0;QS=1,0;MQ0F=0 PL:AD 0,190,255:63,0 -000000F 479 . T G,<*> 0 . DP=68;I16=36,29,0,1,2467,98357,12,144,3900,234000,60,3600,1416,33712,21,441;QS=0.995159,0.00484066,0;SGB=-0.379885;RPBZ=-0.787962;MQBZ=0;MQSBZ=0;BQBZ=-1.86106;NMBZ=-1.44958;SCBZ=-0.927153;FS=0;MQ0F=0 PL:AD 0,180,255,196,255,255:65,1,0 +000000F 479 . T G,<*> 0 . DP=68;I16=36,29,0,1,2467,98357,12,144,3900,234000,60,3600,1416,33712,21,441;QS=0.995159,0.00484066,0;SGB=-0.379885;RPBZ=-0.787962;MQBZ=0;MQSBZ=0;BQBZ=-1.86106;SCBZ=-0.927153;FS=0;MQ0F=0 PL:AD 0,180,255,196,255,255:65,1,0 000000F 480 . G <*> 0 . DP=70;I16=38,30,0,0,2563,101527,0,0,4080,244800,0,0,1495,35435,0,0;QS=1,0;MQ0F=0 PL:AD 0,205,255:68,0 000000F 481 . T <*> 0 . DP=70;I16=38,30,0,0,2521,98551,0,0,4080,244800,0,0,1514,35994,0,0;QS=1,0;MQ0F=0 PL:AD 0,205,255:68,0 -000000F 482 . T G,<*> 0 . DP=70;I16=37,30,1,0,2575,103005,12,144,4020,241200,60,3600,1518,36344,14,196;QS=0.995361,0.00463858,0;SGB=-0.379885;RPBZ=-0.892198;MQBZ=0;MQSBZ=0;BQBZ=-1.93937;NMBZ=-0.332412;SCBZ=-0.948507;FS=0;MQ0F=0 PL:AD 0,186,255,202,255,255:67,1,0 +000000F 482 . T G,<*> 0 . DP=70;I16=37,30,1,0,2575,103005,12,144,4020,241200,60,3600,1518,36344,14,196;QS=0.995361,0.00463858,0;SGB=-0.379885;RPBZ=-0.892198;MQBZ=0;MQSBZ=0;BQBZ=-1.93937;SCBZ=-0.948507;FS=0;MQ0F=0 PL:AD 0,186,255,202,255,255:67,1,0 000000F 483 . T <*> 0 . DP=70;I16=38,30,0,0,2646,106206,0,0,4080,244800,0,0,1549,37071,0,0;QS=1,0;MQ0F=0 PL:AD 0,205,255:68,0 000000F 484 . G <*> 0 . DP=70;I16=38,30,0,0,2659,107225,0,0,4080,244800,0,0,1565,37585,0,0;QS=1,0;MQ0F=0 PL:AD 0,205,255:68,0 000000F 485 . T <*> 0 . DP=70;I16=38,30,0,0,2618,104932,0,0,4080,244800,0,0,1578,37978,0,0;QS=1,0;MQ0F=0 PL:AD 0,205,255:68,0 000000F 486 . T <*> 0 . DP=70;I16=38,30,0,0,2589,103545,0,0,4080,244800,0,0,1589,38295,0,0;QS=1,0;MQ0F=0 PL:AD 0,205,255:68,0 000000F 487 . T <*> 0 . DP=73;I16=38,33,0,0,2694,107284,0,0,4260,255600,0,0,1599,38583,0,0;QS=1,0;MQ0F=0 PL:AD 0,214,255:71,0 -000000F 488 . A G,<*> 0 . DP=76;I16=41,32,0,1,2640,102296,8,64,4380,262800,60,3600,1679,40447,1,1;QS=0.996979,0.00302115,0;SGB=-0.379885;RPBZ=-1.52228;MQBZ=0;MQSBZ=0;BQBZ=-1.89405;NMBZ=-0.328825;SCBZ=-0.946449;FS=0;MQ0F=0 PL:AD 0,204,255,220,255,255:73,1,0 -000000F 489 . C A,<*> 0 . DP=79;I16=43,33,0,1,2694,103126,12,144,4560,273600,60,3600,1715,41273,25,625;QS=0.995565,0.00443459,0;SGB=-0.379885;RPBZ=-0.495167;MQBZ=0;MQSBZ=0;BQBZ=-1.58784;NMBZ=-0.135403;SCBZ=-0.974263;FS=0;MQ0F=0 PL:AD 0,213,255,229,255,255:76,1,0 +000000F 488 . A G,<*> 0 . DP=76;I16=41,32,0,1,2640,102296,8,64,4380,262800,60,3600,1679,40447,1,1;QS=0.996979,0.00302115,0;SGB=-0.379885;RPBZ=-1.52228;MQBZ=0;MQSBZ=0;BQBZ=-1.89405;SCBZ=-0.946449;FS=0;MQ0F=0 PL:AD 0,204,255,220,255,255:73,1,0 +000000F 489 . C A,<*> 0 . DP=79;I16=43,33,0,1,2694,103126,12,144,4560,273600,60,3600,1715,41273,25,625;QS=0.995565,0.00443459,0;SGB=-0.379885;RPBZ=-0.495167;MQBZ=0;MQSBZ=0;BQBZ=-1.58784;SCBZ=-0.974263;FS=0;MQ0F=0 PL:AD 0,213,255,229,255,255:76,1,0 000000F 490 . C <*> 0 . DP=80;I16=43,35,0,0,2796,107040,0,0,4680,280800,0,0,1782,43020,0,0;QS=1,0;MQ0F=0 PL:AD 0,235,255:78,0 000000F 491 . T <*> 0 . DP=80;I16=43,35,0,0,2910,113818,0,0,4680,280800,0,0,1798,43500,0,0;QS=1,0;MQ0F=0 PL:AD 0,235,255:78,0 000000F 492 . G <*> 0 . DP=81;I16=43,35,0,0,3089,125687,0,0,4680,280800,0,0,1814,44012,0,0;QS=1,0;MQ0F=0 PL:AD 0,235,255:78,0 @@ -128,83 +127,83 @@ 000000F 496 . T <*> 0 . DP=87;I16=47,37,0,0,3238,128760,0,0,5040,302400,0,0,1917,46777,0,0;QS=1,0;MQ0F=0 PL:AD 0,253,255:84,0 000000F 497 . G <*> 0 . DP=87;I16=47,37,0,0,3280,132640,0,0,5040,302400,0,0,1933,47227,0,0;QS=1,0;MQ0F=0 PL:AD 0,253,255:84,0 000000F 498 . T <*> 0 . DP=88;I16=48,37,0,0,3081,120187,0,0,5100,306000,0,0,1971,48181,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:85,0 -000000F 499 . T C,<*> 0 . DP=89;I16=48,36,0,1,3190,126958,8,64,5040,302400,60,3600,1957,47809,25,625;QS=0.997498,0.00250156,0;SGB=-0.379885;RPBZ=-0.305833;MQBZ=0;MQSBZ=0;BQBZ=-1.95559;NMBZ=-0.286188;SCBZ=-1.05778;FS=0;MQ0F=0 PL:AD 0,237,255,253,255,255:84,1,0 -000000F 500 . T G,A,<*> 0 . DP=92;I16=50,37,1,1,3308,133104,24,288,5220,313200,120,7200,1986,48376,50,1250;QS=0.992797,0.00360144,0.00360144,0;VDB=0.32;SGB=-0.453602;RPBZ=0.41539;MQBZ=0;MQSBZ=0;BQBZ=-2.60206;NMBZ=-0.583258;SCBZ=-1.0009;FS=0;MQ0F=0 PL:AD 0,245,255,245,255,255,255,255,255,255:87,1,1,0 +000000F 499 . T C,<*> 0 . DP=89;I16=48,36,0,1,3190,126958,8,64,5040,302400,60,3600,1957,47809,25,625;QS=0.997498,0.00250156,0;SGB=-0.379885;RPBZ=-0.305833;MQBZ=0;MQSBZ=0;BQBZ=-1.95559;SCBZ=-1.05778;FS=0;MQ0F=0 PL:AD 0,237,255,253,255,255:84,1,0 +000000F 500 . T G,A,<*> 0 . DP=92;I16=50,37,1,1,3308,133104,24,288,5220,313200,120,7200,1986,48376,50,1250;QS=0.992797,0.00360144,0.00360144,0;VDB=0.32;SGB=-0.453602;RPBZ=0.41539;MQBZ=0;MQSBZ=0;BQBZ=-2.60206;SCBZ=-1.0009;FS=0;MQ0F=0 PL:AD 0,245,255,245,255,255,255,255,255,255:87,1,1,0 000000F 501 . G <*> 0 . DP=97;I16=53,40,0,0,3485,138049,0,0,5580,334800,0,0,2050,49962,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:93,0 -000000F 502 . T A,<*> 0 . DP=98;I16=53,40,1,0,3391,132771,12,144,5580,334800,60,3600,2065,50183,25,625;QS=0.996476,0.00352423,0;SGB=-0.379885;RPBZ=1.67751;MQBZ=0;MQSBZ=0;BQBZ=-1.7355;NMBZ=0.221736;SCBZ=0.856937;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:93,1,0 +000000F 502 . T A,<*> 0 . DP=98;I16=53,40,1,0,3391,132771,12,144,5580,334800,60,3600,2065,50183,25,625;QS=0.996476,0.00352423,0;SGB=-0.379885;RPBZ=1.67751;MQBZ=0;MQSBZ=0;BQBZ=-1.7355;SCBZ=0.856937;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:93,1,0 000000F 503 . G <*> 0 . DP=98;I16=54,40,0,0,3540,140610,0,0,5640,338400,0,0,2108,51206,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:94,0 -000000F 504 . T C,A,<*> 0 . DP=102;I16=53,42,1,1,3464,137680,20,208,5700,342000,120,7200,2099,50913,25,625;QS=0.994259,0.00344432,0.00229621,0;VDB=0.92;SGB=-0.453602;RPBZ=0.0126977;MQBZ=0;MQSBZ=0;BQBZ=-2.43319;NMBZ=1.20903;SCBZ=0.512446;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:95,1,1,0 +000000F 504 . T C,A,<*> 0 . DP=102;I16=53,42,1,1,3464,137680,20,208,5700,342000,120,7200,2099,50913,25,625;QS=0.994259,0.00344432,0.00229621,0;VDB=0.92;SGB=-0.453602;RPBZ=0.0126977;MQBZ=0;MQSBZ=0;BQBZ=-2.43319;SCBZ=0.512446;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:95,1,1,0 000000F 505 . G <*> 0 . DP=102;I16=54,43,0,0,3640,144678,0,0,5820,349200,0,0,2141,51803,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:97,0 -000000F 506 . C G,<*> 0 . DP=103;I16=54,43,0,1,3621,145273,12,144,5820,349200,60,3600,2138,51502,25,625;QS=0.996697,0.00330306,0;SGB=-0.379885;RPBZ=0.194473;MQBZ=0;MQSBZ=0;BQBZ=-1.75415;NMBZ=-0.425375;SCBZ=-1.07827;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:97,1,0 +000000F 506 . C G,<*> 0 . DP=103;I16=54,43,0,1,3621,145273,12,144,5820,349200,60,3600,2138,51502,25,625;QS=0.996697,0.00330306,0;SGB=-0.379885;RPBZ=0.194473;MQBZ=0;MQSBZ=0;BQBZ=-1.75415;SCBZ=-1.07827;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:97,1,0 000000F 507 . T <*> 0 . DP=103;I16=54,44,0,0,3520,139202,0,0,5880,352800,0,0,2181,52471,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:98,0 -000000F 508 . C T,<*> 0 . DP=103;I16=54,43,0,1,3476,137498,12,144,5820,349200,60,3600,2174,52226,25,625;QS=0.99656,0.00344037,0;SGB=-0.379885;RPBZ=0.265217;MQBZ=0;MQSBZ=0;BQBZ=-1.63996;NMBZ=-0.425375;SCBZ=-1.07818;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:97,1,0 +000000F 508 . C T,<*> 0 . DP=103;I16=54,43,0,1,3476,137498,12,144,5820,349200,60,3600,2174,52226,25,625;QS=0.99656,0.00344037,0;SGB=-0.379885;RPBZ=0.265217;MQBZ=0;MQSBZ=0;BQBZ=-1.63996;SCBZ=-1.07818;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:97,1,0 000000F 509 . C <*> 0 . DP=103;I16=54,44,0,0,3580,142206,0,0,5880,352800,0,0,2217,53267,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:98,0 -000000F 510 . C A,G,<*> 0 . DP=106;I16=54,43,1,2,3646,145190,42,692,5820,349200,180,10800,2189,52645,67,1515;QS=0.988612,0.00921909,0.0021692,0;VDB=0.401962;SGB=-0.511536;RPBZ=-0.707412;MQBZ=0;MQSBZ=0;BQBZ=-3.02794;NMBZ=-0.678755;SCBZ=-0.99293;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:97,2,1,0 -000000F 511 . T A,<*> 0 . DP=107;I16=55,45,0,1,3663,144413,12,144,6000,360000,60,3600,2251,54067,25,625;QS=0.996735,0.00326531,0;SGB=-0.379885;RPBZ=-0.0343102;MQBZ=0;MQSBZ=0;BQBZ=-1.71065;NMBZ=-0.343991;SCBZ=-1.08137;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:100,1,0 -000000F 512 . C A,G,<*> 0 . DP=107;I16=55,43,1,3,3657,146609,54,836,5880,352800,240,14400,2238,53902,83,1939;QS=0.985449,0.0123956,0.00215575,0;VDB=0.681156;SGB=-0.556411;RPBZ=-0.465574;MQBZ=0;MQSBZ=0;BQBZ=-3.45917;NMBZ=0.121004;SCBZ=-0.667699;FS=0;MQ0F=0 PL:AD 0,248,255,255,255,255,255,255,255,255:98,3,1,0 -000000F 513 . T G,<*> 0 . DP=108;I16=56,46,0,1,3774,150038,7,49,6120,367200,60,3600,2340,56352,0,0;QS=0.998149,0.00185136,0;SGB=-0.379885;RPBZ=-1.71577;MQBZ=0;MQSBZ=0;BQBZ=-1.90666;NMBZ=-0.303554;SCBZ=-1.07835;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:102,1,0 -000000F 514 . G T,<*> 0 . DP=110;I16=56,47,1,1,3763,148539,20,208,6180,370800,120,7200,2348,56422,25,625;QS=0.994713,0.00528681,0;VDB=0.44;SGB=-0.453602;RPBZ=-1.58286;MQBZ=0;MQSBZ=0;BQBZ=-2.48498;NMBZ=0.481867;SCBZ=0.0121282;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:103,2,0 -000000F 515 . C G,<*> 0 . DP=110;I16=57,47,0,1,3848,153002,12,144,6240,374400,60,3600,2367,56887,25,625;QS=0.996891,0.00310881,0;SGB=-0.379885;RPBZ=0.263997;MQBZ=0;MQSBZ=0;BQBZ=-1.75323;NMBZ=-0.446607;SCBZ=-1.07538;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:104,1,0 -000000F 516 . G T,<*> 0 . DP=111;I16=57,48,0,1,3969,158573,12,144,6300,378000,60,3600,2411,58015,0,0;QS=0.996986,0.00301432,0;SGB=-0.379885;RPBZ=-1.71626;MQBZ=0;MQSBZ=0;BQBZ=-1.8341;NMBZ=-0.409591;SCBZ=-1.06697;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:105,1,0 -000000F 517 . T C,<*> 0 . DP=112;I16=56,50,1,0,3850,151946,12,144,6360,381600,60,3600,2408,58016,21,441;QS=0.996893,0.0031072,0;SGB=-0.379885;RPBZ=-0.7772;MQBZ=0;MQSBZ=0;BQBZ=-1.67048;NMBZ=1.60672;SCBZ=0.856997;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:106,1,0 +000000F 510 . C A,G,<*> 0 . DP=106;I16=54,43,1,2,3646,145190,42,692,5820,349200,180,10800,2189,52645,67,1515;QS=0.988612,0.00921909,0.0021692,0;VDB=0.401962;SGB=-0.511536;RPBZ=-0.707412;MQBZ=0;MQSBZ=0;BQBZ=-3.02794;SCBZ=-0.99293;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:97,2,1,0 +000000F 511 . T A,<*> 0 . DP=107;I16=55,45,0,1,3663,144413,12,144,6000,360000,60,3600,2251,54067,25,625;QS=0.996735,0.00326531,0;SGB=-0.379885;RPBZ=-0.0343102;MQBZ=0;MQSBZ=0;BQBZ=-1.71065;SCBZ=-1.08137;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:100,1,0 +000000F 512 . C A,G,<*> 0 . DP=107;I16=55,43,1,3,3657,146609,54,836,5880,352800,240,14400,2238,53902,83,1939;QS=0.985449,0.0123956,0.00215575,0;VDB=0.681156;SGB=-0.556411;RPBZ=-0.465574;MQBZ=0;MQSBZ=0;BQBZ=-3.45917;SCBZ=-0.667699;FS=0;MQ0F=0 PL:AD 0,248,255,255,255,255,255,255,255,255:98,3,1,0 +000000F 513 . T G,<*> 0 . DP=108;I16=56,46,0,1,3774,150038,7,49,6120,367200,60,3600,2340,56352,0,0;QS=0.998149,0.00185136,0;SGB=-0.379885;RPBZ=-1.71577;MQBZ=0;MQSBZ=0;BQBZ=-1.90666;SCBZ=-1.07835;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:102,1,0 +000000F 514 . G T,<*> 0 . DP=110;I16=56,47,1,1,3763,148539,20,208,6180,370800,120,7200,2348,56422,25,625;QS=0.994713,0.00528681,0;VDB=0.44;SGB=-0.453602;RPBZ=-1.58286;MQBZ=0;MQSBZ=0;BQBZ=-2.48498;SCBZ=0.0121282;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:103,2,0 +000000F 515 . C G,<*> 0 . DP=110;I16=57,47,0,1,3848,153002,12,144,6240,374400,60,3600,2367,56887,25,625;QS=0.996891,0.00310881,0;SGB=-0.379885;RPBZ=0.263997;MQBZ=0;MQSBZ=0;BQBZ=-1.75323;SCBZ=-1.07538;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:104,1,0 +000000F 516 . G T,<*> 0 . DP=111;I16=57,48,0,1,3969,158573,12,144,6300,378000,60,3600,2411,58015,0,0;QS=0.996986,0.00301432,0;SGB=-0.379885;RPBZ=-1.71626;MQBZ=0;MQSBZ=0;BQBZ=-1.8341;SCBZ=-1.06697;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:105,1,0 +000000F 517 . T C,<*> 0 . DP=112;I16=56,50,1,0,3850,151946,12,144,6360,381600,60,3600,2408,58016,21,441;QS=0.996893,0.0031072,0;SGB=-0.379885;RPBZ=-0.7772;MQBZ=0;MQSBZ=0;BQBZ=-1.67048;SCBZ=0.856997;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:106,1,0 000000F 518 . G <*> 0 . DP=115;I16=59,50,0,0,3977,155237,0,0,6540,392400,0,0,2447,58891,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:109,0 -000000F 519 . C A,<*> 0 . DP=116;I16=60,49,0,1,4018,159736,12,144,6540,392400,60,3600,2443,58747,25,625;QS=0.997022,0.00297767,0;SGB=-0.379885;RPBZ=0.110257;MQBZ=0;MQSBZ=0;BQBZ=-1.72465;NMBZ=-0.268336;SCBZ=-1.03419;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:109,1,0 -000000F 520 . T G,C,A 0 . DP=116;I16=59,48,1,2,4046,162680,48,1152,6420,385200,180,10800,2436,58644,53,1259;QS=0.988276,0.00781632,0.00195408,0.00195408;VDB=0.913952;SGB=-0.511536;RPBZ=0.578224;MQBZ=0;MQSBZ=0;BQBZ=-2.88822;NMBZ=-0.570213;SCBZ=-0.373153;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:107,1,1,1 -000000F 521 . G A,T,<*> 0 . DP=118;I16=61,48,1,2,4131,166701,36,432,6540,392400,180,10800,2454,59246,53,1089;QS=0.991361,0.00575954,0.00287977,0;VDB=0.251321;SGB=-0.511536;RPBZ=-1.60419;MQBZ=0;MQSBZ=0;BQBZ=-3.05428;NMBZ=-0.614138;SCBZ=-0.836529;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:109,2,1,0 +000000F 519 . C A,<*> 0 . DP=116;I16=60,49,0,1,4018,159736,12,144,6540,392400,60,3600,2443,58747,25,625;QS=0.997022,0.00297767,0;SGB=-0.379885;RPBZ=0.110257;MQBZ=0;MQSBZ=0;BQBZ=-1.72465;SCBZ=-1.03419;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:109,1,0 +000000F 520 . T G,C,A 0 . DP=116;I16=59,48,1,2,4046,162680,48,1152,6420,385200,180,10800,2436,58644,53,1259;QS=0.988276,0.00781632,0.00195408,0.00195408;VDB=0.913952;SGB=-0.511536;RPBZ=0.578224;MQBZ=0;MQSBZ=0;BQBZ=-2.88822;SCBZ=-0.373153;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:107,1,1,1 +000000F 521 . G A,T,<*> 0 . DP=118;I16=61,48,1,2,4131,166701,36,432,6540,392400,180,10800,2454,59246,53,1089;QS=0.991361,0.00575954,0.00287977,0;VDB=0.251321;SGB=-0.511536;RPBZ=-1.60419;MQBZ=0;MQSBZ=0;BQBZ=-3.05428;SCBZ=-0.836529;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:109,2,1,0 000000F 522 . G <*> 0 . DP=118;I16=62,50,0,0,4076,161128,0,0,6720,403200,0,0,2525,60719,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:112,0 -000000F 523 . C A,<*> 0 . DP=119;I16=63,49,0,1,4174,166860,12,144,6720,403200,60,3600,2518,60530,25,625;QS=0.997133,0.0028667,0;SGB=-0.379885;RPBZ=-0.13799;MQBZ=0;MQSBZ=0;BQBZ=-1.80506;NMBZ=-0.875769;SCBZ=-1.02482;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:112,1,0 -000000F 524 . T G,<*> 0 . DP=119;I16=62,50,1,0,4191,166163,27,729,6720,403200,60,3600,2537,61019,25,625;QS=0.993599,0.00640114,0;SGB=-0.379885;RPBZ=-0.82791;MQBZ=0;MQSBZ=0;BQBZ=-1.39926;NMBZ=0.35334;SCBZ=0.0480382;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:112,1,0 -000000F 525 . A C,G,<*> 0 . DP=119;I16=62,48,1,2,4098,163296,36,432,6600,396000,180,10800,2509,60447,71,1691;QS=0.991292,0.00580552,0.00290276,0;VDB=0.199299;SGB=-0.511536;RPBZ=-1.60781;MQBZ=0;MQSBZ=0;BQBZ=-2.97339;NMBZ=1.00241;SCBZ=1.45142;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:110,2,1,0 -000000F 526 . T A,<*> 0 . DP=120;I16=63,49,0,1,4180,166064,12,144,6720,403200,60,3600,2570,61910,25,625;QS=0.997137,0.0028626,0;SGB=-0.379885;RPBZ=-1.2266;MQBZ=0;MQSBZ=0;BQBZ=-1.74833;NMBZ=-0.245826;SCBZ=0.367327;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:112,1,0 -000000F 527 . C G,A,<*> 0 . DP=120;I16=62,49,1,1,4246,172572,24,288,6660,399600,120,7200,2557,61573,48,1154;QS=0.994379,0.0028103,0.0028103,0;VDB=0.18;SGB=-0.453602;RPBZ=-1.28504;MQBZ=0;MQSBZ=0;BQBZ=-2.51884;NMBZ=2.22611;SCBZ=1.10043;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:111,1,1,0 -000000F 528 . A G,<*> 0 . DP=121;I16=62,51,1,0,4295,173733,12,144,6780,406800,60,3600,2588,62236,25,625;QS=0.997214,0.00278616,0;SGB=-0.379885;RPBZ=-0.805477;MQBZ=0;MQSBZ=0;BQBZ=-1.82642;NMBZ=0.365458;SCBZ=0.0634184;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:113,1,0 -000000F 529 . T C,<*> 0 . DP=123;I16=65,50,0,1,4363,176845,8,64,6900,414000,60,3600,2639,63305,25,625;QS=0.99817,0.00183024,0;SGB=-0.379885;RPBZ=-1.04546;MQBZ=0;MQSBZ=0;BQBZ=-1.9592;NMBZ=-0.733499;SCBZ=-1.04156;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:115,1,0 +000000F 523 . C A,<*> 0 . DP=119;I16=63,49,0,1,4174,166860,12,144,6720,403200,60,3600,2518,60530,25,625;QS=0.997133,0.0028667,0;SGB=-0.379885;RPBZ=-0.13799;MQBZ=0;MQSBZ=0;BQBZ=-1.80506;SCBZ=-1.02482;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:112,1,0 +000000F 524 . T G,<*> 0 . DP=119;I16=62,50,1,0,4191,166163,27,729,6720,403200,60,3600,2537,61019,25,625;QS=0.993599,0.00640114,0;SGB=-0.379885;RPBZ=-0.82791;MQBZ=0;MQSBZ=0;BQBZ=-1.39926;SCBZ=0.0480382;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:112,1,0 +000000F 525 . A C,G,<*> 0 . DP=119;I16=62,48,1,2,4098,163296,36,432,6600,396000,180,10800,2509,60447,71,1691;QS=0.991292,0.00580552,0.00290276,0;VDB=0.199299;SGB=-0.511536;RPBZ=-1.60781;MQBZ=0;MQSBZ=0;BQBZ=-2.97339;SCBZ=1.45142;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:110,2,1,0 +000000F 526 . T A,<*> 0 . DP=120;I16=63,49,0,1,4180,166064,12,144,6720,403200,60,3600,2570,61910,25,625;QS=0.997137,0.0028626,0;SGB=-0.379885;RPBZ=-1.2266;MQBZ=0;MQSBZ=0;BQBZ=-1.74833;SCBZ=0.367327;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:112,1,0 +000000F 527 . C G,A,<*> 0 . DP=120;I16=62,49,1,1,4246,172572,24,288,6660,399600,120,7200,2557,61573,48,1154;QS=0.994379,0.0028103,0.0028103,0;VDB=0.18;SGB=-0.453602;RPBZ=-1.28504;MQBZ=0;MQSBZ=0;BQBZ=-2.51884;SCBZ=1.10043;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:111,1,1,0 +000000F 528 . A G,<*> 0 . DP=121;I16=62,51,1,0,4295,173733,12,144,6780,406800,60,3600,2588,62236,25,625;QS=0.997214,0.00278616,0;SGB=-0.379885;RPBZ=-0.805477;MQBZ=0;MQSBZ=0;BQBZ=-1.82642;SCBZ=0.0634184;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:113,1,0 +000000F 529 . T C,<*> 0 . DP=123;I16=65,50,0,1,4363,176845,8,64,6900,414000,60,3600,2639,63305,25,625;QS=0.99817,0.00183024,0;SGB=-0.379885;RPBZ=-1.04546;MQBZ=0;MQSBZ=0;BQBZ=-1.9592;SCBZ=-1.04156;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:115,1,0 000000F 530 . G <*> 0 . DP=123;I16=65,51,0,0,4357,176035,0,0,6960,417600,0,0,2672,64088,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:116,0 -000000F 531 . T A,G,<*> 0 . DP=123;I16=63,49,2,2,4199,169729,48,576,6720,403200,240,14400,2579,61741,100,2500;QS=0.988698,0.00847657,0.00282552,0;VDB=0.0550934;SGB=-0.556411;RPBZ=-0.650816;MQBZ=0;MQSBZ=0;BQBZ=-3.46139;NMBZ=0.401901;SCBZ=-0.463641;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:112,3,1,0 -000000F 532 . C A,G,<*> 0 . DP=124;I16=65,49,0,3,4352,176182,36,432,6840,410400,180,10800,2640,63492,45,897;QS=0.991796,0.00546946,0.00273473,0;VDB=0.588406;SGB=-0.511536;RPBZ=-1.58686;MQBZ=0;MQSBZ=0;BQBZ=-3.10955;NMBZ=-0.942115;SCBZ=-1.82952;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:114,2,1,0 +000000F 531 . T A,G,<*> 0 . DP=123;I16=63,49,2,2,4199,169729,48,576,6720,403200,240,14400,2579,61741,100,2500;QS=0.988698,0.00847657,0.00282552,0;VDB=0.0550934;SGB=-0.556411;RPBZ=-0.650816;MQBZ=0;MQSBZ=0;BQBZ=-3.46139;SCBZ=-0.463641;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:112,3,1,0 +000000F 532 . C A,G,<*> 0 . DP=124;I16=65,49,0,3,4352,176182,36,432,6840,410400,180,10800,2640,63492,45,897;QS=0.991796,0.00546946,0.00273473,0;VDB=0.588406;SGB=-0.511536;RPBZ=-1.58686;MQBZ=0;MQSBZ=0;BQBZ=-3.10955;SCBZ=-1.82952;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:114,2,1,0 000000F 533 . A <*> 0 . DP=124;I16=65,52,0,0,4235,168199,0,0,7020,421200,0,0,2692,64582,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:117,0 -000000F 534 . G A,<*> 0 . DP=124;I16=65,51,0,1,4319,173543,12,144,6960,417600,60,3600,2677,64331,21,441;QS=0.997229,0.00277072,0;SGB=-0.379885;RPBZ=-1.3327;MQBZ=0;MQSBZ=0;BQBZ=-1.72023;NMBZ=-0.148409;SCBZ=-1.04702;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:116,1,0 -000000F 535 . G A,<*> 0 . DP=125;I16=65,52,0,1,4309,171791,12,144,7020,421200,60,3600,2679,64385,25,625;QS=0.997223,0.00277713,0;SGB=-0.379885;RPBZ=-1.10121;MQBZ=0;MQSBZ=0;BQBZ=-1.74874;NMBZ=-0.250141;SCBZ=0.0762649;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:117,1,0 -000000F 536 . T G,A,<*> 0 . DP=125;I16=65,51,0,2,4274,171298,24,288,6960,417600,120,7200,2661,64041,48,1154;QS=0.994416,0.002792,0.002792,0;VDB=0.1;SGB=-0.453602;RPBZ=-1.74128;MQBZ=0;MQSBZ=0;BQBZ=-2.39373;NMBZ=-0.292578;SCBZ=-0.693187;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:116,1,1,0 +000000F 534 . G A,<*> 0 . DP=124;I16=65,51,0,1,4319,173543,12,144,6960,417600,60,3600,2677,64331,21,441;QS=0.997229,0.00277072,0;SGB=-0.379885;RPBZ=-1.3327;MQBZ=0;MQSBZ=0;BQBZ=-1.72023;SCBZ=-1.04702;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:116,1,0 +000000F 535 . G A,<*> 0 . DP=125;I16=65,52,0,1,4309,171791,12,144,7020,421200,60,3600,2679,64385,25,625;QS=0.997223,0.00277713,0;SGB=-0.379885;RPBZ=-1.10121;MQBZ=0;MQSBZ=0;BQBZ=-1.74874;SCBZ=0.0762649;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:117,1,0 +000000F 536 . T G,A,<*> 0 . DP=125;I16=65,51,0,2,4274,171298,24,288,6960,417600,120,7200,2661,64041,48,1154;QS=0.994416,0.002792,0.002792,0;VDB=0.1;SGB=-0.453602;RPBZ=-1.74128;MQBZ=0;MQSBZ=0;BQBZ=-2.39373;SCBZ=-0.693187;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:116,1,1,0 000000F 537 . A <*> 0 . DP=125;I16=65,53,0,0,4390,175290,0,0,7080,424800,0,0,2713,65375,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:118,0 -000000F 537 . AC A 0 . INDEL;IDV=60;IMF=0.48;DP=125;I16=36,26,30,27,2480,99200,2280,91200,3720,223200,3420,205200,1433,34549,1298,31150;QS=0.263673,0.736327;VDB=0.383756;SGB=-0.693147;RPBZ=-0.543708;MQBZ=0;MQSBZ=0;BQBZ=-2.39373;NMBZ=0.25078;SCBZ=0.641853;FS=0;MQ0F=0 PL:AD 255,0,28:62,57 +000000F 537 . AC A 0 . INDEL;IDV=60;IMF=0.48;DP=125;I16=36,26,30,27,2480,99200,2280,91200,3720,223200,3420,205200,1433,34549,1298,31150;QS=0.263673,0.736327;VDB=0.383756;SGB=-0.693147;RPBZ=-0.543708;MQBZ=0;MQSBZ=0;BQBZ=-2.39373;SCBZ=0.641853;FS=0;MQ0F=0 PL:AD 255,0,28:62,57 000000F 538 . C <*> 0 . DP=65;I16=36,26,0,0,2195,86349,0,0,3720,223200,0,0,1432,34600,0,0;QS=1,0;MQ0F=0 PL:AD 0,187,255:62,0 -000000F 538 . CT C 0 . INDEL;IDV=64;IMF=0.512;DP=125;I16=30,26,36,25,2240,89600,2440,97600,3360,201600,3660,219600,1277,30663,1380,33214;QS=0.22136,0.77864;VDB=0.00357075;SGB=-0.693147;RPBZ=0.242079;MQBZ=0;MQSBZ=0;BQBZ=-2.39373;NMBZ=-2.25501;SCBZ=-0.994262;FS=0;MQ0F=0 PL:AD 255,0,28:56,61 +000000F 538 . CT C 0 . INDEL;IDV=64;IMF=0.512;DP=125;I16=30,26,36,25,2240,89600,2440,97600,3360,201600,3660,219600,1277,30663,1380,33214;QS=0.22136,0.77864;VDB=0.00357075;SGB=-0.693147;RPBZ=0.242079;MQBZ=0;MQSBZ=0;BQBZ=-2.39373;SCBZ=-0.994262;FS=0;MQ0F=0 PL:AD 255,0,28:56,61 000000F 539 . T <*> 0 . DP=60;I16=29,26,0,0,2120,86238,0,0,3300,198000,0,0,1260,30374,0,0;QS=1,0;MQ0F=0 PL:AD 0,166,255:55,0 000000F 540 . G <*> 0 . DP=124;I16=64,53,0,0,4130,161310,0,0,7020,421200,0,0,2703,65511,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:117,0 000000F 541 . G <*> 0 . DP=124;I16=64,53,0,0,4143,160525,0,0,7020,421200,0,0,2705,65703,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:117,0 -000000F 542 . T G,A,<*> 0 . DP=124;I16=63,52,1,1,4035,156631,24,288,6900,414000,120,7200,2657,64685,50,1250;QS=0.994087,0.00295639,0.00295639,0;VDB=0.26;SGB=-0.453602;RPBZ=-1.44078;MQBZ=0;MQSBZ=0;BQBZ=-2.25702;NMBZ=0.136979;SCBZ=-0.906022;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:115,1,1,0 -000000F 543 . C G,A,<*> 0 . DP=122;I16=62,53,1,1,4006,154170,24,288,6900,414000,120,7200,2673,65063,50,1250;QS=0.994045,0.00297767,0.00297767,0;VDB=0.22;SGB=-0.453602;RPBZ=-0.483734;MQBZ=0;MQSBZ=0;BQBZ=-2.21926;NMBZ=0.821994;SCBZ=0.31726;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:115,1,1,0 -000000F 544 . T A,<*> 0 . DP=121;I16=62,53,0,1,4151,162625,12,144,6900,414000,60,3600,2697,65733,25,625;QS=0.997117,0.00288254,0;SGB=-0.379885;RPBZ=0.238977;MQBZ=0;MQSBZ=0;BQBZ=-1.67238;NMBZ=-0.224501;SCBZ=-1.05505;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:115,1,0 -000000F 545 . G A,<*> 0 . DP=121;I16=62,53,0,1,4078,158586,12,144,6900,414000,60,3600,2710,66228,8,64;QS=0.997066,0.00293399,0;SGB=-0.379885;RPBZ=1.6131;MQBZ=0;MQSBZ=0;BQBZ=-1.61213;NMBZ=-0.568741;SCBZ=-1.05503;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:115,1,0 -000000F 546 . G A,<*> 0 . DP=121;I16=62,53,0,1,4230,164790,12,144,6900,414000,60,3600,2689,65637,25,625;QS=0.997171,0.00282885,0;SGB=-0.379885;RPBZ=-0.97077;MQBZ=0;MQSBZ=0;BQBZ=-1.77555;NMBZ=-0.718441;SCBZ=-1.0549;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:115,1,0 -000000F 547 . A C,<*> 0 . DP=119;I16=62,51,0,1,4105,158737,12,144,6780,406800,60,3600,2686,65592,25,625;QS=0.997085,0.00291474,0;SGB=-0.379885;RPBZ=-0.896646;MQBZ=0;MQSBZ=0;BQBZ=-1.70779;NMBZ=1.50766;SCBZ=0.0314879;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:113,1,0 -000000F 548 . C G,<*> 0 . DP=119;I16=62,51,0,1,4014,154686,12,144,6780,406800,60,3600,2681,65479,25,625;QS=0.997019,0.00298063,0;SGB=-0.379885;RPBZ=-0.896728;MQBZ=0;MQSBZ=0;BQBZ=-1.67128;NMBZ=1.50766;SCBZ=0.0314876;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:113,1,0 -000000F 549 . C A,<*> 0 . DP=117;I16=33,29,29,22,2214,83510,1893,75363,3720,223200,3060,183600,1463,35977,1212,29370;QS=0.53908,0.46092,0;VDB=0.0978768;SGB=-0.693147;RPBZ=-0.600202;MQBZ=0;MQSBZ=0;BQBZ=1.17837;NMBZ=0.668443;SCBZ=0.928426;FS=0;MQ0F=0 PL:AD 255,0,255,255,255,255:62,51,0 -000000F 550 . G T,<*> 0 . DP=117;I16=62,50,0,1,4113,161301,22,484,6720,403200,60,3600,2641,64473,25,625;QS=0.99468,0.00532044,0;SGB=-0.379885;RPBZ=-0.950536;MQBZ=0;MQSBZ=0;BQBZ=-1.55326;NMBZ=-0.73753;SCBZ=-1.07862;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:112,1,0 -000000F 551 . G T,A,<*> 0 . DP=116;I16=60,50,1,1,4131,164089,24,288,6600,396000,120,7200,2607,63583,50,1250;QS=0.994224,0.00288809,0.00288809,0;VDB=0.32;SGB=-0.453602;RPBZ=-1.01088;MQBZ=0;MQSBZ=0;BQBZ=-2.59034;NMBZ=0.286289;SCBZ=0.329971;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:110,1,1,0 -000000F 552 . A C,<*> 0 . DP=116;I16=60,50,1,1,3927,151331,24,288,6600,396000,120,7200,2598,63352,50,1250;QS=0.993926,0.00607441,0;VDB=0.1;SGB=-0.453602;RPBZ=-1.12079;MQBZ=0;MQSBZ=0;BQBZ=-2.37929;NMBZ=1.33204;SCBZ=-0.136538;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:110,2,0 -000000F 553 . G T,<*> 0 . DP=116;I16=60,51,1,0,4046,158108,12,144,6660,399600,60,3600,2613,63729,25,625;QS=0.997043,0.00295712,0;SGB=-0.379885;RPBZ=-0.35579;MQBZ=0;MQSBZ=0;BQBZ=-1.77886;NMBZ=0.635577;SCBZ=0.688792;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:111,1,0 +000000F 542 . T G,A,<*> 0 . DP=124;I16=63,52,1,1,4035,156631,24,288,6900,414000,120,7200,2657,64685,50,1250;QS=0.994087,0.00295639,0.00295639,0;VDB=0.26;SGB=-0.453602;RPBZ=-1.44078;MQBZ=0;MQSBZ=0;BQBZ=-2.25702;SCBZ=-0.906022;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:115,1,1,0 +000000F 543 . C G,A,<*> 0 . DP=122;I16=62,53,1,1,4006,154170,24,288,6900,414000,120,7200,2673,65063,50,1250;QS=0.994045,0.00297767,0.00297767,0;VDB=0.22;SGB=-0.453602;RPBZ=-0.483734;MQBZ=0;MQSBZ=0;BQBZ=-2.21926;SCBZ=0.31726;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:115,1,1,0 +000000F 544 . T A,<*> 0 . DP=121;I16=62,53,0,1,4151,162625,12,144,6900,414000,60,3600,2697,65733,25,625;QS=0.997117,0.00288254,0;SGB=-0.379885;RPBZ=0.238977;MQBZ=0;MQSBZ=0;BQBZ=-1.67238;SCBZ=-1.05505;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:115,1,0 +000000F 545 . G A,<*> 0 . DP=121;I16=62,53,0,1,4078,158586,12,144,6900,414000,60,3600,2710,66228,8,64;QS=0.997066,0.00293399,0;SGB=-0.379885;RPBZ=1.6131;MQBZ=0;MQSBZ=0;BQBZ=-1.61213;SCBZ=-1.05503;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:115,1,0 +000000F 546 . G A,<*> 0 . DP=121;I16=62,53,0,1,4230,164790,12,144,6900,414000,60,3600,2689,65637,25,625;QS=0.997171,0.00282885,0;SGB=-0.379885;RPBZ=-0.97077;MQBZ=0;MQSBZ=0;BQBZ=-1.77555;SCBZ=-1.0549;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:115,1,0 +000000F 547 . A C,<*> 0 . DP=119;I16=62,51,0,1,4105,158737,12,144,6780,406800,60,3600,2686,65592,25,625;QS=0.997085,0.00291474,0;SGB=-0.379885;RPBZ=-0.896646;MQBZ=0;MQSBZ=0;BQBZ=-1.70779;SCBZ=0.0314879;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:113,1,0 +000000F 548 . C G,<*> 0 . DP=119;I16=62,51,0,1,4014,154686,12,144,6780,406800,60,3600,2681,65479,25,625;QS=0.997019,0.00298063,0;SGB=-0.379885;RPBZ=-0.896728;MQBZ=0;MQSBZ=0;BQBZ=-1.67128;SCBZ=0.0314876;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:113,1,0 +000000F 549 . C A,<*> 0 . DP=117;I16=33,29,29,22,2214,83510,1893,75363,3720,223200,3060,183600,1463,35977,1212,29370;QS=0.53908,0.46092,0;VDB=0.0978768;SGB=-0.693147;RPBZ=-0.600202;MQBZ=0;MQSBZ=0;BQBZ=1.17837;SCBZ=0.928426;FS=0;MQ0F=0 PL:AD 255,0,255,255,255,255:62,51,0 +000000F 550 . G T,<*> 0 . DP=117;I16=62,50,0,1,4113,161301,22,484,6720,403200,60,3600,2641,64473,25,625;QS=0.99468,0.00532044,0;SGB=-0.379885;RPBZ=-0.950536;MQBZ=0;MQSBZ=0;BQBZ=-1.55326;SCBZ=-1.07862;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:112,1,0 +000000F 551 . G T,A,<*> 0 . DP=116;I16=60,50,1,1,4131,164089,24,288,6600,396000,120,7200,2607,63583,50,1250;QS=0.994224,0.00288809,0.00288809,0;VDB=0.32;SGB=-0.453602;RPBZ=-1.01088;MQBZ=0;MQSBZ=0;BQBZ=-2.59034;SCBZ=0.329971;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:110,1,1,0 +000000F 552 . A C,<*> 0 . DP=116;I16=60,50,1,1,3927,151331,24,288,6600,396000,120,7200,2598,63352,50,1250;QS=0.993926,0.00607441,0;VDB=0.1;SGB=-0.453602;RPBZ=-1.12079;MQBZ=0;MQSBZ=0;BQBZ=-2.37929;SCBZ=-0.136538;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:110,2,0 +000000F 553 . G T,<*> 0 . DP=116;I16=60,51,1,0,4046,158108,12,144,6660,399600,60,3600,2613,63729,25,625;QS=0.997043,0.00295712,0;SGB=-0.379885;RPBZ=-0.35579;MQBZ=0;MQSBZ=0;BQBZ=-1.77886;SCBZ=0.688792;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:111,1,0 000000F 554 . A <*> 0 . DP=113;I16=60,50,0,0,4046,159278,0,0,6600,396000,0,0,2629,64087,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:110,0 000000F 555 . G <*> 0 . DP=112;I16=60,49,0,0,4016,156988,0,0,6540,392400,0,0,2600,63438,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:109,0 000000F 556 . A <*> 0 . DP=112;I16=60,49,0,0,3915,151463,0,0,6540,392400,0,0,2588,63068,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:109,0 000000F 557 . A <*> 0 . DP=112;I16=60,49,0,0,3957,151889,0,0,6540,392400,0,0,2575,62681,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:109,0 -000000F 558 . A G,<*> 0 . DP=112;I16=60,47,0,2,3726,140280,24,288,6420,385200,120,7200,2510,60980,50,1250;QS=0.9936,0.0064,0;VDB=0.22;SGB=-0.453602;RPBZ=-1.14043;MQBZ=0;MQSBZ=0;BQBZ=-2.29525;NMBZ=0.294161;SCBZ=-0.444037;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:107,2,0 -000000F 559 . C T,<*> 0 . DP=112;I16=59,49,1,0,3985,155617,12,144,6480,388800,60,3600,2518,61092,25,625;QS=0.996998,0.00300225,0;SGB=-0.379885;RPBZ=0.731168;MQBZ=0;MQSBZ=0;BQBZ=-1.78272;NMBZ=-0.36631;SCBZ=-1.08527;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:108,1,0 +000000F 558 . A G,<*> 0 . DP=112;I16=60,47,0,2,3726,140280,24,288,6420,385200,120,7200,2510,60980,50,1250;QS=0.9936,0.0064,0;VDB=0.22;SGB=-0.453602;RPBZ=-1.14043;MQBZ=0;MQSBZ=0;BQBZ=-2.29525;SCBZ=-0.444037;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:107,2,0 +000000F 559 . C T,<*> 0 . DP=112;I16=59,49,1,0,3985,155617,12,144,6480,388800,60,3600,2518,61092,25,625;QS=0.996998,0.00300225,0;SGB=-0.379885;RPBZ=0.731168;MQBZ=0;MQSBZ=0;BQBZ=-1.78272;SCBZ=-1.08527;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:108,1,0 000000F 560 . T <*> 0 . DP=110;I16=59,48,0,0,3896,150870,0,0,6420,385200,0,0,2507,60841,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:107,0 000000F 561 . G <*> 0 . DP=110;I16=59,48,0,0,3921,153367,0,0,6420,385200,0,0,2492,60440,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:107,0 -000000F 562 . T C,A,<*> 0 . DP=110;I16=58,47,1,1,3748,143542,24,288,6300,378000,120,7200,2425,58723,50,1250;QS=0.993637,0.00318134,0.00318134,0;VDB=0.32;SGB=-0.453602;RPBZ=1.03535;MQBZ=0;MQSBZ=0;BQBZ=-2.35872;NMBZ=-0.461089;SCBZ=-0.452888;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:105,1,1,0 -000000F 563 . G A,<*> 0 . DP=109;I16=59,45,0,2,3881,153011,24,288,6240,374400,120,7200,2384,57712,50,1250;QS=0.993854,0.00614597,0;VDB=0.06;SGB=-0.453602;RPBZ=-1.81161;MQBZ=0;MQSBZ=0;BQBZ=-2.59069;NMBZ=-0.314161;SCBZ=-0.927311;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:104,2,0 +000000F 562 . T C,A,<*> 0 . DP=110;I16=58,47,1,1,3748,143542,24,288,6300,378000,120,7200,2425,58723,50,1250;QS=0.993637,0.00318134,0.00318134,0;VDB=0.32;SGB=-0.453602;RPBZ=1.03535;MQBZ=0;MQSBZ=0;BQBZ=-2.35872;SCBZ=-0.452888;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:105,1,1,0 +000000F 563 . G A,<*> 0 . DP=109;I16=59,45,0,2,3881,153011,24,288,6240,374400,120,7200,2384,57712,50,1250;QS=0.993854,0.00614597,0;VDB=0.06;SGB=-0.453602;RPBZ=-1.81161;MQBZ=0;MQSBZ=0;BQBZ=-2.59069;SCBZ=-0.927311;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:104,2,0 000000F 564 . G <*> 0 . DP=109;I16=59,47,0,0,3954,155218,0,0,6360,381600,0,0,2417,58561,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:106,0 -000000F 565 . A G,<*> 0 . DP=108;I16=59,44,0,2,3818,150006,24,288,6180,370800,120,7200,2351,56943,50,1250;QS=0.993753,0.00624675,0;VDB=0.52;SGB=-0.453602;RPBZ=-0.0703536;MQBZ=0;MQSBZ=0;BQBZ=-2.43017;NMBZ=0.434607;SCBZ=-0.752998;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:103,2,0 +000000F 565 . A G,<*> 0 . DP=108;I16=59,44,0,2,3818,150006,24,288,6180,370800,120,7200,2351,56943,50,1250;QS=0.993753,0.00624675,0;VDB=0.52;SGB=-0.453602;RPBZ=-0.0703536;MQBZ=0;MQSBZ=0;BQBZ=-2.43017;SCBZ=-0.752998;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:103,2,0 000000F 566 . T <*> 0 . DP=108;I16=59,46,0,0,3981,157549,0,0,6300,378000,0,0,2384,57808,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:105,0 -000000F 567 . G T,C,<*> 0 . DP=108;I16=57,46,2,0,3847,151871,20,208,6180,370800,120,7200,2318,56254,48,1154;QS=0.994828,0.00310318,0.00206879,0;VDB=0.7;SGB=-0.453602;RPBZ=0.128964;MQBZ=0;MQSBZ=0;BQBZ=-2.74966;NMBZ=-0.822312;SCBZ=-0.146119;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:103,1,1,0 -000000F 568 . T C,<*> 0 . DP=106;I16=56,47,1,0,3763,145559,8,64,6180,370800,60,3600,2349,56993,25,625;QS=0.997879,0.00212145,0;SGB=-0.379885;RPBZ=0.983018;MQBZ=0;MQSBZ=0;BQBZ=-1.93576;NMBZ=-1.60247;SCBZ=-1.05631;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:103,1,0 -000000F 569 . C G,A,<*> 0 . DP=104;I16=55,45,0,2,3734,146948,24,288,6000,360000,120,7200,2309,55985,50,1250;QS=0.993614,0.00319319,0.00319319,0;VDB=0.58;SGB=-0.453602;RPBZ=-0.543243;MQBZ=0;MQSBZ=0;BQBZ=-2.54989;NMBZ=-0.193493;SCBZ=-1.48352;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:100,1,1,0 +000000F 567 . G T,C,<*> 0 . DP=108;I16=57,46,2,0,3847,151871,20,208,6180,370800,120,7200,2318,56254,48,1154;QS=0.994828,0.00310318,0.00206879,0;VDB=0.7;SGB=-0.453602;RPBZ=0.128964;MQBZ=0;MQSBZ=0;BQBZ=-2.74966;SCBZ=-0.146119;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:103,1,1,0 +000000F 568 . T C,<*> 0 . DP=106;I16=56,47,1,0,3763,145559,8,64,6180,370800,60,3600,2349,56993,25,625;QS=0.997879,0.00212145,0;SGB=-0.379885;RPBZ=0.983018;MQBZ=0;MQSBZ=0;BQBZ=-1.93576;SCBZ=-1.05631;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:103,1,0 +000000F 569 . C G,A,<*> 0 . DP=104;I16=55,45,0,2,3734,146948,24,288,6000,360000,120,7200,2309,55985,50,1250;QS=0.993614,0.00319319,0.00319319,0;VDB=0.58;SGB=-0.453602;RPBZ=-0.543243;MQBZ=0;MQSBZ=0;BQBZ=-2.54989;SCBZ=-1.48352;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:100,1,1,0 000000F 570 . T <*> 0 . DP=104;I16=55,47,0,0,3862,151566,0,0,6120,367200,0,0,2342,56784,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:102,0 000000F 571 . G <*> 0 . DP=104;I16=55,47,0,0,3733,145003,0,0,6120,367200,0,0,2325,56367,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:102,0 -000000F 572 . T A,G,<*> 0 . DP=103;I16=53,46,1,1,3664,142548,34,628,5940,356400,120,7200,2259,54733,50,1250;QS=0.990806,0.00594916,0.003245,0;VDB=0.22;SGB=-0.453602;RPBZ=0.219457;MQBZ=0;MQSBZ=0;BQBZ=-2.44659;NMBZ=1.02598;SCBZ=0.216127;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:99,1,1,0 -000000F 573 . C G,<*> 0 . DP=103;I16=54,46,0,1,3749,146645,12,144,6000,360000,60,3600,2267,54957,25,625;QS=0.996809,0.00319064,0;SGB=-0.379885;RPBZ=-0.428856;MQBZ=0;MQSBZ=0;BQBZ=-1.85387;NMBZ=-0.446862;SCBZ=-1.03794;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:100,1,0 +000000F 572 . T A,G,<*> 0 . DP=103;I16=53,46,1,1,3664,142548,34,628,5940,356400,120,7200,2259,54733,50,1250;QS=0.990806,0.00594916,0.003245,0;VDB=0.22;SGB=-0.453602;RPBZ=0.219457;MQBZ=0;MQSBZ=0;BQBZ=-2.44659;SCBZ=0.216127;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:99,1,1,0 +000000F 573 . C G,<*> 0 . DP=103;I16=54,46,0,1,3749,146645,12,144,6000,360000,60,3600,2267,54957,25,625;QS=0.996809,0.00319064,0;SGB=-0.379885;RPBZ=-0.428856;MQBZ=0;MQSBZ=0;BQBZ=-1.85387;SCBZ=-1.03794;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:100,1,0 000000F 574 . A <*> 0 . DP=102;I16=54,46,0,0,3671,141999,0,0,6000,360000,0,0,2275,55165,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:100,0 000000F 575 . A <*> 0 . DP=101;I16=53,46,0,0,3653,142115,0,0,5940,356400,0,0,2259,54781,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:99,0 000000F 576 . C <*> 0 . DP=99;I16=52,45,0,0,3665,144129,0,0,5820,349200,0,0,2229,54203,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:97,0 @@ -214,84 +213,84 @@ 000000F 580 . A <*> 0 . DP=98;I16=51,45,0,0,3569,139629,0,0,5760,345600,0,0,2141,51599,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:96,0 000000F 581 . C <*> 0 . DP=95;I16=49,44,0,0,3512,137782,0,0,5580,334800,0,0,2096,50392,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:93,0 000000F 582 . A <*> 0 . DP=94;I16=49,43,0,0,3411,135315,0,0,5520,331200,0,0,2073,49673,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:92,0 -000000F 583 . G C,<*> 0 . DP=90;I16=46,41,1,0,3292,129550,12,144,5220,313200,60,3600,1985,47479,25,625;QS=0.996368,0.00363196,0;SGB=-0.379885;RPBZ=0.334737;MQBZ=0;MQSBZ=0;BQBZ=-1.89321;NMBZ=-0.512824;SCBZ=-1.01118;FS=0;MQ0F=0 PL:AD 0,245,255,255,255,255:87,1,0 +000000F 583 . G C,<*> 0 . DP=90;I16=46,41,1,0,3292,129550,12,144,5220,313200,60,3600,1985,47479,25,625;QS=0.996368,0.00363196,0;SGB=-0.379885;RPBZ=0.334737;MQBZ=0;MQSBZ=0;BQBZ=-1.89321;SCBZ=-1.01118;FS=0;MQ0F=0 PL:AD 0,245,255,255,255,255:87,1,0 000000F 584 . A <*> 0 . DP=87;I16=45,40,0,0,3152,123280,0,0,5100,306000,0,0,1940,46204,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:85,0 000000F 585 . A <*> 0 . DP=88;I16=44,40,0,0,3202,127432,0,0,5040,302400,0,0,1914,45520,0,0;QS=1,0;MQ0F=0 PL:AD 0,253,255:84,0 -000000F 586 . A G,<*> 0 . DP=88;I16=43,40,1,0,2964,114852,12,144,4980,298800,60,3600,1875,44509,16,256;QS=0.995968,0.00403226,0;SGB=-0.379885;RPBZ=0.866495;MQBZ=0;MQSBZ=0;BQBZ=-1.73561;NMBZ=1.61188;SCBZ=1.14098;FS=0;MQ0F=0 PL:AD 0,234,255,250,255,255:83,1,0 -000000F 587 . A C,<*> 0 . DP=88;I16=45,40,0,1,2997,115249,12,144,5100,306000,60,3600,1891,44583,25,625;QS=0.996012,0.00398804,0;SGB=-0.379885;RPBZ=-0.584321;MQBZ=0;MQSBZ=0;BQBZ=-1.64438;NMBZ=1.51363;SCBZ=0.548806;FS=0;MQ0F=0 PL:AD 0,240,255,255,255,255:85,1,0 +000000F 586 . A G,<*> 0 . DP=88;I16=43,40,1,0,2964,114852,12,144,4980,298800,60,3600,1875,44509,16,256;QS=0.995968,0.00403226,0;SGB=-0.379885;RPBZ=0.866495;MQBZ=0;MQSBZ=0;BQBZ=-1.73561;SCBZ=1.14098;FS=0;MQ0F=0 PL:AD 0,234,255,250,255,255:83,1,0 +000000F 587 . A C,<*> 0 . DP=88;I16=45,40,0,1,2997,115249,12,144,5100,306000,60,3600,1891,44583,25,625;QS=0.996012,0.00398804,0;SGB=-0.379885;RPBZ=-0.584321;MQBZ=0;MQSBZ=0;BQBZ=-1.64438;SCBZ=0.548806;FS=0;MQ0F=0 PL:AD 0,240,255,255,255,255:85,1,0 000000F 588 . A <*> 0 . DP=87;I16=45,40,0,0,2971,113817,0,0,5100,306000,0,0,1891,44401,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:85,0 -000000F 589 . G A,<*> 0 . DP=87;I16=44,40,1,0,3059,117323,12,144,5040,302400,60,3600,1840,42970,25,625;QS=0.996092,0.00390752,0;SGB=-0.379885;RPBZ=0.550542;MQBZ=0;MQSBZ=0;BQBZ=-1.79452;NMBZ=1.61324;SCBZ=1.68471;FS=0;MQ0F=0 PL:AD 0,237,255,253,255,255:84,1,0 +000000F 589 . G A,<*> 0 . DP=87;I16=44,40,1,0,3059,117323,12,144,5040,302400,60,3600,1840,42970,25,625;QS=0.996092,0.00390752,0;SGB=-0.379885;RPBZ=0.550542;MQBZ=0;MQSBZ=0;BQBZ=-1.79452;SCBZ=1.68471;FS=0;MQ0F=0 PL:AD 0,237,255,253,255,255:84,1,0 000000F 590 . T <*> 0 . DP=87;I16=45,40,0,0,3019,114421,0,0,5100,306000,0,0,1839,42841,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:85,0 -000000F 591 . G C,<*> 0 . DP=86;I16=43,40,1,0,3033,117015,12,144,4980,298800,60,3600,1807,42121,3,9;QS=0.996059,0.00394089,0;SGB=-0.379885;RPBZ=1.67089;MQBZ=0;MQSBZ=0;BQBZ=-1.80181;NMBZ=-1.0334;SCBZ=-1.01597;FS=0;MQ0F=0 PL:AD 0,234,255,250,255,255:83,1,0 -000000F 592 . A C,<*> 0 . DP=85;I16=44,38,0,2,2821,106231,24,288,4920,295200,120,7200,1748,40690,36,746;QS=0.991564,0.00843585,0;VDB=0.5;SGB=-0.453602;RPBZ=0.484389;MQBZ=0;MQSBZ=0;BQBZ=-2.1998;NMBZ=0.823216;SCBZ=-0.0922779;FS=0;MQ0F=0 PL:AD 0,217,255,247,255,255:82,2,0 -000000F 593 . C G,A,<*> 0 . DP=84;I16=42,39,1,1,2912,110366,24,288,4860,291600,120,7200,1709,39543,50,1250;QS=0.991826,0.00408719,0.00408719,0;VDB=0.36;SGB=-0.453602;RPBZ=-0.0891287;MQBZ=0;MQSBZ=0;BQBZ=-2.57106;NMBZ=0.699311;SCBZ=-0.108692;FS=0;MQ0F=0 PL:AD 0,228,255,228,255,255,244,255,255,255:81,1,1,0 +000000F 591 . G C,<*> 0 . DP=86;I16=43,40,1,0,3033,117015,12,144,4980,298800,60,3600,1807,42121,3,9;QS=0.996059,0.00394089,0;SGB=-0.379885;RPBZ=1.67089;MQBZ=0;MQSBZ=0;BQBZ=-1.80181;SCBZ=-1.01597;FS=0;MQ0F=0 PL:AD 0,234,255,250,255,255:83,1,0 +000000F 592 . A C,<*> 0 . DP=85;I16=44,38,0,2,2821,106231,24,288,4920,295200,120,7200,1748,40690,36,746;QS=0.991564,0.00843585,0;VDB=0.5;SGB=-0.453602;RPBZ=0.484389;MQBZ=0;MQSBZ=0;BQBZ=-2.1998;SCBZ=-0.0922779;FS=0;MQ0F=0 PL:AD 0,217,255,247,255,255:82,2,0 +000000F 593 . C G,A,<*> 0 . DP=84;I16=42,39,1,1,2912,110366,24,288,4860,291600,120,7200,1709,39543,50,1250;QS=0.991826,0.00408719,0.00408719,0;VDB=0.36;SGB=-0.453602;RPBZ=-0.0891287;MQBZ=0;MQSBZ=0;BQBZ=-2.57106;SCBZ=-0.108692;FS=0;MQ0F=0 PL:AD 0,228,255,228,255,255,244,255,255,255:81,1,1,0 000000F 594 . T <*> 0 . DP=84;I16=43,40,0,0,2911,110919,0,0,4980,298800,0,0,1733,40151,0,0;QS=1,0;MQ0F=0 PL:AD 0,250,255:83,0 000000F 595 . G <*> 0 . DP=82;I16=42,39,0,0,2849,108157,0,0,4860,291600,0,0,1681,38837,0,0;QS=1,0;MQ0F=0 PL:AD 0,244,255:81,0 -000000F 596 . A C,<*> 0 . DP=81;I16=42,37,0,1,2846,108902,12,144,4740,284400,60,3600,1613,37303,25,625;QS=0.995801,0.00419874,0;SGB=-0.379885;RPBZ=-0.9748;MQBZ=0;MQSBZ=0;BQBZ=-1.73819;NMBZ=0.130213;SCBZ=0.250526;FS=0;MQ0F=0 PL:AD 0,222,255,238,255,255:79,1,0 -000000F 597 . T G,<*> 0 . DP=80;I16=42,36,0,1,2742,102116,12,144,4680,280800,60,3600,1574,36614,15,225;QS=0.995643,0.0043573,0;SGB=-0.379885;RPBZ=0.833621;MQBZ=0;MQSBZ=0;BQBZ=-1.70797;NMBZ=-0.131854;SCBZ=0.254296;FS=0;MQ0F=0 PL:AD 0,219,255,235,255,255:78,1,0 +000000F 596 . A C,<*> 0 . DP=81;I16=42,37,0,1,2846,108902,12,144,4740,284400,60,3600,1613,37303,25,625;QS=0.995801,0.00419874,0;SGB=-0.379885;RPBZ=-0.9748;MQBZ=0;MQSBZ=0;BQBZ=-1.73819;SCBZ=0.250526;FS=0;MQ0F=0 PL:AD 0,222,255,238,255,255:79,1,0 +000000F 597 . T G,<*> 0 . DP=80;I16=42,36,0,1,2742,102116,12,144,4680,280800,60,3600,1574,36614,15,225;QS=0.995643,0.0043573,0;SGB=-0.379885;RPBZ=0.833621;MQBZ=0;MQSBZ=0;BQBZ=-1.70797;SCBZ=0.254296;FS=0;MQ0F=0 PL:AD 0,219,255,235,255,255:78,1,0 000000F 598 . T <*> 0 . DP=79;I16=41,37,0,0,2839,109553,0,0,4680,280800,0,0,1562,36238,0,0;QS=1,0;MQ0F=0 PL:AD 0,235,255:78,0 000000F 599 . A <*> 0 . DP=77;I16=40,36,0,0,2770,106710,0,0,4560,273600,0,0,1528,35518,0,0;QS=1,0;MQ0F=0 PL:AD 0,229,255:76,0 000000F 600 . G <*> 0 . DP=77;I16=40,36,0,0,2714,103152,0,0,4560,273600,0,0,1498,34792,0,0;QS=1,0;MQ0F=0 PL:AD 0,229,255:76,0 -000000F 601 . T G,C,<*> 0 . DP=77;I16=39,35,1,1,2583,97801,24,288,4440,266400,120,7200,1417,32827,50,1250;QS=0.990798,0.00460123,0.00460123,0;VDB=0.1;SGB=-0.453602;RPBZ=-0.795612;MQBZ=0;MQSBZ=0;BQBZ=-2.28816;NMBZ=0.569195;SCBZ=0.0680273;FS=0;MQ0F=0 PL:AD 0,207,255,207,255,255,223,255,255,255:74,1,1,0 -000000F 602 . T A,C,<*> 0 . DP=74;I16=37,33,1,2,2416,90472,61,1657,4200,252000,180,10800,1357,31631,60,1350;QS=0.975373,0.019782,0.00484457,0;VDB=0.568985;SGB=-0.511536;RPBZ=0.333732;MQBZ=0;MQSBZ=0;BQBZ=-2.13242;NMBZ=0.306281;SCBZ=0.845379;FS=0;MQ0F=0 PL:AD 0,164,255,195,255,255,211,255,255,255:70,2,1,0 -000000F 603 . A C,<*> 0 . DP=68;I16=35,30,1,0,2312,88408,12,144,3900,234000,60,3600,1347,31297,25,625;QS=0.994837,0.00516351,0;SGB=-0.379885;RPBZ=-0.131301;MQBZ=0;MQSBZ=0;BQBZ=-1.66952;NMBZ=0.526139;SCBZ=-1.04349;FS=0;MQ0F=0 PL:AD 0,180,255,196,255,255:65,1,0 +000000F 601 . T G,C,<*> 0 . DP=77;I16=39,35,1,1,2583,97801,24,288,4440,266400,120,7200,1417,32827,50,1250;QS=0.990798,0.00460123,0.00460123,0;VDB=0.1;SGB=-0.453602;RPBZ=-0.795612;MQBZ=0;MQSBZ=0;BQBZ=-2.28816;SCBZ=0.0680273;FS=0;MQ0F=0 PL:AD 0,207,255,207,255,255,223,255,255,255:74,1,1,0 +000000F 602 . T A,C,<*> 0 . DP=74;I16=37,33,1,2,2416,90472,61,1657,4200,252000,180,10800,1357,31631,60,1350;QS=0.975373,0.019782,0.00484457,0;VDB=0.568985;SGB=-0.511536;RPBZ=0.333732;MQBZ=0;MQSBZ=0;BQBZ=-2.13242;SCBZ=0.845379;FS=0;MQ0F=0 PL:AD 0,164,255,195,255,255,211,255,255,255:70,2,1,0 +000000F 603 . A C,<*> 0 . DP=68;I16=35,30,1,0,2312,88408,12,144,3900,234000,60,3600,1347,31297,25,625;QS=0.994837,0.00516351,0;SGB=-0.379885;RPBZ=-0.131301;MQBZ=0;MQSBZ=0;BQBZ=-1.66952;SCBZ=-1.04349;FS=0;MQ0F=0 PL:AD 0,180,255,196,255,255:65,1,0 000000F 604 . G <*> 0 . DP=67;I16=36,30,0,0,2403,93039,0,0,3960,237600,0,0,1349,31351,0,0;QS=1,0;MQ0F=0 PL:AD 0,199,255:66,0 -000000F 605 . A G,<*> 0 . DP=66;I16=35,28,1,1,2254,85780,24,288,3780,226800,120,7200,1292,30038,33,689;QS=0.989464,0.0105356,0;VDB=0.36;SGB=-0.453602;RPBZ=0.589131;MQBZ=0;MQSBZ=0;BQBZ=-2.37279;NMBZ=2.34191;SCBZ=1.62638;FS=0;MQ0F=0 PL:AD 0,162,255,190,255,255:63,2,0 -000000F 606 . T G,<*> 0 . DP=65;I16=34,29,1,0,2247,87073,22,484,3780,226800,60,3600,1287,29883,13,169;QS=0.990304,0.0096959,0;SGB=-0.379885;RPBZ=1.00206;MQBZ=0;MQSBZ=0;BQBZ=-1.38823;NMBZ=-0.596984;SCBZ=-1.04683;FS=0;MQ0F=0 PL:AD 0,170,255,190,255,255:63,1,0 +000000F 605 . A G,<*> 0 . DP=66;I16=35,28,1,1,2254,85780,24,288,3780,226800,120,7200,1292,30038,33,689;QS=0.989464,0.0105356,0;VDB=0.36;SGB=-0.453602;RPBZ=0.589131;MQBZ=0;MQSBZ=0;BQBZ=-2.37279;SCBZ=1.62638;FS=0;MQ0F=0 PL:AD 0,162,255,190,255,255:63,2,0 +000000F 606 . T G,<*> 0 . DP=65;I16=34,29,1,0,2247,87073,22,484,3780,226800,60,3600,1287,29883,13,169;QS=0.990304,0.0096959,0;SGB=-0.379885;RPBZ=1.00206;MQBZ=0;MQSBZ=0;BQBZ=-1.38823;SCBZ=-1.04683;FS=0;MQ0F=0 PL:AD 0,170,255,190,255,255:63,1,0 000000F 607 . G <*> 0 . DP=64;I16=35,28,0,0,2255,86451,0,0,3780,226800,0,0,1255,29027,0,0;QS=1,0;MQ0F=0 PL:AD 0,190,255:63,0 -000000F 608 . T G,<*> 0 . DP=62;I16=33,27,1,0,2177,84023,8,64,3600,216000,60,3600,1182,27240,25,625;QS=0.996339,0.00366133,0;SGB=-0.379885;RPBZ=0.0852552;MQBZ=0;MQSBZ=0;BQBZ=-1.89659;NMBZ=0.540939;SCBZ=-1.04111;FS=0;MQ0F=0 PL:AD 0,166,255,181,255,255:60,1,0 -000000F 609 . A G,<*> 0 . DP=60;I16=33,25,0,1,2036,77468,12,144,3480,208800,60,3600,1139,26307,25,625;QS=0.994141,0.00585938,0;SGB=-0.379885;RPBZ=-0.0881423;MQBZ=0;MQSBZ=0;BQBZ=-1.68674;NMBZ=1.64902;SCBZ=1.23654;FS=0;MQ0F=0 PL:AD 0,160,255,175,255,255:58,1,0 +000000F 608 . T G,<*> 0 . DP=62;I16=33,27,1,0,2177,84023,8,64,3600,216000,60,3600,1182,27240,25,625;QS=0.996339,0.00366133,0;SGB=-0.379885;RPBZ=0.0852552;MQBZ=0;MQSBZ=0;BQBZ=-1.89659;SCBZ=-1.04111;FS=0;MQ0F=0 PL:AD 0,166,255,181,255,255:60,1,0 +000000F 609 . A G,<*> 0 . DP=60;I16=33,25,0,1,2036,77468,12,144,3480,208800,60,3600,1139,26307,25,625;QS=0.994141,0.00585938,0;SGB=-0.379885;RPBZ=-0.0881423;MQBZ=0;MQSBZ=0;BQBZ=-1.68674;SCBZ=1.23654;FS=0;MQ0F=0 PL:AD 0,160,255,175,255,255:58,1,0 000000F 610 . A <*> 0 . DP=59;I16=33,25,0,0,2025,77505,0,0,3480,208800,0,0,1144,26524,0,0;QS=1,0;MQ0F=0 PL:AD 0,175,255:58,0 -000000F 611 . C T,<*> 0 . DP=55;I16=14,12,16,12,990,39320,1009,38281,1560,93600,1680,100800,576,13946,550,12206;QS=0.495248,0.504752,0;VDB=1.84196e-06;SGB=-0.693054;RPBZ=1.75927;MQBZ=0;MQSBZ=0;BQBZ=-0.270305;NMBZ=-0.720132;SCBZ=-0.614376;FS=0;MQ0F=0 PL:AD 255,0,255,255,255,255:26,28,0 +000000F 611 . C T,<*> 0 . DP=55;I16=14,12,16,12,990,39320,1009,38281,1560,93600,1680,100800,576,13946,550,12206;QS=0.495248,0.504752,0;VDB=1.84196e-06;SGB=-0.693054;RPBZ=1.75927;MQBZ=0;MQSBZ=0;BQBZ=-0.270305;SCBZ=-0.614376;FS=0;MQ0F=0 PL:AD 255,0,255,255,255,255:26,28,0 000000F 612 . T <*> 0 . DP=54;I16=29,24,0,0,1898,72790,0,0,3180,190800,0,0,1111,25815,0,0;QS=1,0;MQ0F=0 PL:AD 0,160,255:53,0 -000000F 613 . A G,C,<*> 0 . DP=54;I16=27,24,2,0,1946,77058,24,288,3060,183600,120,7200,1046,24258,50,1250;QS=0.987817,0.00609137,0.00609137,0;VDB=0.06;SGB=-0.453602;RPBZ=0.537207;MQBZ=0;MQSBZ=0;BQBZ=-2.67554;NMBZ=0.842481;SCBZ=0.495445;FS=0;MQ0F=0 PL:AD 0,139,255,139,255,255,154,255,255,255:51,1,1,0 -000000F 614 . A C,<*> 0 . DP=53;I16=28,23,0,1,1870,73000,12,144,3060,183600,60,3600,1054,24458,25,625;QS=0.993624,0.0063762,0;SGB=-0.379885;RPBZ=0.033359;MQBZ=0;MQSBZ=0;BQBZ=-1.88;NMBZ=1.70474;SCBZ=1.24225;FS=0;MQ0F=0 PL:AD 0,139,255,154,255,255:51,1,0 +000000F 613 . A G,C,<*> 0 . DP=54;I16=27,24,2,0,1946,77058,24,288,3060,183600,120,7200,1046,24258,50,1250;QS=0.987817,0.00609137,0.00609137,0;VDB=0.06;SGB=-0.453602;RPBZ=0.537207;MQBZ=0;MQSBZ=0;BQBZ=-2.67554;SCBZ=0.495445;FS=0;MQ0F=0 PL:AD 0,139,255,139,255,255,154,255,255,255:51,1,1,0 +000000F 614 . A C,<*> 0 . DP=53;I16=28,23,0,1,1870,73000,12,144,3060,183600,60,3600,1054,24458,25,625;QS=0.993624,0.0063762,0;SGB=-0.379885;RPBZ=0.033359;MQBZ=0;MQSBZ=0;BQBZ=-1.88;SCBZ=1.24225;FS=0;MQ0F=0 PL:AD 0,139,255,154,255,255:51,1,0 000000F 615 . T <*> 0 . DP=53;I16=28,24,0,0,1924,74686,0,0,3120,187200,0,0,1061,24643,0,0;QS=1,0;MQ0F=0 PL:AD 0,157,255:52,0 -000000F 616 . T G,<*> 0 . DP=53;I16=28,23,0,1,1815,69225,12,144,3060,183600,60,3600,1017,23565,25,625;QS=0.993432,0.00656814,0;SGB=-0.379885;RPBZ=-0.833529;MQBZ=0;MQSBZ=0;BQBZ=-1.66586;NMBZ=-0.200558;SCBZ=0.352496;FS=0;MQ0F=0 PL:AD 0,139,255,154,255,255:51,1,0 +000000F 616 . T G,<*> 0 . DP=53;I16=28,23,0,1,1815,69225,12,144,3060,183600,60,3600,1017,23565,25,625;QS=0.993432,0.00656814,0;SGB=-0.379885;RPBZ=-0.833529;MQBZ=0;MQSBZ=0;BQBZ=-1.66586;SCBZ=0.352496;FS=0;MQ0F=0 PL:AD 0,139,255,154,255,255:51,1,0 000000F 617 . T <*> 0 . DP=52;I16=27,24,0,0,1844,70962,0,0,3060,183600,0,0,1024,23774,0,0;QS=1,0;MQ0F=0 PL:AD 0,154,255:51,0 000000F 618 . C <*> 0 . DP=52;I16=27,24,0,0,1782,67390,0,0,3060,183600,0,0,1005,23345,0,0;QS=1,0;MQ0F=0 PL:AD 0,154,255:51,0 -000000F 619 . A C,<*> 0 . DP=52;I16=26,24,1,0,1756,66842,12,144,3000,180000,60,3600,961,22329,25,625;QS=0.993213,0.00678733,0;SGB=-0.379885;RPBZ=0.612053;MQBZ=0;MQSBZ=0;BQBZ=-1.58836;NMBZ=0.647334;SCBZ=1.65684;FS=0;MQ0F=0 PL:AD 0,136,255,151,255,255:50,1,0 +000000F 619 . A C,<*> 0 . DP=52;I16=26,24,1,0,1756,66842,12,144,3000,180000,60,3600,961,22329,25,625;QS=0.993213,0.00678733,0;SGB=-0.379885;RPBZ=0.612053;MQBZ=0;MQSBZ=0;BQBZ=-1.58836;SCBZ=1.65684;FS=0;MQ0F=0 PL:AD 0,136,255,151,255,255:50,1,0 000000F 620 . A <*> 0 . DP=50;I16=25,24,0,0,1670,63616,0,0,2940,176400,0,0,969,22599,0,0;QS=1,0;MQ0F=0 PL:AD 0,148,255:49,0 000000F 621 . C <*> 0 . DP=49;I16=24,24,0,0,1738,67580,0,0,2880,172800,0,0,953,22277,0,0;QS=1,0;MQ0F=0 PL:AD 0,144,255:48,0 000000F 622 . T <*> 0 . DP=47;I16=23,23,0,0,1642,63060,0,0,2760,165600,0,0,921,21681,0,0;QS=1,0;MQ0F=0 PL:AD 0,138,255:46,0 -000000F 623 . A G,C,<*> 0 . DP=46;I16=22,21,1,1,1593,61369,24,288,2580,154800,120,7200,862,20368,44,986;QS=0.985158,0.00742115,0.00742115,0;VDB=0.28;SGB=-0.453602;RPBZ=0.110272;MQBZ=0;MQSBZ=0;BQBZ=-2.46441;NMBZ=0.552785;SCBZ=-0.699329;FS=0;MQ0F=0 PL:AD 0,116,255,116,255,255,129,255,255,255:43,1,1,0 +000000F 623 . A G,C,<*> 0 . DP=46;I16=22,21,1,1,1593,61369,24,288,2580,154800,120,7200,862,20368,44,986;QS=0.985158,0.00742115,0.00742115,0;VDB=0.28;SGB=-0.453602;RPBZ=0.110272;MQBZ=0;MQSBZ=0;BQBZ=-2.46441;SCBZ=-0.699329;FS=0;MQ0F=0 PL:AD 0,116,255,116,255,255,129,255,255,255:43,1,1,0 000000F 624 . T <*> 0 . DP=45;I16=22,22,0,0,1522,57304,0,0,2640,158400,0,0,892,21056,0,0;QS=1,0;MQ0F=0 PL:AD 0,132,255:44,0 000000F 625 . C <*> 0 . DP=43;I16=20,23,0,0,1462,54230,0,0,2580,154800,0,0,905,21409,0,0;QS=1,0;MQ0F=0 PL:AD 0,129,255:43,0 -000000F 626 . T A,<*> 0 . DP=42;I16=19,22,0,1,1407,52739,12,144,2460,147600,60,3600,869,20535,25,625;QS=0.991543,0.00845666,0;SGB=-0.379885;RPBZ=0.0826192;MQBZ=0;MQSBZ=0;BQBZ=-1.63079;NMBZ=-0.0413668;SCBZ=-0.998652;FS=0;MQ0F=0 PL:AD 0,110,255,123,255,255:41,1,0 +000000F 626 . T A,<*> 0 . DP=42;I16=19,22,0,1,1407,52739,12,144,2460,147600,60,3600,869,20535,25,625;QS=0.991543,0.00845666,0;SGB=-0.379885;RPBZ=0.0826192;MQBZ=0;MQSBZ=0;BQBZ=-1.63079;SCBZ=-0.998652;FS=0;MQ0F=0 PL:AD 0,110,255,123,255,255:41,1,0 000000F 627 . A <*> 0 . DP=42;I16=19,23,0,0,1458,54660,0,0,2520,151200,0,0,880,20786,0,0;QS=1,0;MQ0F=0 PL:AD 0,126,255:42,0 -000000F 628 . G C,<*> 0 . DP=41;I16=17,23,1,0,1491,57863,12,144,2400,144000,60,3600,838,19618,24,576;QS=0.992016,0.00798403,0;SGB=-0.379885;RPBZ=0.296217;MQBZ=0;MQSBZ=0;BQBZ=-1.99912;NMBZ=-0.720676;SCBZ=-0.981384;FS=0;MQ0F=0 PL:AD 0,107,255,120,255,255:40,1,0 +000000F 628 . G C,<*> 0 . DP=41;I16=17,23,1,0,1491,57863,12,144,2400,144000,60,3600,838,19618,24,576;QS=0.992016,0.00798403,0;SGB=-0.379885;RPBZ=0.296217;MQBZ=0;MQSBZ=0;BQBZ=-1.99912;SCBZ=-0.981384;FS=0;MQ0F=0 PL:AD 0,107,255,120,255,255:40,1,0 000000F 629 . T <*> 0 . DP=40;I16=18,22,0,0,1452,55272,0,0,2400,144000,0,0,827,19349,0,0;QS=1,0;MQ0F=0 PL:AD 0,120,255:40,0 000000F 630 . C <*> 0 . DP=38;I16=16,22,0,0,1338,50174,0,0,2280,136800,0,0,812,18860,0,0;QS=1,0;MQ0F=0 PL:AD 0,114,255:38,0 -000000F 631 . T G,<*> 0 . DP=37;I16=14,22,1,0,1280,48224,32,1024,2160,129600,60,3600,783,18083,11,121;QS=0.97561,0.0243902,0;SGB=-0.379885;RPBZ=1.36088;MQBZ=0;MQSBZ=0;BQBZ=-1.06419;NMBZ=0.939374;SCBZ=-0.906765;FS=0;MQ0F=0 PL:AD 0,79,255,108,255,255:36,1,0 +000000F 631 . T G,<*> 0 . DP=37;I16=14,22,1,0,1280,48224,32,1024,2160,129600,60,3600,783,18083,11,121;QS=0.97561,0.0243902,0;SGB=-0.379885;RPBZ=1.36088;MQBZ=0;MQSBZ=0;BQBZ=-1.06419;SCBZ=-0.906765;FS=0;MQ0F=0 PL:AD 0,79,255,108,255,255:36,1,0 000000F 632 . T <*> 0 . DP=36;I16=15,21,0,0,1320,50548,0,0,2160,129600,0,0,761,17359,0,0;QS=1,0;MQ0F=0 PL:AD 0,108,255:36,0 -000000F 633 . C A,<*> 0 . DP=35;I16=14,19,0,2,1183,44803,24,288,1980,118800,120,7200,678,15322,47,1109;QS=0.980116,0.019884,0;VDB=0.26;SGB=-0.453602;RPBZ=0.463397;MQBZ=0;MQSBZ=0;BQBZ=-2.3085;NMBZ=1.56853;SCBZ=1.47371;FS=0;MQ0F=0 PL:AD 0,76,255,99,255,255:33,2,0 +000000F 633 . C A,<*> 0 . DP=35;I16=14,19,0,2,1183,44803,24,288,1980,118800,120,7200,678,15322,47,1109;QS=0.980116,0.019884,0;VDB=0.26;SGB=-0.453602;RPBZ=0.463397;MQBZ=0;MQSBZ=0;BQBZ=-2.3085;SCBZ=1.47371;FS=0;MQ0F=0 PL:AD 0,76,255,99,255,255:33,2,0 000000F 634 . C <*> 0 . DP=35;I16=14,21,0,0,1290,49572,0,0,2100,126000,0,0,708,15898,0,0;QS=1,0;MQ0F=0 PL:AD 0,105,255:35,0 000000F 635 . T <*> 0 . DP=35;I16=14,21,0,0,1242,47888,0,0,2100,126000,0,0,691,15399,0,0;QS=1,0;MQ0F=0 PL:AD 0,105,255:35,0 -000000F 636 . C T,<*> 0 . DP=34;I16=13,20,1,0,1163,44105,12,144,1980,118800,60,3600,643,14453,16,256;QS=0.989787,0.0102128,0;SGB=-0.379885;RPBZ=0.66524;MQBZ=0;MQSBZ=0;BQBZ=-1.57615;NMBZ=-0.511566;SCBZ=-0.84147;FS=0;MQ0F=0 PL:AD 0,87,255,99,255,255:33,1,0 +000000F 636 . C T,<*> 0 . DP=34;I16=13,20,1,0,1163,44105,12,144,1980,118800,60,3600,643,14453,16,256;QS=0.989787,0.0102128,0;SGB=-0.379885;RPBZ=0.66524;MQBZ=0;MQSBZ=0;BQBZ=-1.57615;SCBZ=-0.84147;FS=0;MQ0F=0 PL:AD 0,87,255,99,255,255:33,1,0 000000F 637 . T <*> 0 . DP=33;I16=14,19,0,0,1151,43717,0,0,1980,118800,0,0,627,14033,0,0;QS=1,0;MQ0F=0 PL:AD 0,99,255:33,0 000000F 638 . A <*> 0 . DP=32;I16=13,19,0,0,1113,41153,0,0,1920,115200,0,0,605,13531,0,0;QS=1,0;MQ0F=0 PL:AD 0,96,255:32,0 -000000F 639 . A T,<*> 0 . DP=30;I16=13,16,0,1,965,34529,12,144,1740,104400,60,3600,577,12917,13,169;QS=0.987718,0.0122825,0;SGB=-0.379885;RPBZ=0.988773;MQBZ=0;MQSBZ=0;BQBZ=-1.63451;NMBZ=0.405999;SCBZ=-0.878553;FS=0;MQ0F=0 PL:AD 0,75,255,87,255,255:29,1,0 +000000F 639 . A T,<*> 0 . DP=30;I16=13,16,0,1,965,34529,12,144,1740,104400,60,3600,577,12917,13,169;QS=0.987718,0.0122825,0;SGB=-0.379885;RPBZ=0.988773;MQBZ=0;MQSBZ=0;BQBZ=-1.63451;SCBZ=-0.878553;FS=0;MQ0F=0 PL:AD 0,75,255,87,255,255:29,1,0 000000F 640 . A <*> 0 . DP=29;I16=12,17,0,0,994,36924,0,0,1740,104400,0,0,575,12621,0,0;QS=1,0;MQ0F=0 PL:AD 0,87,255:29,0 -000000F 641 . G T,<*> 0 . DP=27;I16=11,15,0,1,869,31995,12,144,1560,93600,60,3600,529,11623,11,121;QS=0.986379,0.0136209,0;SGB=-0.379885;RPBZ=1.35554;MQBZ=0;MQSBZ=0;BQBZ=-1.5086;NMBZ=-0.322848;SCBZ=-0.793551;FS=0;MQ0F=0 PL:AD 0,66,255,78,255,255:26,1,0 -000000F 642 . A C,<*> 0 . DP=26;I16=11,14,0,1,850,31010,22,484,1500,90000,60,3600,504,11078,9,81;QS=0.974771,0.0252294,0;SGB=-0.379885;RPBZ=1.41458;MQBZ=0;MQSBZ=0;BQBZ=-1.18957;NMBZ=1.27431;SCBZ=0.532911;FS=0;MQ0F=0 PL:AD 0,56,255,75,255,255:25,1,0 +000000F 641 . G T,<*> 0 . DP=27;I16=11,15,0,1,869,31995,12,144,1560,93600,60,3600,529,11623,11,121;QS=0.986379,0.0136209,0;SGB=-0.379885;RPBZ=1.35554;MQBZ=0;MQSBZ=0;BQBZ=-1.5086;SCBZ=-0.793551;FS=0;MQ0F=0 PL:AD 0,66,255,78,255,255:26,1,0 +000000F 642 . A C,<*> 0 . DP=26;I16=11,14,0,1,850,31010,22,484,1500,90000,60,3600,504,11078,9,81;QS=0.974771,0.0252294,0;SGB=-0.379885;RPBZ=1.41458;MQBZ=0;MQSBZ=0;BQBZ=-1.18957;SCBZ=0.532911;FS=0;MQ0F=0 PL:AD 0,56,255,75,255,255:25,1,0 000000F 643 . C <*> 0 . DP=26;I16=11,15,0,0,912,34334,0,0,1560,93600,0,0,499,10747,0,0;QS=1,0;MQ0F=0 PL:AD 0,78,255:26,0 -000000F 644 . C A,<*> 0 . DP=26;I16=11,14,0,1,869,31707,12,144,1500,90000,60,3600,464,9914,20,400;QS=0.986379,0.0136209,0;SGB=-0.379885;RPBZ=0.268045;MQBZ=0;MQSBZ=0;BQBZ=-1.6731;NMBZ=1.00586;SCBZ=0.989693;FS=0;MQ0F=0 PL:AD 0,63,255,75,255,255:25,1,0 +000000F 644 . C A,<*> 0 . DP=26;I16=11,14,0,1,869,31707,12,144,1500,90000,60,3600,464,9914,20,400;QS=0.986379,0.0136209,0;SGB=-0.379885;RPBZ=0.268045;MQBZ=0;MQSBZ=0;BQBZ=-1.6731;SCBZ=0.989693;FS=0;MQ0F=0 PL:AD 0,63,255,75,255,255:25,1,0 000000F 645 . C <*> 0 . DP=26;I16=11,15,0,0,911,33421,0,0,1560,93600,0,0,466,9764,0,0;QS=1,0;MQ0F=0 PL:AD 0,78,255:26,0 000000F 646 . C <*> 0 . DP=26;I16=11,15,0,0,850,29718,0,0,1560,93600,0,0,447,9201,0,0;QS=1,0;MQ0F=0 PL:AD 0,78,255:26,0 -000000F 647 . T C,<*> 0 . DP=26;I16=11,14,0,1,898,34076,12,144,1500,90000,60,3600,423,8651,5,25;QS=0.986813,0.0131868,0;SGB=-0.379885;RPBZ=1.14097;MQBZ=0;MQSBZ=0;BQBZ=-1.57982;NMBZ=0.737633;SCBZ=-0.760963;FS=0;MQ0F=0 PL:AD 0,63,255,75,255,255:25,1,0 +000000F 647 . T C,<*> 0 . DP=26;I16=11,14,0,1,898,34076,12,144,1500,90000,60,3600,423,8651,5,25;QS=0.986813,0.0131868,0;SGB=-0.379885;RPBZ=1.14097;MQBZ=0;MQSBZ=0;BQBZ=-1.57982;SCBZ=-0.760963;FS=0;MQ0F=0 PL:AD 0,63,255,75,255,255:25,1,0 000000F 648 . A <*> 0 . DP=26;I16=11,15,0,0,870,32110,0,0,1560,93600,0,0,407,8091,0,0;QS=1,0;MQ0F=0 PL:AD 0,78,255:26,0 000000F 649 . C <*> 0 . DP=26;I16=11,15,0,0,928,35102,0,0,1560,93600,0,0,386,7548,0,0;QS=1,0;MQ0F=0 PL:AD 0,78,255:26,0 -000000F 650 . T C,<*> 0 . DP=26;I16=11,14,0,1,897,33867,12,144,1500,90000,60,3600,359,6973,5,25;QS=0.986799,0.0132013,0;SGB=-0.379885;RPBZ=0.874779;MQBZ=0;MQSBZ=0;BQBZ=-1.67266;NMBZ=-1.4745;SCBZ=-0.760963;FS=0;MQ0F=0 PL:AD 0,63,255,75,255,255:25,1,0 +000000F 650 . T C,<*> 0 . DP=26;I16=11,14,0,1,897,33867,12,144,1500,90000,60,3600,359,6973,5,25;QS=0.986799,0.0132013,0;SGB=-0.379885;RPBZ=0.874779;MQBZ=0;MQSBZ=0;BQBZ=-1.67266;SCBZ=-0.760963;FS=0;MQ0F=0 PL:AD 0,63,255,75,255,255:25,1,0 000000F 651 . T <*> 0 . DP=26;I16=11,15,0,0,905,33255,0,0,1560,93600,0,0,342,6492,0,0;QS=1,0;MQ0F=0 PL:AD 0,78,255:26,0 000000F 652 . T <*> 0 . DP=25;I16=11,14,0,0,891,32693,0,0,1500,90000,0,0,321,6029,0,0;QS=1,0;MQ0F=0 PL:AD 0,75,255:25,0 000000F 653 . A <*> 0 . DP=21;I16=9,12,0,0,804,31130,0,0,1260,75600,0,0,303,5555,0,0;QS=1,0;MQ0F=0 PL:AD 0,63,255:21,0 000000F 654 . A <*> 0 . DP=21;I16=9,12,0,0,659,22061,0,0,1260,75600,0,0,285,5117,0,0;QS=1,0;MQ0F=0 PL:AD 0,63,255:21,0 000000F 655 . C <*> 0 . DP=21;I16=9,12,0,0,664,22342,0,0,1260,75600,0,0,266,4666,0,0;QS=1,0;MQ0F=0 PL:AD 0,63,255:21,0 -000000F 655 . CACAATACAA CACAA 0 . INDEL;IDV=6;IMF=0.285714;DP=21;I16=4,11,5,1,1800,216000,720,86400,900,54000,360,21600,166,2878,100,1788;QS=0.371728,0.628272;VDB=0.00189453;SGB=-0.616816;RPBZ=-2.81289;MQBZ=0;MQSBZ=0;BQBZ=-1.67266;NMBZ=-2.79934;SCBZ=-2.52262;FS=0;MQ0F=0 PL:AD 129,0,28:15,6 +000000F 655 . CACAATACAA CACAA 0 . INDEL;IDV=6;IMF=0.285714;DP=21;I16=4,11,5,1,1800,216000,720,86400,900,54000,360,21600,166,2878,100,1788;QS=0.371728,0.628272;VDB=0.00189453;SGB=-0.616816;RPBZ=-2.81289;MQBZ=0;MQSBZ=0;BQBZ=-1.67266;SCBZ=-2.52262;FS=0;MQ0F=0 PL:AD 129,0,28:15,6 000000F 656 . A <*> 0 . DP=11;I16=4,7,0,0,404,15690,0,0,660,39600,0,0,141,2411,0,0;QS=1,0;MQ0F=0 PL:AD 0,33,255:11,0 000000F 657 . C <*> 0 . DP=11;I16=4,7,0,0,413,15607,0,0,660,39600,0,0,131,2189,0,0;QS=1,0;MQ0F=0 PL:AD 0,33,255:11,0 000000F 658 . A <*> 0 . DP=10;I16=3,7,0,0,121,1651,0,0,600,36000,0,0,122,1986,0,0;QS=1,0;MQ0F=0 PL:AD 0,30,79:10,0 -000000F 658 . AA AAATTA 0 . INDEL;IDV=2;IMF=0.125;DP=16;I16=5,6,1,2,1100,110000,300,30000,660,39600,180,10800,141,2389,50,902;QS=0.418605,0.581395;VDB=0.045681;SGB=-0.511536;RPBZ=-1.70026;MQBZ=0;MQSBZ=0;BQBZ=-1.67266;NMBZ=-1.17947;SCBZ=-1.35678;FS=0;MQ0F=0 PL:AD 76,0,29:11,3 +000000F 658 . AA AAATTA 0 . INDEL;IDV=2;IMF=0.125;DP=16;I16=5,6,1,2,1100,110000,300,30000,660,39600,180,10800,141,2389,50,902;QS=0.418605,0.581395;VDB=0.045681;SGB=-0.511536;RPBZ=-1.70026;MQBZ=0;MQSBZ=0;BQBZ=-1.67266;SCBZ=-1.35678;FS=0;MQ0F=0 PL:AD 76,0,29:11,3 000000F 659 . A <*> 0 . DP=10;I16=3,5,0,0,86,1088,0,0,480,28800,0,0,75,1077,0,0;QS=1,0;MQ0F=0 PL:AD 0,24,63:8,0 000000F 660 . T <*> 0 . DP=2;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;QS=0,0;MQ0F=0 PL:AD 0,0,0:0,0 000000F 661 . A <*> 0 . DP=8;I16=0,2,0,0,8,32,0,0,120,7200,0,0,26,340,0,0;QS=1,0;MQ0F=0 PL:AD 0,6,7:2,0 diff --git a/test/mpileup/indel-AD.2.out b/test/mpileup/indel-AD.2.out index 6d84471e9..23b51dda6 100644 --- a/test/mpileup/indel-AD.2.out +++ b/test/mpileup/indel-AD.2.out @@ -11,7 +11,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -22,4 +21,4 @@ ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample 11 75 . G <*> 0 . DP=68;I16=6,62,0,0,2437,87909,0,0,3770,217210,0,0,838,15940,0,0;QS=1,0;MQ0F=0 PL:AD 0,205,255:68,0 -11 75 . GTAAAATAAAATAAAATAAAATAAA GTAAAATAAAATAAAATAAAATAAAATAAA 0 . INDEL;IDV=6;IMF=0.0882353;DP=68;I16=5,57,1,5,7440,892800,720,86400,3596,212164,174,5046,691,12331,147,3609;QS=0.834915,0.165085;VDB=0.00452698;SGB=-0.616816;RPBZ=-3.24592;MQBZ=-6.13241;MQSBZ=0;BQBZ=0;NMBZ=-0.546919;SCBZ=-0.546919;FS=0;MQ0F=0 PL:AD 0,54,150:62,6 +11 75 . GTAAAATAAAATAAAATAAAATAAA GTAAAATAAAATAAAATAAAATAAAATAAA 0 . INDEL;IDV=6;IMF=0.0882353;DP=68;I16=5,57,1,5,7440,892800,720,86400,3596,212164,174,5046,691,12331,147,3609;QS=0.834915,0.165085;VDB=0.00452698;SGB=-0.616816;RPBZ=-3.24592;MQBZ=-6.13241;MQSBZ=0;BQBZ=0;SCBZ=-0.546919;FS=0;MQ0F=0 PL:AD 0,54,150:62,6 diff --git a/test/mpileup/indel-AD.3.out b/test/mpileup/indel-AD.3.out index 6d84471e9..23b51dda6 100644 --- a/test/mpileup/indel-AD.3.out +++ b/test/mpileup/indel-AD.3.out @@ -11,7 +11,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -22,4 +21,4 @@ ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample 11 75 . G <*> 0 . DP=68;I16=6,62,0,0,2437,87909,0,0,3770,217210,0,0,838,15940,0,0;QS=1,0;MQ0F=0 PL:AD 0,205,255:68,0 -11 75 . GTAAAATAAAATAAAATAAAATAAA GTAAAATAAAATAAAATAAAATAAAATAAA 0 . INDEL;IDV=6;IMF=0.0882353;DP=68;I16=5,57,1,5,7440,892800,720,86400,3596,212164,174,5046,691,12331,147,3609;QS=0.834915,0.165085;VDB=0.00452698;SGB=-0.616816;RPBZ=-3.24592;MQBZ=-6.13241;MQSBZ=0;BQBZ=0;NMBZ=-0.546919;SCBZ=-0.546919;FS=0;MQ0F=0 PL:AD 0,54,150:62,6 +11 75 . GTAAAATAAAATAAAATAAAATAAA GTAAAATAAAATAAAATAAAATAAAATAAA 0 . INDEL;IDV=6;IMF=0.0882353;DP=68;I16=5,57,1,5,7440,892800,720,86400,3596,212164,174,5046,691,12331,147,3609;QS=0.834915,0.165085;VDB=0.00452698;SGB=-0.616816;RPBZ=-3.24592;MQBZ=-6.13241;MQSBZ=0;BQBZ=0;SCBZ=-0.546919;FS=0;MQ0F=0 PL:AD 0,54,150:62,6 diff --git a/test/mpileup/indel-AD.4.out b/test/mpileup/indel-AD.4.out index 6d84471e9..23b51dda6 100644 --- a/test/mpileup/indel-AD.4.out +++ b/test/mpileup/indel-AD.4.out @@ -11,7 +11,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -22,4 +21,4 @@ ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample 11 75 . G <*> 0 . DP=68;I16=6,62,0,0,2437,87909,0,0,3770,217210,0,0,838,15940,0,0;QS=1,0;MQ0F=0 PL:AD 0,205,255:68,0 -11 75 . GTAAAATAAAATAAAATAAAATAAA GTAAAATAAAATAAAATAAAATAAAATAAA 0 . INDEL;IDV=6;IMF=0.0882353;DP=68;I16=5,57,1,5,7440,892800,720,86400,3596,212164,174,5046,691,12331,147,3609;QS=0.834915,0.165085;VDB=0.00452698;SGB=-0.616816;RPBZ=-3.24592;MQBZ=-6.13241;MQSBZ=0;BQBZ=0;NMBZ=-0.546919;SCBZ=-0.546919;FS=0;MQ0F=0 PL:AD 0,54,150:62,6 +11 75 . GTAAAATAAAATAAAATAAAATAAA GTAAAATAAAATAAAATAAAATAAAATAAA 0 . INDEL;IDV=6;IMF=0.0882353;DP=68;I16=5,57,1,5,7440,892800,720,86400,3596,212164,174,5046,691,12331,147,3609;QS=0.834915,0.165085;VDB=0.00452698;SGB=-0.616816;RPBZ=-3.24592;MQBZ=-6.13241;MQSBZ=0;BQBZ=0;SCBZ=-0.546919;FS=0;MQ0F=0 PL:AD 0,54,150:62,6 diff --git a/test/mpileup/mpileup-SCR.out b/test/mpileup/mpileup-SCR.out index 31eea650e..1134b26a6 100644 --- a/test/mpileup/mpileup-SCR.out +++ b/test/mpileup/mpileup-SCR.out @@ -11,7 +11,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -33,7 +32,7 @@ 1 72 . C <*> 0 . DP=9;SCR=3;I16=6,3,0,0,318,11254,0,0,456,24672,0,0,82,1074,0,0;QS=1,0;MQ0F=0 PL:SCR 0,27,216:3 1 73 . C <*> 0 . DP=10;SCR=3;I16=7,3,0,0,348,12146,0,0,516,28272,0,0,91,1247,0,0;QS=1,0;MQ0F=0 PL:SCR 0,30,224:3 1 74 . C <*> 0 . DP=10;SCR=3;I16=7,3,0,0,350,12278,0,0,516,28272,0,0,100,1388,0,0;QS=1,0;MQ0F=0 PL:SCR 0,30,228:3 -1 75 . C G,<*> 0 . DP=12;SCR=4;I16=6,2,3,1,274,9444,132,4392,480,28800,119,3601,55,501,54,1046;QS=0.697201,0.302799,0;VDB=0.0533436;SGB=-0.556411;RPBZ=1.63069;MQBZ=-3.26599;MQSBZ=0.111111;BQBZ=-0.515877;NMBZ=3.31662;SCBZ=3.23349;FS=0;MQ0F=0 PL:SCR 73,0,170,97,182,252:4 +1 75 . C G,<*> 0 . DP=12;SCR=4;I16=6,2,3,1,274,9444,132,4392,480,28800,119,3601,55,501,54,1046;QS=0.697201,0.302799,0;VDB=0.0533436;SGB=-0.556411;RPBZ=1.63069;MQBZ=-3.26599;MQSBZ=0.111111;BQBZ=-0.515877;SCBZ=3.23349;FS=0;MQ0F=0 PL:SCR 73,0,170,97,182,252:4 1 76 . C <*> 0 . DP=12;SCR=4;I16=9,3,0,0,410,14076,0,0,599,32401,0,0,120,1726,0,0;QS=1,0;MQ0F=0 PL:SCR 0,36,233:4 1 77 . G <*> 0 . DP=12;SCR=4;I16=9,3,0,0,385,12495,0,0,599,32401,0,0,131,1927,0,0;QS=1,0;MQ0F=0 PL:SCR 0,36,225:4 1 78 . T <*> 0 . DP=12;SCR=4;I16=9,3,0,0,365,11201,0,0,599,32401,0,0,142,2150,0,0;QS=1,0;MQ0F=0 PL:SCR 0,36,213:4 diff --git a/test/mpileup/mpileup-filter.1.out b/test/mpileup/mpileup-filter.1.out index b3aacdc87..ecd87f1f8 100644 --- a/test/mpileup/mpileup-filter.1.out +++ b/test/mpileup/mpileup-filter.1.out @@ -11,7 +11,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= diff --git a/test/mpileup/mpileup-filter.2.out b/test/mpileup/mpileup-filter.2.out index 6e8064a6e..dcd95f2fe 100644 --- a/test/mpileup/mpileup-filter.2.out +++ b/test/mpileup/mpileup-filter.2.out @@ -11,7 +11,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= diff --git a/test/mpileup/mpileup.1.out b/test/mpileup/mpileup.1.out index 7f63e9d69..93b366e20 100644 --- a/test/mpileup/mpileup.1.out +++ b/test/mpileup/mpileup.1.out @@ -11,7 +11,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -23,29 +22,29 @@ 17 100 . C <*> 0 . DP=18;I16=16,1,0,0,672,27586,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0 PL 0,27,189 0,9,118 0,15,134 17 101 . C <*> 0 . DP=18;I16=16,1,0,0,630,24730,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL 0,27,182 0,9,108 0,15,132 17 102 . C <*> 0 . DP=18;I16=16,1,0,0,676,27812,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL 0,27,188 0,9,121 0,15,139 -17 103 . T C,<*> 0 . DP=18;I16=15,1,1,0,668,28542,6,36,929,54841,29,841,323,7035,6,36;QS=2.98256,0.0174419,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64924;NMBZ=2.45514;SCBZ=4;FS=0;MQ0F=0 PL 0,17,184,24,187,185 0,9,118,9,118,118 0,15,147,15,147,147 -17 104 . G C,<*> 0 . DP=18;I16=15,1,1,0,601,24163,3,9,929,54841,29,841,320,6884,7,49;QS=2.98726,0.0127389,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64309;NMBZ=2.45514;SCBZ=4;FS=0;MQ0F=0 PL 0,18,173,24,176,173 0,9,101,9,101,101 0,15,133,15,133,133 +17 103 . T C,<*> 0 . DP=18;I16=15,1,1,0,668,28542,6,36,929,54841,29,841,323,7035,6,36;QS=2.98256,0.0174419,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64924;SCBZ=4;FS=0;MQ0F=0 PL 0,17,184,24,187,185 0,9,118,9,118,118 0,15,147,15,147,147 +17 104 . G C,<*> 0 . DP=18;I16=15,1,1,0,601,24163,3,9,929,54841,29,841,320,6884,7,49;QS=2.98726,0.0127389,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64309;SCBZ=4;FS=0;MQ0F=0 PL 0,18,173,24,176,173 0,9,101,9,101,101 0,15,133,15,133,133 17 105 . G <*> 0 . DP=19;I16=17,1,0,0,603,22351,0,0,1018,59282,0,0,325,6815,0,0;QS=3,0;MQ0F=0 PL 0,30,171 0,9,106 0,15,125 17 106 . G <*> 0 . DP=19;I16=17,1,0,0,636,25058,0,0,1018,59282,0,0,324,6718,0,0;QS=3,0;MQ0F=0 PL 0,30,190 0,9,92 0,15,124 17 107 . C <*> 0 . DP=19;I16=17,1,0,0,686,27952,0,0,1018,59282,0,0,323,6643,0,0;QS=3,0;MQ0F=0 PL 0,30,192 0,9,119 0,15,136 17 108 . C <*> 0 . DP=19;I16=17,1,0,0,681,27429,0,0,1018,59282,0,0,322,6590,0,0;QS=3,0;MQ0F=0 PL 0,30,190 0,9,119 0,15,135 -17 109 . T C,<*> 0 . DP=19;I16=16,1,1,0,716,30648,2,4,989,58441,29,841,309,6415,12,144;QS=2.98922,0.0107817,0;SGB=-0.556633;RPBZ=-0.674966;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.6661;NMBZ=2.52179;SCBZ=3;FS=0;MQ0F=0 PL 0,20,191,27,194,191 0,9,120,9,120,120 0,15,150,15,150,150 +17 109 . T C,<*> 0 . DP=19;I16=16,1,1,0,716,30648,2,4,989,58441,29,841,309,6415,12,144;QS=2.98922,0.0107817,0;SGB=-0.556633;RPBZ=-0.674966;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.6661;SCBZ=3;FS=0;MQ0F=0 PL 0,20,191,27,194,191 0,9,120,9,120,120 0,15,150,15,150,150 17 110 . G <*> 0 . DP=19;I16=17,1,0,0,688,28036,0,0,1018,59282,0,0,320,6550,0,0;QS=3,0;MQ0F=0 PL 0,30,194 0,9,113 0,15,136 17 111 . G <*> 0 . DP=19;I16=17,1,0,0,573,21453,0,0,1018,59282,0,0,318,6514,0,0;QS=3,0;MQ0F=0 PL 0,30,167 0,9,95 0,15,119 -17 112 . C G,<*> 0 . DP=19;I16=16,1,1,0,657,26565,2,4,989,58441,29,841,301,6277,15,225;QS=2.98907,0.010929,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65292;NMBZ=2.52179;SCBZ=3;FS=0;MQ0F=0 PL 0,20,187,27,190,187 0,9,103,9,103,103 0,15,135,15,135,135 -17 113 . A G,<*> 0 . DP=19;I16=16,1,1,0,635,25055,4,16,989,58441,29,841,297,6207,16,256;QS=2.98817,0.0118343,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65205;NMBZ=2.52179;SCBZ=3;FS=0;MQ0F=0 PL 0,20,172,27,175,172 0,9,102,9,102,102 0,15,139,15,139,139 +17 112 . C G,<*> 0 . DP=19;I16=16,1,1,0,657,26565,2,4,989,58441,29,841,301,6277,15,225;QS=2.98907,0.010929,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65292;SCBZ=3;FS=0;MQ0F=0 PL 0,20,187,27,190,187 0,9,103,9,103,103 0,15,135,15,135,135 +17 113 . A G,<*> 0 . DP=19;I16=16,1,1,0,635,25055,4,16,989,58441,29,841,297,6207,16,256;QS=2.98817,0.0118343,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65205;SCBZ=3;FS=0;MQ0F=0 PL 0,20,172,27,175,172 0,9,102,9,102,102 0,15,139,15,139,139 17 114 . C <*> 0 . DP=19;I16=17,1,0,0,660,25876,0,0,1018,59282,0,0,310,6446,0,0;QS=3,0;MQ0F=0 PL 0,30,181 0,9,113 0,15,133 -17 115 . C A,<*> 0 . DP=21;I16=17,2,1,0,688,27426,12,144,1078,62882,29,841,283,5827,25,625;QS=2.88785,0.11215,0;SGB=-0.556633;RPBZ=0.260329;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.47798;NMBZ=2.3712;SCBZ=-0.418446;FS=0;MQ0F=0 PL 0,30,189,30,189,189 3,0,86,9,89,93 0,21,153,21,153,153 -17 116 . A C,<*> 0 . DP=21;I16=17,2,1,0,705,27791,2,4,1078,62882,29,841,287,6073,19,361;QS=2.98873,0.0112676,0;SGB=-0.556633;RPBZ=0.0867763;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.65814;NMBZ=2.65016;SCBZ=2.65016;FS=0;MQ0F=0 PL 0,20,179,27,182,179 0,9,102,9,102,102 0,21,175,21,175,175 +17 115 . C A,<*> 0 . DP=21;I16=17,2,1,0,688,27426,12,144,1078,62882,29,841,283,5827,25,625;QS=2.88785,0.11215,0;SGB=-0.556633;RPBZ=0.260329;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.47798;SCBZ=-0.418446;FS=0;MQ0F=0 PL 0,30,189,30,189,189 3,0,86,9,89,93 0,21,153,21,153,153 +17 116 . A C,<*> 0 . DP=21;I16=17,2,1,0,705,27791,2,4,1078,62882,29,841,287,6073,19,361;QS=2.98873,0.0112676,0;SGB=-0.556633;RPBZ=0.0867763;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.65814;SCBZ=2.65016;FS=0;MQ0F=0 PL 0,20,179,27,182,179 0,9,102,9,102,102 0,21,175,21,175,175 17 117 . G <*> 0 . DP=21;I16=18,2,0,0,715,28045,0,0,1107,63723,0,0,304,6444,0,0;QS=3,0;MQ0F=0 PL 0,30,185 0,9,97 0,21,177 17 118 . G <*> 0 . DP=20;I16=17,2,0,0,620,23470,0,0,1047,60123,0,0,303,6481,0,0;QS=3,0;MQ0F=0 PL 0,27,175 0,9,65 0,21,162 17 119 . G <*> 0 . DP=19;I16=16,2,0,0,619,23459,0,0,987,56523,0,0,301,6493,0,0;QS=3,0;MQ0F=0 PL 0,27,176 0,6,76 0,21,160 -17 120 . A G,<*> 0 . DP=19;I16=15,2,1,0,646,25392,4,16,958,55682,29,841,277,5999,23,529;QS=2.9873,0.0126984,0;SGB=-0.556633;RPBZ=0.28942;MQBZ=-2.23607;MQSBZ=-1.30384;BQBZ=-1.6486;NMBZ=3;SCBZ=3;FS=0;MQ0F=0 PL 0,18,171,24,174,171 0,6,88,6,88,88 0,21,171,21,171,171 +17 120 . A G,<*> 0 . DP=19;I16=15,2,1,0,646,25392,4,16,958,55682,29,841,277,5999,23,529;QS=2.9873,0.0126984,0;SGB=-0.556633;RPBZ=0.28942;MQBZ=-2.23607;MQSBZ=-1.30384;BQBZ=-1.6486;SCBZ=3;FS=0;MQ0F=0 PL 0,18,171,24,174,171 0,6,88,6,88,88 0,21,171,21,171,171 17 121 . G <*> 0 . DP=19;I16=16,2,0,0,650,25148,0,0,987,56523,0,0,298,6534,0,0;QS=3,0;MQ0F=0 PL 0,27,181 0,6,84 0,21,168 17 122 . C <*> 0 . DP=20;I16=17,2,0,0,696,27784,0,0,1047,60123,0,0,296,6560,0,0;QS=3,0;MQ0F=0 PL 0,27,180 0,9,107 0,21,178 17 123 . T <*> 0 . DP=18;I16=15,2,0,0,647,26145,0,0,927,52923,0,0,296,6554,0,0;QS=3,0;MQ0F=0 PL 0,24,170 0,9,123 0,18,166 17 124 . T <*> 0 . DP=19;I16=16,2,0,0,606,22002,0,0,987,56523,0,0,296,6564,0,0;QS=3,0;MQ0F=0 PL 0,27,154 0,9,114 0,18,154 -17 125 . A T,<*> 0 . DP=18;I16=14,2,1,0,589,22565,4,16,898,52082,29,841,272,5916,25,625;QS=2.98444,0.0155642,0;SGB=-0.556633;RPBZ=1.02125;MQBZ=-2.16025;MQSBZ=-1.23956;BQBZ=-1.64106;NMBZ=2.91548;SCBZ=2.91548;FS=0;MQ0F=0 PL 0,15,149,21,152,149 0,9,114,9,114,114 0,18,162,18,162,162 +17 125 . A T,<*> 0 . DP=18;I16=14,2,1,0,589,22565,4,16,898,52082,29,841,272,5916,25,625;QS=2.98444,0.0155642,0;SGB=-0.556633;RPBZ=1.02125;MQBZ=-2.16025;MQSBZ=-1.23956;BQBZ=-1.64106;SCBZ=2.91548;FS=0;MQ0F=0 PL 0,15,149,21,152,149 0,9,114,9,114,114 0,18,162,18,162,162 17 126 . A <*> 0 . DP=18;I16=15,2,0,0,629,24725,0,0,927,52923,0,0,298,6536,0,0;QS=3,0;MQ0F=0 PL 0,24,162 0,9,117 0,18,174 17 127 . C <*> 0 . DP=18;I16=15,2,0,0,627,24331,0,0,927,52923,0,0,299,6549,0,0;QS=3,0;MQ0F=0 PL 0,24,163 0,9,119 0,18,160 17 128 . A <*> 0 . DP=18;I16=15,2,0,0,660,26364,0,0,927,52923,0,0,300,6580,0,0;QS=3,0;MQ0F=0 PL 0,24,169 0,9,121 0,18,168 diff --git a/test/mpileup/mpileup.10.out b/test/mpileup/mpileup.10.out index bfd47a969..3328e27d8 100644 --- a/test/mpileup/mpileup.10.out +++ b/test/mpileup/mpileup.10.out @@ -11,7 +11,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -23,29 +22,29 @@ 17 100 . C <*> 0 . DP=16;I16=14,1,0,0,593,24461,0,0,838,48482,0,0,310,7132,0,0;QS=5,0;MQ0F=0 PL 0,3,19 0,6,78 0,12,128 0,9,118 0,15,134 17 101 . C <*> 0 . DP=16;I16=14,1,0,0,567,22633,0,0,838,48482,0,0,309,7011,0,0;QS=5,0;MQ0F=0 PL 0,3,22 0,6,79 0,12,123 0,9,108 0,15,132 17 102 . C <*> 0 . DP=16;I16=14,1,0,0,602,25074,0,0,838,48482,0,0,308,6904,0,0;QS=5,0;MQ0F=0 PL 0,3,20 0,6,78 0,12,129 0,9,121 0,15,139 -17 103 . T C,<*> 0 . DP=16;I16=13,1,1,0,588,25334,6,36,809,47641,29,841,301,6775,6,36;QS=4,1,0;SGB=-0.587685;RPBZ=-1.15831;MQBZ=-2.54951;MQSBZ=0.392232;BQBZ=-1.64233;NMBZ=2.31624;SCBZ=3.74166;FS=0;MQ0F=0 PL 6,3,0,6,3,6 0,6,79,6,79,79 0,12,131,12,131,131 0,9,118,9,118,118 0,15,147,15,147,147 -17 104 . G C,<*> 0 . DP=16;I16=13,1,1,0,536,21966,3,9,809,47641,29,841,298,6634,7,49;QS=4,1,0;SGB=-0.587685;RPBZ=-1.15831;MQBZ=-2.54951;MQSBZ=0.392232;BQBZ=-1.63041;NMBZ=2.31624;SCBZ=3.74166;FS=0;MQ0F=0 PL 4,3,0,4,3,4 0,6,78,6,78,78 0,12,123,12,123,123 0,9,101,9,101,101 0,15,133,15,133,133 +17 103 . T C,<*> 0 . DP=16;I16=13,1,1,0,588,25334,6,36,809,47641,29,841,301,6775,6,36;QS=4,1,0;SGB=-0.587685;RPBZ=-1.15831;MQBZ=-2.54951;MQSBZ=0.392232;BQBZ=-1.64233;SCBZ=3.74166;FS=0;MQ0F=0 PL 6,3,0,6,3,6 0,6,79,6,79,79 0,12,131,12,131,131 0,9,118,9,118,118 0,15,147,15,147,147 +17 104 . G C,<*> 0 . DP=16;I16=13,1,1,0,536,21966,3,9,809,47641,29,841,298,6634,7,49;QS=4,1,0;SGB=-0.587685;RPBZ=-1.15831;MQBZ=-2.54951;MQSBZ=0.392232;BQBZ=-1.63041;SCBZ=3.74166;FS=0;MQ0F=0 PL 4,3,0,4,3,4 0,6,78,6,78,78 0,12,123,12,123,123 0,9,101,9,101,101 0,15,133,15,133,133 17 105 . G <*> 0 . DP=17;I16=15,1,0,0,541,20301,0,0,898,52082,0,0,303,6571,0,0;QS=5,0;MQ0F=0 PL 0,6,35 0,6,77 0,12,106 0,9,106 0,15,125 17 106 . G <*> 0 . DP=17;I16=15,1,0,0,562,22318,0,0,898,52082,0,0,302,6476,0,0;QS=5,0;MQ0F=0 PL 0,6,44 0,6,75 0,12,130 0,9,92 0,15,124 17 107 . C <*> 0 . DP=17;I16=15,1,0,0,606,24752,0,0,898,52082,0,0,301,6399,0,0;QS=5,0;MQ0F=0 PL 0,6,36 0,6,77 0,12,130 0,9,119 0,15,136 17 108 . C <*> 0 . DP=17;I16=15,1,0,0,604,24464,0,0,898,52082,0,0,300,6340,0,0;QS=5,0;MQ0F=0 PL 0,6,37 0,6,78 0,12,128 0,9,119 0,15,135 -17 109 . T C,<*> 0 . DP=17;I16=14,1,1,0,639,27679,2,4,869,51241,29,841,287,6155,12,144;QS=4.89189,0.108108,0;SGB=-0.587685;RPBZ=-0.759816;MQBZ=-2.64575;MQSBZ=0.377964;BQBZ=-1.6641;NMBZ=2.38667;SCBZ=2.82843;FS=0;MQ0F=0 PL 0,1,28,3,31,30 0,6,77,6,77,77 0,12,133,12,133,133 0,9,120,9,120,120 0,15,150,15,150,150 +17 109 . T C,<*> 0 . DP=17;I16=14,1,1,0,639,27679,2,4,869,51241,29,841,287,6155,12,144;QS=4.89189,0.108108,0;SGB=-0.587685;RPBZ=-0.759816;MQBZ=-2.64575;MQSBZ=0.377964;BQBZ=-1.6641;SCBZ=2.82843;FS=0;MQ0F=0 PL 0,1,28,3,31,30 0,6,77,6,77,77 0,12,133,12,133,133 0,9,120,9,120,120 0,15,150,15,150,150 17 110 . G <*> 0 . DP=17;I16=15,1,0,0,608,24834,0,0,898,52082,0,0,298,6276,0,0;QS=5,0;MQ0F=0 PL 0,6,40 0,6,78 0,12,130 0,9,113 0,15,136 17 111 . G <*> 0 . DP=17;I16=15,1,0,0,503,18985,0,0,898,52082,0,0,296,6222,0,0;QS=5,0;MQ0F=0 PL 0,6,45 0,6,75 0,12,92 0,9,95 0,15,119 -17 112 . C G,<*> 0 . DP=17;I16=14,1,1,0,577,23365,2,4,869,51241,29,841,279,5963,15,225;QS=4.88235,0.117647,0;SGB=-0.587685;RPBZ=-0.542725;MQBZ=-2.64575;MQSBZ=0.377964;BQBZ=-1.63663;NMBZ=2.38667;SCBZ=2.82843;FS=0;MQ0F=0 PL 0,1,25,3,28,27 0,6,77,6,77,77 0,12,129,12,129,129 0,9,103,9,103,103 0,15,135,15,135,135 -17 113 . A G,<*> 0 . DP=17;I16=14,1,1,0,565,22603,4,16,869,51241,29,841,275,5867,16,256;QS=4.88235,0.117647,0;SGB=-0.587685;RPBZ=-0.542725;MQBZ=-2.64575;MQSBZ=0.377964;BQBZ=-1.64646;NMBZ=2.38667;SCBZ=2.82843;FS=0;MQ0F=0 PL 0,1,25,3,28,27 0,6,71,6,71,71 0,12,120,12,120,120 0,9,102,9,102,102 0,15,139,15,139,139 +17 112 . C G,<*> 0 . DP=17;I16=14,1,1,0,577,23365,2,4,869,51241,29,841,279,5963,15,225;QS=4.88235,0.117647,0;SGB=-0.587685;RPBZ=-0.542725;MQBZ=-2.64575;MQSBZ=0.377964;BQBZ=-1.63663;SCBZ=2.82843;FS=0;MQ0F=0 PL 0,1,25,3,28,27 0,6,77,6,77,77 0,12,129,12,129,129 0,9,103,9,103,103 0,15,135,15,135,135 +17 113 . A G,<*> 0 . DP=17;I16=14,1,1,0,565,22603,4,16,869,51241,29,841,275,5867,16,256;QS=4.88235,0.117647,0;SGB=-0.587685;RPBZ=-0.542725;MQBZ=-2.64575;MQSBZ=0.377964;BQBZ=-1.64646;SCBZ=2.82843;FS=0;MQ0F=0 PL 0,1,25,3,28,27 0,6,71,6,71,71 0,12,120,12,120,120 0,9,102,9,102,102 0,15,139,15,139,139 17 114 . C <*> 0 . DP=17;I16=15,1,0,0,581,22755,0,0,898,52082,0,0,288,6076,0,0;QS=5,0;MQ0F=0 PL 0,6,38 0,6,75 0,12,118 0,9,113 0,15,133 -17 115 . C A,<*> 0 . DP=19;I16=15,2,1,0,615,24761,12,144,958,55682,29,841,261,5423,25,625;QS=4.88785,0.11215,0;SGB=-0.587685;RPBZ=0.28942;MQBZ=-2.23607;MQSBZ=-1.30384;BQBZ=-1.4501;NMBZ=2.22511;SCBZ=-0.445021;FS=0;MQ0F=0 PL 0,6,43,6,43,43 0,6,80,6,80,80 0,12,123,12,123,123 3,0,86,9,89,93 0,21,153,21,153,153 -17 116 . A C,<*> 0 . DP=19;I16=15,2,1,0,631,25045,2,4,958,55682,29,841,265,5631,19,361;QS=4.90244,0.097561,0;SGB=-0.587685;RPBZ=0.0964735;MQBZ=-2.23607;MQSBZ=-1.30384;BQBZ=-1.65205;NMBZ=2.52179;SCBZ=2.52179;FS=0;MQ0F=0 PL 0,1,32,3,35,34 0,6,75,6,75,75 0,12,121,12,121,121 0,9,102,9,102,102 0,21,175,21,175,175 +17 115 . C A,<*> 0 . DP=19;I16=15,2,1,0,615,24761,12,144,958,55682,29,841,261,5423,25,625;QS=4.88785,0.11215,0;SGB=-0.587685;RPBZ=0.28942;MQBZ=-2.23607;MQSBZ=-1.30384;BQBZ=-1.4501;SCBZ=-0.445021;FS=0;MQ0F=0 PL 0,6,43,6,43,43 0,6,80,6,80,80 0,12,123,12,123,123 3,0,86,9,89,93 0,21,153,21,153,153 +17 116 . A C,<*> 0 . DP=19;I16=15,2,1,0,631,25045,2,4,958,55682,29,841,265,5631,19,361;QS=4.90244,0.097561,0;SGB=-0.587685;RPBZ=0.0964735;MQBZ=-2.23607;MQSBZ=-1.30384;BQBZ=-1.65205;SCBZ=2.52179;FS=0;MQ0F=0 PL 0,1,32,3,35,34 0,6,75,6,75,75 0,12,121,12,121,121 0,9,102,9,102,102 0,21,175,21,175,175 17 117 . G <*> 0 . DP=19;I16=16,2,0,0,635,24843,0,0,987,56523,0,0,282,5960,0,0;QS=5,0;MQ0F=0 PL 0,6,42 0,6,77 0,12,117 0,9,97 0,21,177 17 118 . G <*> 0 . DP=19;I16=16,2,0,0,583,22101,0,0,987,56523,0,0,280,5952,0,0;QS=5,0;MQ0F=0 PL 0,6,43 0,6,77 0,12,116 0,9,65 0,21,162 17 119 . G <*> 0 . DP=18;I16=15,2,0,0,581,22015,0,0,927,52923,0,0,277,5917,0,0;QS=5,0;MQ0F=0 PL 0,6,47 0,6,78 0,12,114 0,6,76 0,21,160 -17 120 . A G,<*> 0 . DP=18;I16=14,2,1,0,608,23948,4,16,898,52082,29,841,252,5374,23,529;QS=4.91111,0.0888889,0;SGB=-0.587685;RPBZ=0.204375;MQBZ=-2.16025;MQSBZ=-1.23956;BQBZ=-1.64411;NMBZ=2.91548;SCBZ=2.91548;FS=0;MQ0F=0 PL 0,1,36,3,39,38 0,6,75,6,75,75 0,12,116,12,116,116 0,6,88,6,88,88 0,21,171,21,171,171 +17 120 . A G,<*> 0 . DP=18;I16=14,2,1,0,608,23948,4,16,898,52082,29,841,252,5374,23,529;QS=4.91111,0.0888889,0;SGB=-0.587685;RPBZ=0.204375;MQBZ=-2.16025;MQSBZ=-1.23956;BQBZ=-1.64411;SCBZ=2.91548;FS=0;MQ0F=0 PL 0,1,36,3,39,38 0,6,75,6,75,75 0,12,116,12,116,116 0,6,88,6,88,88 0,21,171,21,171,171 17 121 . G <*> 0 . DP=18;I16=15,2,0,0,619,24187,0,0,927,52923,0,0,273,5909,0,0;QS=5,0;MQ0F=0 PL 0,6,48 0,6,80 0,12,121 0,6,84 0,21,168 17 122 . C <*> 0 . DP=19;I16=16,2,0,0,655,26103,0,0,987,56523,0,0,271,5935,0,0;QS=5,0;MQ0F=0 PL 0,6,42 0,6,78 0,12,119 0,9,107 0,21,178 17 123 . T <*> 0 . DP=17;I16=14,2,0,0,610,24776,0,0,867,49323,0,0,271,5929,0,0;QS=5,0;MQ0F=0 PL 0,6,48 0,6,75 0,9,99 0,9,123 0,18,166 17 124 . T <*> 0 . DP=17;I16=14,2,0,0,547,20261,0,0,867,49323,0,0,271,5939,0,0;QS=5,0;MQ0F=0 PL 0,6,33 0,6,70 0,9,89 0,9,114 0,18,154 -17 125 . A T,<*> 0 . DP=16;I16=12,2,1,0,522,20316,4,16,778,44882,29,841,246,5290,25,625;QS=4.90476,0.0952381,0;SGB=-0.587685;RPBZ=0.926648;MQBZ=-2;MQSBZ=-1.1007;BQBZ=-1.62747;NMBZ=2.73861;SCBZ=2.73861;FS=0;MQ0F=0 PL 0,1,33,3,36,35 0,6,72,6,72,72 0,6,63,6,63,63 0,9,114,9,114,114 0,18,162,18,162,162 +17 125 . A T,<*> 0 . DP=16;I16=12,2,1,0,522,20316,4,16,778,44882,29,841,246,5290,25,625;QS=4.90476,0.0952381,0;SGB=-0.587685;RPBZ=0.926648;MQBZ=-2;MQSBZ=-1.1007;BQBZ=-1.62747;SCBZ=2.73861;FS=0;MQ0F=0 PL 0,1,33,3,36,35 0,6,72,6,72,72 0,6,63,6,63,63 0,9,114,9,114,114 0,18,162,18,162,162 17 126 . A <*> 0 . DP=16;I16=13,2,0,0,558,22192,0,0,807,45723,0,0,271,5907,0,0;QS=5,0;MQ0F=0 PL 0,6,50 0,6,72 0,6,67 0,9,117 0,18,174 17 127 . C <*> 0 . DP=16;I16=13,2,0,0,554,21662,0,0,807,45723,0,0,271,5915,0,0;QS=5,0;MQ0F=0 PL 0,6,46 0,6,69 0,6,75 0,9,119 0,18,160 17 128 . A <*> 0 . DP=16;I16=13,2,0,0,588,23772,0,0,807,45723,0,0,271,5939,0,0;QS=5,0;MQ0F=0 PL 0,6,59 0,6,74 0,6,72 0,9,121 0,18,168 diff --git a/test/mpileup/mpileup.11.out b/test/mpileup/mpileup.11.out index 5780a46e1..adee2884f 100644 --- a/test/mpileup/mpileup.11.out +++ b/test/mpileup/mpileup.11.out @@ -11,7 +11,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -178,7 +177,7 @@ 17 156 . C <*> 0 . DP=5;I16=4,1,0,0,190,7238,0,0,269,15241,0,0,101,2311,0,0;QS=1,0;MQ0F=0 PL 0,15,150 17 157 . C <*> 0 . DP=5;I16=4,1,0,0,192,7384,0,0,269,15241,0,0,101,2341,0,0;QS=1,0;MQ0F=0 PL 0,15,149 17 158 . T <*> 0 . DP=5;I16=4,1,0,0,205,8455,0,0,269,15241,0,0,101,2375,0,0;QS=1,0;MQ0F=0 PL 0,15,159 -17 159 . A G,<*> 0 . DP=6;I16=4,1,1,0,179,6513,5,25,269,15241,60,3600,101,2413,0,0;QS=0.97076,0.0292398,0;SGB=-0.379885;RPBZ=-1.46385;MQBZ=0.447214;MQSBZ=-2.23607;BQBZ=-1.46385;NMBZ=0;SCBZ=0;FS=0;MQ0F=0 PL 0,10,129,15,132,129 +17 159 . A G,<*> 0 . DP=6;I16=4,1,1,0,179,6513,5,25,269,15241,60,3600,101,2413,0,0;QS=0.97076,0.0292398,0;SGB=-0.379885;RPBZ=-1.46385;MQBZ=0.447214;MQSBZ=-2.23607;BQBZ=-1.46385;SCBZ=0;FS=0;MQ0F=0 PL 0,10,129,15,132,129 17 160 . G <*> 0 . DP=6;I16=5,1,0,0,187,6199,0,0,329,18841,0,0,102,2456,0,0;QS=1,0;MQ0F=0 PL 0,18,139 17 161 . A <*> 0 . DP=6;I16=5,1,0,0,225,8479,0,0,329,18841,0,0,103,2505,0,0;QS=1,0;MQ0F=0 PL 0,18,162 17 162 . A <*> 0 . DP=6;I16=5,1,0,0,233,9149,0,0,329,18841,0,0,103,2509,0,0;QS=1,0;MQ0F=0 PL 0,18,167 @@ -209,7 +208,7 @@ 17 187 . C <*> 0 . DP=7;I16=6,1,0,0,252,9238,0,0,389,22441,0,0,142,3234,0,0;QS=1,0;MQ0F=0 PL 0,21,172 17 188 . C <*> 0 . DP=7;I16=6,1,0,0,239,8387,0,0,389,22441,0,0,143,3297,0,0;QS=1,0;MQ0F=0 PL 0,21,162 17 189 . C <*> 0 . DP=7;I16=6,1,0,0,247,8819,0,0,389,22441,0,0,144,3366,0,0;QS=1,0;MQ0F=0 PL 0,21,167 -17 190 . A C,<*> 0 . DP=7;I16=5,1,1,0,219,8109,5,25,329,18841,60,3600,118,2716,25,625;QS=0.976636,0.0233645,0;SGB=-0.379885;RPBZ=0;MQBZ=0.408248;MQSBZ=-2.44949;BQBZ=-1.51357;NMBZ=-0.408248;SCBZ=0;FS=0;MQ0F=0 PL 0,12,153,18,156,153 +17 190 . A C,<*> 0 . DP=7;I16=5,1,1,0,219,8109,5,25,329,18841,60,3600,118,2716,25,625;QS=0.976636,0.0233645,0;SGB=-0.379885;RPBZ=0;MQBZ=0.408248;MQSBZ=-2.44949;BQBZ=-1.51357;SCBZ=0;FS=0;MQ0F=0 PL 0,12,153,18,156,153 17 191 . T <*> 0 . DP=7;I16=6,1,0,0,247,8853,0,0,389,22441,0,0,141,3273,0,0;QS=1,0;MQ0F=0 PL 0,21,169 17 192 . G <*> 0 . DP=7;I16=6,1,0,0,221,7309,0,0,389,22441,0,0,139,3213,0,0;QS=1,0;MQ0F=0 PL 0,21,151 17 193 . T <*> 0 . DP=7;I16=6,1,0,0,229,8027,0,0,389,22441,0,0,137,3161,0,0;QS=1,0;MQ0F=0 PL 0,21,157 @@ -245,7 +244,7 @@ 17 223 . G <*> 0 . DP=4;I16=4,0,0,0,104,2810,0,0,240,14400,0,0,88,2044,0,0;QS=1,0;MQ0F=0 PL 0,12,81 17 224 . G <*> 0 . DP=4;I16=4,0,0,0,89,2077,0,0,240,14400,0,0,87,2019,0,0;QS=1,0;MQ0F=0 PL 0,12,70 17 225 . C <*> 0 . DP=4;I16=4,0,0,0,107,3369,0,0,240,14400,0,0,86,1996,0,0;QS=1,0;MQ0F=0 PL 0,12,86 -17 226 . A G,<*> 0 . DP=4;I16=3,0,1,0,98,3430,3,9,180,10800,60,3600,60,1350,25,625;QS=0.960784,0.0392157,0;SGB=-0.379885;RPBZ=-0.447214;MQBZ=0;BQBZ=-1.34164;NMBZ=0;SCBZ=0;FS=0;MQ0F=0 PL 0,5,79,9,82,80 +17 226 . A G,<*> 0 . DP=4;I16=3,0,1,0,98,3430,3,9,180,10800,60,3600,60,1350,25,625;QS=0.960784,0.0392157,0;SGB=-0.379885;RPBZ=-0.447214;MQBZ=0;BQBZ=-1.34164;SCBZ=0;FS=0;MQ0F=0 PL 0,5,79,9,82,80 17 227 . C <*> 0 . DP=4;I16=4,0,0,0,91,2685,0,0,240,14400,0,0,84,1956,0,0;QS=1,0;MQ0F=0 PL 0,12,75 17 228 . C <*> 0 . DP=4;I16=4,0,0,0,121,3947,0,0,240,14400,0,0,83,1939,0,0;QS=1,0;MQ0F=0 PL 0,12,96 17 229 . G <*> 0 . DP=4;I16=4,0,0,0,91,2097,0,0,240,14400,0,0,82,1924,0,0;QS=1,0;MQ0F=0 PL 0,12,70 @@ -256,7 +255,7 @@ 17 234 . A <*> 0 . DP=5;I16=5,0,0,0,170,5930,0,0,300,18000,0,0,79,1883,0,0;QS=1,0;MQ0F=0 PL 0,15,123 17 235 . A <*> 0 . DP=5;I16=5,0,0,0,155,5325,0,0,300,18000,0,0,78,1836,0,0;QS=1,0;MQ0F=0 PL 0,15,115 17 236 . G <*> 0 . DP=5;I16=5,0,0,0,141,4187,0,0,300,18000,0,0,77,1795,0,0;QS=1,0;MQ0F=0 PL 0,15,103 -17 237 . A C,<*> 0 . DP=4;I16=3,0,1,0,109,4005,8,64,180,10800,60,3600,52,1134,25,625;QS=0.931624,0.0683761,0;SGB=-0.379885;RPBZ=0.447214;MQBZ=0;BQBZ=-1.34164;NMBZ=0;SCBZ=0;FS=0;MQ0F=0 PL 0,3,84,9,87,87 +17 237 . A C,<*> 0 . DP=4;I16=3,0,1,0,109,4005,8,64,180,10800,60,3600,52,1134,25,625;QS=0.931624,0.0683761,0;SGB=-0.379885;RPBZ=0.447214;MQBZ=0;BQBZ=-1.34164;SCBZ=0;FS=0;MQ0F=0 PL 0,3,84,9,87,87 17 238 . C <*> 0 . DP=4;I16=4,0,0,0,104,2856,0,0,240,14400,0,0,77,1727,0,0;QS=1,0;MQ0F=0 PL 0,12,82 17 239 . A <*> 0 . DP=4;I16=4,0,0,0,138,4886,0,0,240,14400,0,0,77,1699,0,0;QS=1,0;MQ0F=0 PL 0,12,108 17 240 . C <*> 0 . DP=4;I16=4,0,0,0,136,4700,0,0,240,14400,0,0,76,1626,0,0;QS=1,0;MQ0F=0 PL 0,12,106 @@ -355,7 +354,7 @@ 17 332 . A <*> 0 . DP=11;I16=4,7,0,0,411,15645,0,0,598,34082,0,0,189,4043,0,0;QS=1,0;MQ0F=0 PL 0,33,255 17 333 . A <*> 0 . DP=11;I16=4,7,0,0,405,15523,0,0,598,34082,0,0,191,4029,0,0;QS=1,0;MQ0F=0 PL 0,33,255 17 334 . A <*> 0 . DP=11;I16=4,7,0,0,404,15090,0,0,598,34082,0,0,193,4027,0,0;QS=1,0;MQ0F=0 PL 0,33,255 -17 335 . A G,<*> 0 . DP=12;I16=4,7,1,0,382,13732,4,16,598,34082,60,3600,195,4037,0,0;QS=0.989189,0.0108108,0;SGB=-0.379885;RPBZ=-1.59605;MQBZ=0.447214;MQSBZ=-1.25357;BQBZ=-1.59886;NMBZ=-0.301511;SCBZ=-0.301511;FS=0;MQ0F=0 PL 0,25,245,33,248,245 +17 335 . A G,<*> 0 . DP=12;I16=4,7,1,0,382,13732,4,16,598,34082,60,3600,195,4037,0,0;QS=0.989189,0.0108108,0;SGB=-0.379885;RPBZ=-1.59605;MQBZ=0.447214;MQSBZ=-1.25357;BQBZ=-1.59886;SCBZ=-0.301511;FS=0;MQ0F=0 PL 0,25,245,33,248,245 17 336 . A <*> 0 . DP=12;I16=5,7,0,0,382,12810,0,0,658,37682,0,0,198,4060,0,0;QS=1,0;MQ0F=0 PL 0,36,255 17 337 . C <*> 0 . DP=12;I16=5,7,0,0,443,16735,0,0,658,37682,0,0,200,4048,0,0;QS=1,0;MQ0F=0 PL 0,36,255 17 338 . T <*> 0 . DP=12;I16=5,7,0,0,482,19532,0,0,658,37682,0,0,202,4052,0,0;QS=1,0;MQ0F=0 PL 0,36,255 @@ -395,7 +394,7 @@ 17 372 . C <*> 0 . DP=11;I16=5,6,0,0,422,16450,0,0,660,39600,0,0,212,4894,0,0;QS=1,0;MQ0F=0 PL 0,33,255 17 373 . A <*> 0 . DP=11;I16=5,6,0,0,416,16096,0,0,660,39600,0,0,211,4831,0,0;QS=1,0;MQ0F=0 PL 0,33,255 17 374 . T <*> 0 . DP=11;I16=5,6,0,0,395,14795,0,0,660,39600,0,0,210,4778,0,0;QS=1,0;MQ0F=0 PL 0,33,255 -17 375 . A T,<*> 0 . DP=11;I16=5,5,0,1,399,15985,14,196,600,36000,60,3600,205,4719,4,16;QS=0.966102,0.0338983,0;SGB=-0.379885;RPBZ=-1.58474;MQBZ=0;MQSBZ=0;BQBZ=-1.59942;NMBZ=1.87617;SCBZ=0;FS=0;MQ0F=0 PL 0,18,255,30,255,255 +17 375 . A T,<*> 0 . DP=11;I16=5,5,0,1,399,15985,14,196,600,36000,60,3600,205,4719,4,16;QS=0.966102,0.0338983,0;SGB=-0.379885;RPBZ=-1.58474;MQBZ=0;MQSBZ=0;BQBZ=-1.59942;SCBZ=0;FS=0;MQ0F=0 PL 0,18,255,30,255,255 17 376 . G <*> 0 . DP=11;I16=5,6,0,0,419,16089,0,0,660,39600,0,0,208,4702,0,0;QS=1,0;MQ0F=0 PL 0,33,255 17 377 . T <*> 0 . DP=11;I16=5,6,0,0,414,16104,0,0,660,39600,0,0,207,4679,0,0;QS=1,0;MQ0F=0 PL 0,33,255 17 378 . T <*> 0 . DP=10;I16=5,5,0,0,399,16003,0,0,600,36000,0,0,207,4665,0,0;QS=1,0;MQ0F=0 PL 0,30,255 @@ -421,7 +420,7 @@ 17 398 . A <*> 0 . DP=10;I16=6,4,0,0,397,15817,0,0,569,33241,0,0,193,4447,0,0;QS=1,0;MQ0F=0 PL 0,30,255 17 399 . A <*> 0 . DP=10;I16=6,4,0,0,400,16172,0,0,569,33241,0,0,193,4417,0,0;QS=1,0;MQ0F=0 PL 0,30,255 17 400 . A <*> 0 . DP=11;I16=6,5,0,0,425,16735,0,0,629,36841,0,0,191,4297,0,0;QS=1,0;MQ0F=0 PL 0,33,255 -17 401 . A C,<*> 0 . DP=11;I16=6,4,0,1,396,15798,8,64,569,33241,60,3600,165,3565,25,625;QS=0.979849,0.0201511,0;SGB=-0.379885;RPBZ=-0.633898;MQBZ=0.316228;MQSBZ=0.912871;BQBZ=-1.58838;NMBZ=3.16228;SCBZ=0;FS=0;MQ0F=0 PL 0,22,255,30,255,255 +17 401 . A C,<*> 0 . DP=11;I16=6,4,0,1,396,15798,8,64,569,33241,60,3600,165,3565,25,625;QS=0.979849,0.0201511,0;SGB=-0.379885;RPBZ=-0.633898;MQBZ=0.316228;MQSBZ=0.912871;BQBZ=-1.58838;SCBZ=0;FS=0;MQ0F=0 PL 0,22,255,30,255,255 17 402 . T <*> 0 . DP=11;I16=6,5,0,0,415,15961,0,0,629,36841,0,0,189,4097,0,0;QS=1,0;MQ0F=0 PL 0,33,255 17 403 . T <*> 0 . DP=11;I16=6,5,0,0,426,16580,0,0,629,36841,0,0,188,4018,0,0;QS=1,0;MQ0F=0 PL 0,33,255 17 404 . G <*> 0 . DP=11;I16=6,5,0,0,421,16197,0,0,629,36841,0,0,187,3953,0,0;QS=1,0;MQ0F=0 PL 0,33,255 @@ -457,7 +456,7 @@ 17 434 . T <*> 0 . DP=10;I16=5,5,0,0,339,11787,0,0,538,30482,0,0,191,4285,0,0;QS=1,0;MQ0F=0 PL 0,30,243 17 435 . A <*> 0 . DP=10;I16=5,5,0,0,346,12322,0,0,538,30482,0,0,192,4318,0,0;QS=1,0;MQ0F=0 PL 0,30,237 17 436 . T <*> 0 . DP=9;I16=4,5,0,0,305,10551,0,0,478,26882,0,0,194,4360,0,0;QS=1,0;MQ0F=0 PL 0,27,223 -17 437 . T G,<*> 0 . DP=9;I16=3,5,1,0,271,9505,6,36,449,26041,29,841,180,4154,16,256;QS=0.978102,0.0218978,0;SGB=-0.379885;RPBZ=-1.36123;MQBZ=-1.87083;MQSBZ=1.69031;BQBZ=-1.55569;NMBZ=-0.353553;SCBZ=0;FS=0;MQ0F=0 PL 0,17,200,24,203,201 +17 437 . T G,<*> 0 . DP=9;I16=3,5,1,0,271,9505,6,36,449,26041,29,841,180,4154,16,256;QS=0.978102,0.0218978,0;SGB=-0.379885;RPBZ=-1.36123;MQBZ=-1.87083;MQSBZ=1.69031;BQBZ=-1.55569;SCBZ=0;FS=0;MQ0F=0 PL 0,17,200,24,203,201 17 438 . A <*> 0 . DP=9;I16=4,5,0,0,298,10570,0,0,478,26882,0,0,198,4468,0,0;QS=1,0;MQ0F=0 PL 0,27,220 17 439 . C <*> 0 . DP=9;I16=4,5,0,0,311,10989,0,0,478,26882,0,0,200,4534,0,0;QS=1,0;MQ0F=0 PL 0,27,224 17 440 . A <*> 0 . DP=9;I16=4,5,0,0,346,13482,0,0,478,26882,0,0,202,4608,0,0;QS=1,0;MQ0F=0 PL 0,27,247 @@ -485,13 +484,13 @@ 17 462 . G <*> 0 . DP=10;I16=5,5,0,0,350,12490,0,0,515,28251,0,0,199,4569,0,0;QS=1,0;MQ0F=0 PL 0,30,241 17 463 . G <*> 0 . DP=10;I16=5,5,0,0,310,10258,0,0,515,28251,0,0,200,4584,0,0;QS=1,0;MQ0F=0 PL 0,30,221 17 464 . A <*> 0 . DP=10;I16=5,5,0,0,304,10594,0,0,515,28251,0,0,201,4605,0,0;QS=1,0;MQ0F=0 PL 0,30,217 -17 465 . C T,<*> 0 . DP=10;I16=5,4,0,1,326,11950,4,16,455,24651,60,3600,196,4596,6,36;QS=0.987342,0.0126582,0;SGB=-0.379885;RPBZ=1.57147;MQBZ=0.645497;MQSBZ=0.903696;BQBZ=-1.61645;NMBZ=2.23607;SCBZ=0;FS=0;MQ0F=0 PL 0,20,224,27,227,224 +17 465 . C T,<*> 0 . DP=10;I16=5,4,0,1,326,11950,4,16,455,24651,60,3600,196,4596,6,36;QS=0.987342,0.0126582,0;SGB=-0.379885;RPBZ=1.57147;MQBZ=0.645497;MQSBZ=0.903696;BQBZ=-1.61645;SCBZ=0;FS=0;MQ0F=0 PL 0,20,224,27,227,224 17 466 . A <*> 0 . DP=10;I16=5,5,0,0,379,14569,0,0,515,28251,0,0,203,4665,0,0;QS=1,0;MQ0F=0 PL 0,30,255 17 467 . A <*> 0 . DP=10;I16=5,5,0,0,367,14303,0,0,515,28251,0,0,203,4655,0,0;QS=1,0;MQ0F=0 PL 0,30,251 17 468 . A <*> 0 . DP=10;I16=5,5,0,0,357,13375,0,0,515,28251,0,0,202,4604,0,0;QS=1,0;MQ0F=0 PL 0,30,251 17 469 . A <*> 0 . DP=10;I16=5,5,0,0,387,15581,0,0,515,28251,0,0,201,4563,0,0;QS=1,0;MQ0F=0 PL 0,30,255 17 470 . G <*> 0 . DP=10;I16=5,5,0,0,328,11334,0,0,515,28251,0,0,200,4532,0,0;QS=1,0;MQ0F=0 PL 0,30,238 -17 471 . T G,C,<*> 0 . DP=11;I16=5,4,0,2,319,11637,18,162,478,26882,97,4969,183,4255,16,256;QS=0.945289,0.0273556,0.0273556,0;VDB=0.96;SGB=-0.453602;RPBZ=0.23624;MQBZ=-0.451335;MQSBZ=1.04881;BQBZ=-2.14585;NMBZ=1.39841;SCBZ=0;FS=0;MQ0F=0 PL 0,19,219,19,221,219,27,222,222,221 +17 471 . T G,C,<*> 0 . DP=11;I16=5,4,0,2,319,11637,18,162,478,26882,97,4969,183,4255,16,256;QS=0.945289,0.0273556,0.0273556,0;VDB=0.96;SGB=-0.453602;RPBZ=0.23624;MQBZ=-0.451335;MQSBZ=1.04881;BQBZ=-2.14585;SCBZ=0;FS=0;MQ0F=0 PL 0,19,219,19,221,219,27,222,222,221 17 472 . T <*> 0 . DP=10;I16=5,5,0,0,340,12388,0,0,515,28251,0,0,200,4500,0,0;QS=1,0;MQ0F=0 PL 0,30,241 17 473 . G <*> 0 . DP=10;I16=5,5,0,0,363,14103,0,0,515,28251,0,0,201,4499,0,0;QS=1,0;MQ0F=0 PL 0,30,250 17 474 . G <*> 0 . DP=11;I16=6,5,0,0,378,13788,0,0,575,31851,0,0,202,4508,0,0;QS=1,0;MQ0F=0 PL 0,33,255 @@ -508,7 +507,7 @@ 17 485 . G <*> 0 . DP=11;I16=6,5,0,0,419,16073,0,0,575,31851,0,0,202,4328,0,0;QS=1,0;MQ0F=0 PL 0,33,255 17 486 . A <*> 0 . DP=11;I16=6,5,0,0,452,18618,0,0,575,31851,0,0,200,4280,0,0;QS=1,0;MQ0F=0 PL 0,33,255 17 487 . G <*> 0 . DP=11;I16=6,5,0,0,403,14875,0,0,575,31851,0,0,198,4244,0,0;QS=1,0;MQ0F=0 PL 0,33,255 -17 488 . A G,<*> 0 . DP=11;I16=5,5,1,0,388,15102,4,16,546,31010,29,841,171,3595,25,625;QS=0.989474,0.0105263,0;SGB=-0.379885;RPBZ=0;MQBZ=-1.81659;MQSBZ=0.699206;BQBZ=-1.60315;NMBZ=0;SCBZ=0;FS=0;MQ0F=0 PL 0,23,255,30,255,255 +17 488 . A G,<*> 0 . DP=11;I16=5,5,1,0,388,15102,4,16,546,31010,29,841,171,3595,25,625;QS=0.989474,0.0105263,0;SGB=-0.379885;RPBZ=0;MQBZ=-1.81659;MQSBZ=0.699206;BQBZ=-1.60315;SCBZ=0;FS=0;MQ0F=0 PL 0,23,255,30,255,255 17 489 . A <*> 0 . DP=11;I16=6,5,0,0,393,14565,0,0,575,31851,0,0,194,4208,0,0;QS=1,0;MQ0F=0 PL 0,33,255 17 490 . A <*> 0 . DP=11;I16=6,5,0,0,401,14927,0,0,575,31851,0,0,192,4208,0,0;QS=1,0;MQ0F=0 PL 0,33,255 17 491 . T <*> 0 . DP=11;I16=6,5,0,0,385,13773,0,0,575,31851,0,0,190,4220,0,0;QS=1,0;MQ0F=0 PL 0,33,255 @@ -624,7 +623,7 @@ 17 601 . T <*> 0 . DP=8;I16=4,4,0,0,305,11697,0,0,480,28800,0,0,132,2768,0,0;QS=1,0;MQ0F=0 PL 0,24,235 17 602 . G <*> 0 . DP=8;I16=4,4,0,0,298,11176,0,0,480,28800,0,0,136,2836,0,0;QS=1,0;MQ0F=0 PL 0,24,229 17 603 . G <*> 0 . DP=8;I16=4,4,0,0,277,9947,0,0,480,28800,0,0,139,2863,0,0;QS=1,0;MQ0F=0 PL 0,24,216 -17 604 . T G,<*> 0 . DP=8;I16=3,4,1,0,265,10121,4,16,420,25200,60,3600,117,2275,25,625;QS=0.98513,0.0148699,0;SGB=-0.379885;RPBZ=0.219529;MQBZ=0;MQSBZ=0;BQBZ=-1.52753;NMBZ=-0.377964;SCBZ=-0.377964;FS=0;MQ0F=0 PL 0,15,205,21,208,205 +17 604 . T G,<*> 0 . DP=8;I16=3,4,1,0,265,10121,4,16,420,25200,60,3600,117,2275,25,625;QS=0.98513,0.0148699,0;SGB=-0.379885;RPBZ=0.219529;MQBZ=0;MQSBZ=0;BQBZ=-1.52753;SCBZ=-0.377964;FS=0;MQ0F=0 PL 0,15,205,21,208,205 17 605 . T <*> 0 . DP=8;I16=4,4,0,0,273,10339,0,0,480,28800,0,0,145,2947,0,0;QS=1,0;MQ0F=0 PL 0,24,215 17 606 . T <*> 0 . DP=8;I16=4,4,0,0,278,9966,0,0,480,28800,0,0,148,3004,0,0;QS=1,0;MQ0F=0 PL 0,24,217 17 607 . A <*> 0 . DP=8;I16=4,4,0,0,288,10428,0,0,480,28800,0,0,151,3071,0,0;QS=1,0;MQ0F=0 PL 0,24,222 @@ -735,7 +734,7 @@ 17 712 . C <*> 0 . DP=6;I16=0,6,0,0,228,8740,0,0,298,16082,0,0,127,2781,0,0;QS=1,0;MQ0F=0 PL 0,18,146 17 713 . T <*> 0 . DP=6;I16=0,6,0,0,225,8639,0,0,298,16082,0,0,130,2888,0,0;QS=1,0;MQ0F=0 PL 0,18,149 17 714 . C <*> 0 . DP=6;I16=0,6,0,0,183,6221,0,0,298,16082,0,0,133,3001,0,0;QS=1,0;MQ0F=0 PL 0,18,127 -17 715 . A C,<*> 0 . DP=6;I16=0,5,0,1,162,5642,6,36,269,15241,29,841,117,2759,19,361;QS=0.964286,0.0357143,0;SGB=-0.379885;RPBZ=-0.87831;MQBZ=-1.41421;BQBZ=-1.48522;NMBZ=1.03923;SCBZ=1.03923;FS=0;MQ0F=0 PL 0,9,114,15,117,115 +17 715 . A C,<*> 0 . DP=6;I16=0,5,0,1,162,5642,6,36,269,15241,29,841,117,2759,19,361;QS=0.964286,0.0357143,0;SGB=-0.379885;RPBZ=-0.87831;MQBZ=-1.41421;BQBZ=-1.48522;SCBZ=1.03923;FS=0;MQ0F=0 PL 0,9,114,15,117,115 17 716 . C <*> 0 . DP=6;I16=0,6,0,0,215,7981,0,0,298,16082,0,0,139,3245,0,0;QS=1,0;MQ0F=0 PL 0,18,145 17 717 . A <*> 0 . DP=6;I16=0,6,0,0,229,9051,0,0,298,16082,0,0,142,3376,0,0;QS=1,0;MQ0F=0 PL 0,18,153 17 718 . G <*> 0 . DP=6;I16=0,6,0,0,209,7521,0,0,298,16082,0,0,145,3513,0,0;QS=1,0;MQ0F=0 PL 0,18,139 @@ -743,17 +742,17 @@ 17 720 . G <*> 0 . DP=6;I16=0,6,0,0,235,9247,0,0,298,16082,0,0,149,3701,0,0;QS=1,0;MQ0F=0 PL 0,18,147 17 721 . C <*> 0 . DP=6;I16=0,6,0,0,227,8683,0,0,298,16082,0,0,150,3750,0,0;QS=1,0;MQ0F=0 PL 0,18,147 17 722 . A <*> 0 . DP=6;I16=0,6,0,0,218,8102,0,0,298,16082,0,0,149,3701,0,0;QS=1,0;MQ0F=0 PL 0,18,143 -17 723 . A G,<*> 0 . DP=6;I16=0,5,0,1,196,7704,7,49,269,15241,29,841,122,2980,25,625;QS=0.964103,0.0358974,0;SGB=-0.379885;RPBZ=-1.46385;MQBZ=-1.41421;BQBZ=-1.48522;NMBZ=1.73205;SCBZ=1.73205;FS=0;MQ0F=0 PL 0,9,129,15,132,130 +17 723 . A G,<*> 0 . DP=6;I16=0,5,0,1,196,7704,7,49,269,15241,29,841,122,2980,25,625;QS=0.964103,0.0358974,0;SGB=-0.379885;RPBZ=-1.46385;MQBZ=-1.41421;BQBZ=-1.48522;SCBZ=1.73205;FS=0;MQ0F=0 PL 0,9,129,15,132,130 17 724 . C <*> 0 . DP=6;I16=0,6,0,0,216,8000,0,0,298,16082,0,0,145,3513,0,0;QS=1,0;MQ0F=0 PL 0,18,140 17 725 . A <*> 0 . DP=6;I16=0,6,0,0,211,7579,0,0,298,16082,0,0,143,3425,0,0;QS=1,0;MQ0F=0 PL 0,18,137 17 726 . C <*> 0 . DP=6;I16=0,6,0,0,199,6927,0,0,298,16082,0,0,141,3341,0,0;QS=1,0;MQ0F=0 PL 0,18,136 -17 727 . A C,<*> 0 . DP=6;I16=0,5,0,1,173,6285,17,289,269,15241,29,841,114,2636,25,625;QS=0.908108,0.0918919,0;SGB=-0.379885;RPBZ=-1.46385;MQBZ=-1.41421;BQBZ=-1.46385;NMBZ=1.03923;SCBZ=1.03923;FS=0;MQ0F=0 PL 0,1,109,15,112,119 +17 727 . A C,<*> 0 . DP=6;I16=0,5,0,1,173,6285,17,289,269,15241,29,841,114,2636,25,625;QS=0.908108,0.0918919,0;SGB=-0.379885;RPBZ=-1.46385;MQBZ=-1.41421;BQBZ=-1.46385;SCBZ=1.03923;FS=0;MQ0F=0 PL 0,1,109,15,112,119 17 728 . C <*> 0 . DP=6;I16=0,6,0,0,214,7890,0,0,298,16082,0,0,137,3185,0,0;QS=1,0;MQ0F=0 PL 0,18,142 17 729 . T <*> 0 . DP=6;I16=0,6,0,0,215,7867,0,0,298,16082,0,0,135,3113,0,0;QS=1,0;MQ0F=0 PL 0,18,142 17 730 . A <*> 0 . DP=6;I16=0,6,0,0,198,7286,0,0,298,16082,0,0,133,3045,0,0;QS=1,0;MQ0F=0 PL 0,18,137 17 731 . T <*> 0 . DP=6;I16=0,6,0,0,219,8327,0,0,298,16082,0,0,131,2981,0,0;QS=1,0;MQ0F=0 PL 0,18,148 17 732 . C <*> 0 . DP=6;I16=0,6,0,0,190,6622,0,0,298,16082,0,0,129,2921,0,0;QS=1,0;MQ0F=0 PL 0,18,132 -17 733 . T C,<*> 0 . DP=6;I16=0,5,0,1,186,7036,4,16,269,15241,29,841,102,2240,25,625;QS=0.978947,0.0210526,0;SGB=-0.379885;RPBZ=-1.46385;MQBZ=-1.41421;BQBZ=-1.48522;NMBZ=1.03923;SCBZ=1.03923;FS=0;MQ0F=0 PL 0,10,128,15,131,129 +17 733 . T C,<*> 0 . DP=6;I16=0,5,0,1,186,7036,4,16,269,15241,29,841,102,2240,25,625;QS=0.978947,0.0210526,0;SGB=-0.379885;RPBZ=-1.46385;MQBZ=-1.41421;BQBZ=-1.48522;SCBZ=1.03923;FS=0;MQ0F=0 PL 0,10,128,15,131,129 17 734 . G <*> 0 . DP=6;I16=0,6,0,0,212,7610,0,0,298,16082,0,0,125,2813,0,0;QS=1,0;MQ0F=0 PL 0,18,139 17 735 . A <*> 0 . DP=7;I16=0,7,0,0,235,8595,0,0,358,19682,0,0,123,2765,0,0;QS=1,0;MQ0F=0 PL 0,21,150 17 736 . C <*> 0 . DP=7;I16=0,7,0,0,239,9173,0,0,358,19682,0,0,122,2722,0,0;QS=1,0;MQ0F=0 PL 0,21,152 @@ -763,7 +762,7 @@ 17 740 . T <*> 0 . DP=7;I16=0,7,0,0,248,9042,0,0,358,19682,0,0,118,2610,0,0;QS=1,0;MQ0F=0 PL 0,21,155 17 741 . T <*> 0 . DP=7;I16=0,7,0,0,244,8970,0,0,358,19682,0,0,116,2548,0,0;QS=1,0;MQ0F=0 PL 0,21,151 17 742 . C <*> 0 . DP=7;I16=0,7,0,0,212,7112,0,0,358,19682,0,0,114,2494,0,0;QS=1,0;MQ0F=0 PL 0,21,138 -17 743 . A C,<*> 0 . DP=7;I16=0,6,0,1,189,6467,10,100,329,18841,29,841,87,1823,25,625;QS=0.949749,0.0502513,0;SGB=-0.379885;RPBZ=-1;MQBZ=-1.58114;BQBZ=-1.5;NMBZ=1.10335;SCBZ=-0.408248;FS=0;MQ0F=0 PL 0,10,123,18,126,126 +17 743 . A C,<*> 0 . DP=7;I16=0,6,0,1,189,6467,10,100,329,18841,29,841,87,1823,25,625;QS=0.949749,0.0502513,0;SGB=-0.379885;RPBZ=-1;MQBZ=-1.58114;BQBZ=-1.5;SCBZ=-0.408248;FS=0;MQ0F=0 PL 0,10,123,18,126,126 17 744 . T <*> 0 . DP=7;I16=0,7,0,0,259,9751,0,0,358,19682,0,0,110,2410,0,0;QS=1,0;MQ0F=0 PL 0,21,154 17 745 . G <*> 0 . DP=8;I16=1,7,0,0,280,10088,0,0,418,23282,0,0,108,2380,0,0;QS=1,0;MQ0F=0 PL 0,24,182 17 746 . G <*> 0 . DP=8;I16=1,7,0,0,274,9756,0,0,418,23282,0,0,107,2359,0,0;QS=1,0;MQ0F=0 PL 0,24,178 @@ -777,14 +776,14 @@ 17 754 . T <*> 0 . DP=6;I16=1,5,0,0,234,9250,0,0,298,16082,0,0,114,2438,0,0;QS=1,0;MQ0F=0 PL 0,18,172 17 755 . G <*> 0 . DP=6;I16=1,5,0,0,220,8164,0,0,298,16082,0,0,115,2475,0,0;QS=1,0;MQ0F=0 PL 0,18,162 17 756 . G <*> 0 . DP=6;I16=1,5,0,0,200,7040,0,0,298,16082,0,0,116,2518,0,0;QS=1,0;MQ0F=0 PL 0,18,157 -17 757 . A C,<*> 0 . DP=6;I16=1,4,0,1,187,7063,9,81,269,15241,29,841,92,1942,25,625;QS=0.953608,0.0463918,0;SGB=-0.379885;RPBZ=-0.29277;MQBZ=-1.41421;MQSBZ=-0.707107;BQBZ=-1.48522;NMBZ=0.904534;SCBZ=-0.447214;FS=0;MQ0F=0 PL 0,8,144,15,147,146 +17 757 . A C,<*> 0 . DP=6;I16=1,4,0,1,187,7063,9,81,269,15241,29,841,92,1942,25,625;QS=0.953608,0.0463918,0;SGB=-0.379885;RPBZ=-0.29277;MQBZ=-1.41421;MQSBZ=-0.707107;BQBZ=-1.48522;SCBZ=-0.447214;FS=0;MQ0F=0 PL 0,8,144,15,147,146 17 758 . A <*> 0 . DP=6;I16=1,5,0,0,205,7219,0,0,298,16082,0,0,118,2622,0,0;QS=1,0;MQ0F=0 PL 0,18,156 -17 759 . A G,<*> 0 . DP=6;I16=1,4,0,1,181,6927,4,16,269,15241,29,841,113,2647,6,36;QS=0.978378,0.0216216,0;SGB=-0.379885;RPBZ=1.46385;MQBZ=-1.41421;MQSBZ=-0.707107;BQBZ=-1.46385;NMBZ=1.50756;SCBZ=2.23607;FS=0;MQ0F=0 PL 0,10,145,15,148,145 +17 759 . A G,<*> 0 . DP=6;I16=1,4,0,1,181,6927,4,16,269,15241,29,841,113,2647,6,36;QS=0.978378,0.0216216,0;SGB=-0.379885;RPBZ=1.46385;MQBZ=-1.41421;MQSBZ=-0.707107;BQBZ=-1.46385;SCBZ=2.23607;FS=0;MQ0F=0 PL 0,10,145,15,148,145 17 760 . C <*> 0 . DP=7;I16=1,6,0,0,171,4987,0,0,358,19682,0,0,120,2750,0,0;QS=1,0;MQ0F=0 PL 0,21,130 17 761 . G <*> 0 . DP=7;I16=1,6,0,0,203,7135,0,0,358,19682,0,0,121,2773,0,0;QS=1,0;MQ0F=0 PL 0,21,155 17 762 . G <*> 0 . DP=7;I16=1,6,0,0,249,9197,0,0,358,19682,0,0,122,2802,0,0;QS=1,0;MQ0F=0 PL 0,21,173 -17 763 . C A,<*> 0 . DP=7;I16=1,5,0,1,223,8479,15,225,329,18841,29,841,121,2833,2,4;QS=0.936975,0.0630252,0;SGB=-0.379885;RPBZ=1.5;MQBZ=-1.58114;MQSBZ=-0.632456;BQBZ=-1.51357;NMBZ=1.57181;SCBZ=2.44949;FS=0;MQ0F=0 PL 0,6,158,18,161,165 -17 764 . A C,<*> 0 . DP=7;I16=1,5,0,1,211,7679,8,64,329,18841,29,841,99,2253,25,625;QS=0.96347,0.0365297,0;SGB=-0.379885;RPBZ=0;MQBZ=-1.58114;MQSBZ=-0.632456;BQBZ=-1.52753;NMBZ=1.04787;SCBZ=-0.408248;FS=0;MQ0F=0 PL 0,11,156,18,159,158 +17 763 . C A,<*> 0 . DP=7;I16=1,5,0,1,223,8479,15,225,329,18841,29,841,121,2833,2,4;QS=0.936975,0.0630252,0;SGB=-0.379885;RPBZ=1.5;MQBZ=-1.58114;MQSBZ=-0.632456;BQBZ=-1.51357;SCBZ=2.44949;FS=0;MQ0F=0 PL 0,6,158,18,161,165 +17 764 . A C,<*> 0 . DP=7;I16=1,5,0,1,211,7679,8,64,329,18841,29,841,99,2253,25,625;QS=0.96347,0.0365297,0;SGB=-0.379885;RPBZ=0;MQBZ=-1.58114;MQSBZ=-0.632456;BQBZ=-1.52753;SCBZ=-0.408248;FS=0;MQ0F=0 PL 0,11,156,18,159,158 17 765 . A <*> 0 . DP=7;I16=1,6,0,0,237,8863,0,0,358,19682,0,0,125,2925,0,0;QS=1,0;MQ0F=0 PL 0,21,170 17 766 . C <*> 0 . DP=6;I16=1,5,0,0,219,8097,0,0,329,18841,0,0,127,2977,0,0;QS=1,0;MQ0F=0 PL 0,18,164 17 767 . A <*> 0 . DP=6;I16=1,5,0,0,187,6311,0,0,329,18841,0,0,129,3033,0,0;QS=1,0;MQ0F=0 PL 0,18,148 @@ -801,7 +800,7 @@ 17 778 . A <*> 0 . DP=6;I16=1,5,0,0,246,10108,0,0,329,18841,0,0,118,2412,0,0;QS=1,0;MQ0F=0 PL 0,18,181 17 779 . G <*> 0 . DP=6;I16=1,5,0,0,219,8227,0,0,329,18841,0,0,116,2352,0,0;QS=1,0;MQ0F=0 PL 0,18,170 17 780 . A <*> 0 . DP=6;I16=1,5,0,0,217,7995,0,0,329,18841,0,0,114,2300,0,0;QS=1,0;MQ0F=0 PL 0,18,166 -17 781 . A C,<*> 0 . DP=6;I16=1,4,0,1,196,7720,10,100,300,18000,29,841,97,2031,15,225;QS=0.951456,0.0485437,0;SGB=-0.379885;RPBZ=0.29277;MQBZ=-2.23607;MQSBZ=-0.447214;BQBZ=-1.48522;NMBZ=1.58114;SCBZ=0;FS=0;MQ0F=0 PL 0,7,150,15,153,154 +17 781 . A C,<*> 0 . DP=6;I16=1,4,0,1,196,7720,10,100,300,18000,29,841,97,2031,15,225;QS=0.951456,0.0485437,0;SGB=-0.379885;RPBZ=0.29277;MQBZ=-2.23607;MQSBZ=-0.447214;BQBZ=-1.48522;SCBZ=0;FS=0;MQ0F=0 PL 0,7,150,15,153,154 17 782 . A <*> 0 . DP=6;I16=1,5,0,0,223,8435,0,0,329,18841,0,0,110,2220,0,0;QS=1,0;MQ0F=0 PL 0,18,171 17 783 . A <*> 0 . DP=7;I16=1,6,0,0,248,9014,0,0,389,22441,0,0,108,2192,0,0;QS=1,0;MQ0F=0 PL 0,21,178 17 784 . C <*> 0 . DP=7;I16=1,6,0,0,259,9613,0,0,389,22441,0,0,107,2173,0,0;QS=1,0;MQ0F=0 PL 0,21,178 @@ -1114,7 +1113,7 @@ 17 1091 . C <*> 0 . DP=9;I16=9,0,0,0,333,12443,0,0,540,32400,0,0,153,3305,0,0;QS=1,0;MQ0F=0 PL 0,27,177 17 1092 . T <*> 0 . DP=9;I16=9,0,0,0,378,15912,0,0,540,32400,0,0,156,3404,0,0;QS=1,0;MQ0F=0 PL 0,27,198 17 1093 . G <*> 0 . DP=9;I16=9,0,0,0,348,13536,0,0,540,32400,0,0,159,3513,0,0;QS=1,0;MQ0F=0 PL 0,27,184 -17 1094 . G T,<*> 0 . DP=9;I16=8,0,1,0,326,13362,12,144,480,28800,60,3600,155,3583,7,49;QS=0.964497,0.035503,0;SGB=-0.379885;RPBZ=-1.55569;MQBZ=0;BQBZ=-1.56227;NMBZ=0;SCBZ=0;FS=0;MQ0F=0 PL 0,14,177,24,180,181 +17 1094 . G T,<*> 0 . DP=9;I16=8,0,1,0,326,13362,12,144,480,28800,60,3600,155,3583,7,49;QS=0.964497,0.035503,0;SGB=-0.379885;RPBZ=-1.55569;MQBZ=0;BQBZ=-1.56227;SCBZ=0;FS=0;MQ0F=0 PL 0,14,177,24,180,181 17 1095 . A <*> 0 . DP=8;I16=8,0,0,0,310,12292,0,0,480,28800,0,0,165,3709,0,0;QS=1,0;MQ0F=0 PL 0,24,178 17 1096 . T <*> 0 . DP=9;I16=9,0,0,0,331,12443,0,0,540,32400,0,0,168,3792,0,0;QS=1,0;MQ0F=0 PL 0,27,178 17 1097 . A <*> 0 . DP=9;I16=9,0,0,0,330,12450,0,0,540,32400,0,0,172,3882,0,0;QS=1,0;MQ0F=0 PL 0,27,177 @@ -1149,7 +1148,7 @@ 17 1126 . C <*> 0 . DP=13;I16=10,2,0,0,507,21851,0,0,720,43200,0,0,225,4893,0,0;QS=1,0;MQ0F=0 PL 0,36,255 17 1127 . T <*> 0 . DP=13;I16=10,2,0,0,513,22447,0,0,720,43200,0,0,227,4945,0,0;QS=1,0;MQ0F=0 PL 0,36,255 17 1128 . G <*> 0 . DP=13;I16=10,2,0,0,501,21369,0,0,720,43200,0,0,229,5009,0,0;QS=1,0;MQ0F=0 PL 0,36,255 -17 1129 . A G,<*> 0 . DP=13;I16=10,1,0,1,463,19969,32,1024,660,39600,60,3600,205,4409,25,625;QS=0.935354,0.0646465,0;SGB=-0.379885;RPBZ=-0.724207;MQBZ=0;MQSBZ=0;BQBZ=-1.31512;NMBZ=0;SCBZ=0;FS=0;MQ0F=0 PL 0,4,230,33,233,251 +17 1129 . A G,<*> 0 . DP=13;I16=10,1,0,1,463,19969,32,1024,660,39600,60,3600,205,4409,25,625;QS=0.935354,0.0646465,0;SGB=-0.379885;RPBZ=-0.724207;MQBZ=0;MQSBZ=0;BQBZ=-1.31512;SCBZ=0;FS=0;MQ0F=0 PL 0,4,230,33,233,251 17 1130 . A <*> 0 . DP=13;I16=10,2,0,0,506,21796,0,0,720,43200,0,0,231,5069,0,0;QS=1,0;MQ0F=0 PL 0,36,255 17 1131 . A <*> 0 . DP=13;I16=10,2,0,0,502,21496,0,0,720,43200,0,0,232,5114,0,0;QS=1,0;MQ0F=0 PL 0,36,255 17 1132 . T <*> 0 . DP=13;I16=10,2,0,0,499,21159,0,0,720,43200,0,0,233,5169,0,0;QS=1,0;MQ0F=0 PL 0,36,255 @@ -1244,7 +1243,7 @@ 17 1221 . A <*> 0 . DP=5;I16=2,3,0,0,186,7098,0,0,300,18000,0,0,100,2500,0,0;QS=1,0;MQ0F=0 PL 0,15,163 17 1222 . T <*> 0 . DP=4;I16=1,3,0,0,161,6531,0,0,240,14400,0,0,100,2500,0,0;QS=1,0;MQ0F=0 PL 0,12,142 17 1223 . T <*> 0 . DP=4;I16=1,3,0,0,136,5460,0,0,240,14400,0,0,100,2500,0,0;QS=1,0;MQ0F=0 PL 0,12,124 -17 1224 . C A,<*> 0 . DP=4;I16=1,2,0,1,119,4723,8,64,180,10800,60,3600,75,1875,25,625;QS=0.937008,0.0629921,0;SGB=-0.379885;RPBZ=1.41421;MQBZ=0;MQSBZ=0;BQBZ=-1.41421;NMBZ=0;SCBZ=0;FS=0;MQ0F=0 PL 0,3,103,9,106,106 +17 1224 . C A,<*> 0 . DP=4;I16=1,2,0,1,119,4723,8,64,180,10800,60,3600,75,1875,25,625;QS=0.937008,0.0629921,0;SGB=-0.379885;RPBZ=1.41421;MQBZ=0;MQSBZ=0;BQBZ=-1.41421;SCBZ=0;FS=0;MQ0F=0 PL 0,3,103,9,106,106 17 1225 . A <*> 0 . DP=4;I16=1,3,0,0,162,6572,0,0,240,14400,0,0,100,2500,0,0;QS=1,0;MQ0F=0 PL 0,12,142 17 1226 . A <*> 0 . DP=4;I16=1,3,0,0,168,7058,0,0,240,14400,0,0,100,2500,0,0;QS=1,0;MQ0F=0 PL 0,12,147 17 1227 . A <*> 0 . DP=4;I16=1,3,0,0,167,6977,0,0,240,14400,0,0,100,2500,0,0;QS=1,0;MQ0F=0 PL 0,12,146 @@ -1387,10 +1386,10 @@ 17 1364 . G <*> 0 . DP=9;I16=1,8,0,0,331,12219,0,0,540,32400,0,0,196,4708,0,0;QS=1,0;MQ0F=0 PL 0,27,200 17 1365 . G <*> 0 . DP=9;I16=1,8,0,0,336,12570,0,0,540,32400,0,0,196,4680,0,0;QS=1,0;MQ0F=0 PL 0,27,202 17 1366 . G <*> 0 . DP=9;I16=1,8,0,0,332,12268,0,0,540,32400,0,0,196,4656,0,0;QS=1,0;MQ0F=0 PL 0,27,199 -17 1367 . G C,<*> 0 . DP=9;I16=1,7,0,1,296,10982,27,729,480,28800,60,3600,181,4411,15,225;QS=0.916409,0.0835913,0;SGB=-0.379885;RPBZ=1.55569;MQBZ=0;MQSBZ=0;BQBZ=-1.58251;NMBZ=-0.353553;SCBZ=0;FS=0;MQ0F=0 PL 0,0,171,24,174,189 +17 1367 . G C,<*> 0 . DP=9;I16=1,7,0,1,296,10982,27,729,480,28800,60,3600,181,4411,15,225;QS=0.916409,0.0835913,0;SGB=-0.379885;RPBZ=1.55569;MQBZ=0;MQSBZ=0;BQBZ=-1.58251;SCBZ=0;FS=0;MQ0F=0 PL 0,0,171,24,174,189 17 1368 . A <*> 0 . DP=9;I16=1,8,0,0,320,11562,0,0,540,32400,0,0,196,4620,0,0;QS=1,0;MQ0F=0 PL 0,27,197 17 1369 . T <*> 0 . DP=9;I16=1,8,0,0,309,10987,0,0,540,32400,0,0,196,4608,0,0;QS=1,0;MQ0F=0 PL 0,27,194 -17 1370 . T C,<*> 0 . DP=10;I16=1,8,0,1,347,13421,2,4,540,32400,60,3600,171,3975,25,625;QS=0.988604,0.011396,0;SGB=-0.379885;RPBZ=-0.873038;MQBZ=0;MQSBZ=0;BQBZ=-1.59599;NMBZ=-0.333333;SCBZ=0;FS=0;MQ0F=0 PL 0,20,208,27,211,208 +17 1370 . T C,<*> 0 . DP=10;I16=1,8,0,1,347,13421,2,4,540,32400,60,3600,171,3975,25,625;QS=0.988604,0.011396,0;SGB=-0.379885;RPBZ=-0.873038;MQBZ=0;MQSBZ=0;BQBZ=-1.59599;SCBZ=0;FS=0;MQ0F=0 PL 0,20,208,27,211,208 17 1371 . C <*> 0 . DP=10;I16=1,9,0,0,338,11742,0,0,600,36000,0,0,197,4597,0,0;QS=1,0;MQ0F=0 PL 0,30,196 17 1372 . C <*> 0 . DP=10;I16=1,9,0,0,343,12099,0,0,600,36000,0,0,198,4600,0,0;QS=1,0;MQ0F=0 PL 0,30,200 17 1373 . C <*> 0 . DP=10;I16=1,9,0,0,332,11388,0,0,600,36000,0,0,198,4560,0,0;QS=1,0;MQ0F=0 PL 0,30,195 @@ -1405,7 +1404,7 @@ 17 1382 . G <*> 0 . DP=12;I16=2,10,0,0,425,15501,0,0,720,43200,0,0,197,4421,0,0;QS=1,0;MQ0F=0 PL 0,36,243 17 1383 . C <*> 0 . DP=11;I16=2,9,0,0,398,14630,0,0,660,39600,0,0,199,4423,0,0;QS=1,0;MQ0F=0 PL 0,33,241 17 1384 . C <*> 0 . DP=11;I16=2,9,0,0,392,14362,0,0,660,39600,0,0,201,4437,0,0;QS=1,0;MQ0F=0 PL 0,33,239 -17 1385 . A C,<*> 0 . DP=11;I16=2,8,0,1,369,13727,2,4,600,36000,60,3600,179,3887,24,576;QS=0.989276,0.0107239,0;SGB=-0.379885;RPBZ=-0.633898;MQBZ=0;MQSBZ=0;BQBZ=-1.59571;NMBZ=-0.316228;SCBZ=0;FS=0;MQ0F=0 PL 0,23,229,30,232,229 +17 1385 . A C,<*> 0 . DP=11;I16=2,8,0,1,369,13727,2,4,600,36000,60,3600,179,3887,24,576;QS=0.989276,0.0107239,0;SGB=-0.379885;RPBZ=-0.633898;MQBZ=0;MQSBZ=0;BQBZ=-1.59571;SCBZ=0;FS=0;MQ0F=0 PL 0,23,229,30,232,229 17 1386 . C <*> 0 . DP=11;I16=2,9,0,0,421,16205,0,0,660,39600,0,0,205,4501,0,0;QS=1,0;MQ0F=0 PL 0,33,254 17 1387 . C <*> 0 . DP=11;I16=2,9,0,0,424,16430,0,0,660,39600,0,0,206,4500,0,0;QS=1,0;MQ0F=0 PL 0,33,252 17 1388 . C <*> 0 . DP=11;I16=2,9,0,0,355,11631,0,0,660,39600,0,0,207,4509,0,0;QS=1,0;MQ0F=0 PL 0,33,211 @@ -1479,10 +1478,10 @@ 17 1456 . T <*> 0 . DP=5;I16=2,3,0,0,197,7771,0,0,300,18000,0,0,80,1592,0,0;QS=1,0;MQ0F=0 PL 0,15,170 17 1457 . G <*> 0 . DP=5;I16=2,3,0,0,189,7193,0,0,300,18000,0,0,77,1481,0,0;QS=1,0;MQ0F=0 PL 0,15,164 17 1458 . T <*> 0 . DP=5;I16=2,3,0,0,190,7292,0,0,300,18000,0,0,74,1380,0,0;QS=1,0;MQ0F=0 PL 0,15,165 -17 1459 . C A,<*> 0 . DP=5;I16=2,2,0,1,164,6734,24,576,240,14400,60,3600,69,1285,2,4;QS=0.87234,0.12766,0;SGB=-0.379885;RPBZ=1.41421;MQBZ=0;MQSBZ=0;BQBZ=-1.41421;NMBZ=-0.5;SCBZ=-0.5;FS=0;MQ0F=0 PL 9,0,135,21,138,152 +17 1459 . C A,<*> 0 . DP=5;I16=2,2,0,1,164,6734,24,576,240,14400,60,3600,69,1285,2,4;QS=0.87234,0.12766,0;SGB=-0.379885;RPBZ=1.41421;MQBZ=0;MQSBZ=0;BQBZ=-1.41421;SCBZ=-0.5;FS=0;MQ0F=0 PL 9,0,135,21,138,152 17 1460 . T <*> 0 . DP=5;I16=2,3,0,0,195,7679,0,0,300,18000,0,0,68,1208,0,0;QS=1,0;MQ0F=0 PL 0,15,170 17 1461 . G <*> 0 . DP=5;I16=2,3,0,0,173,6171,0,0,300,18000,0,0,65,1137,0,0;QS=1,0;MQ0F=0 PL 0,15,152 -17 1462 . C G,<*> 0 . DP=4;I16=1,2,1,0,119,4745,5,25,180,10800,60,3600,46,786,17,289;QS=0.959677,0.0403226,0;SGB=-0.379885;RPBZ=-1.34164;MQBZ=0;MQSBZ=0;BQBZ=-1.34164;NMBZ=-0.57735;SCBZ=-0.57735;FS=0;MQ0F=0 PL 0,5,106,9,109,107 +17 1462 . C G,<*> 0 . DP=4;I16=1,2,1,0,119,4745,5,25,180,10800,60,3600,46,786,17,289;QS=0.959677,0.0403226,0;SGB=-0.379885;RPBZ=-1.34164;MQBZ=0;MQSBZ=0;BQBZ=-1.34164;SCBZ=-0.57735;FS=0;MQ0F=0 PL 0,5,106,9,109,107 17 1463 . T <*> 0 . DP=4;I16=2,2,0,0,151,5805,0,0,240,14400,0,0,61,1021,0,0;QS=1,0;MQ0F=0 PL 0,12,139 17 1464 . G <*> 0 . DP=5;I16=2,3,0,0,165,5535,0,0,300,18000,0,0,59,975,0,0;QS=1,0;MQ0F=0 PL 0,15,144 17 1465 . T <*> 0 . DP=5;I16=2,3,0,0,191,7315,0,0,300,18000,0,0,58,938,0,0;QS=1,0;MQ0F=0 PL 0,15,166 @@ -1636,7 +1635,7 @@ 17 1613 . C <*> 0 . DP=2;I16=1,1,0,0,63,2129,0,0,120,7200,0,0,48,1154,0,0;QS=1,0;MQ0F=0 PL 0,6,63 17 1614 . A <*> 0 . DP=2;I16=1,1,0,0,69,2465,0,0,120,7200,0,0,49,1201,0,0;QS=1,0;MQ0F=0 PL 0,6,69 17 1615 . C <*> 0 . DP=2;I16=1,1,0,0,51,1445,0,0,120,7200,0,0,50,1250,0,0;QS=1,0;MQ0F=0 PL 0,6,51 -17 1616 . T C,<*> 0 . DP=2;I16=1,0,0,1,42,1764,1,1,60,3600,60,3600,25,625,25,625;QS=0.913043,0.0869565,0;SGB=-0.379885;RPBZ=-1;MQBZ=0;MQSBZ=0;BQBZ=-1;NMBZ=0;SCBZ=0;FS=0;MQ0F=0 PL 0,1,37,3,40,39 +17 1616 . T C,<*> 0 . DP=2;I16=1,0,0,1,42,1764,1,1,60,3600,60,3600,25,625,25,625;QS=0.913043,0.0869565,0;SGB=-0.379885;RPBZ=-1;MQBZ=0;MQSBZ=0;BQBZ=-1;SCBZ=0;FS=0;MQ0F=0 PL 0,1,37,3,40,39 17 1617 . C <*> 0 . DP=2;I16=1,1,0,0,53,1885,0,0,120,7200,0,0,50,1250,0,0;QS=1,0;MQ0F=0 PL 0,6,53 17 1618 . A <*> 0 . DP=2;I16=1,1,0,0,81,3281,0,0,120,7200,0,0,49,1201,0,0;QS=1,0;MQ0F=0 PL 0,6,81 17 1619 . G <*> 0 . DP=2;I16=1,1,0,0,67,2269,0,0,120,7200,0,0,48,1154,0,0;QS=1,0;MQ0F=0 PL 0,6,67 @@ -1685,7 +1684,7 @@ 17 1662 . C <*> 0 . DP=4;I16=1,3,0,0,123,3901,0,0,209,11641,0,0,86,1996,0,0;QS=1,0;MQ0F=0 PL 0,12,100 17 1663 . C <*> 0 . DP=4;I16=1,3,0,0,124,3894,0,0,209,11641,0,0,87,2019,0,0;QS=1,0;MQ0F=0 PL 0,12,101 17 1664 . A <*> 0 . DP=4;I16=1,3,0,0,130,4468,0,0,209,11641,0,0,88,2044,0,0;QS=1,0;MQ0F=0 PL 0,12,109 -17 1665 . T C,<*> 0 . DP=4;I16=0,2,1,1,68,2330,58,1924,120,7200,89,4441,50,1250,39,821;QS=0.591304,0.408696,0;VDB=0.1;SGB=-0.453602;RPBZ=-1.54919;MQBZ=-1;MQSBZ=1.73205;BQBZ=0;NMBZ=0;SCBZ=0.408248;FS=0;MQ0F=0 PL 35,0,51,41,57,90 +17 1665 . T C,<*> 0 . DP=4;I16=0,2,1,1,68,2330,58,1924,120,7200,89,4441,50,1250,39,821;QS=0.591304,0.408696,0;VDB=0.1;SGB=-0.453602;RPBZ=-1.54919;MQBZ=-1;MQSBZ=1.73205;BQBZ=0;SCBZ=0.408248;FS=0;MQ0F=0 PL 35,0,51,41,57,90 17 1666 . G <*> 0 . DP=4;I16=1,3,0,0,129,4165,0,0,209,11641,0,0,88,2002,0,0;QS=1,0;MQ0F=0 PL 0,12,111 17 1667 . G <*> 0 . DP=4;I16=1,3,0,0,144,5304,0,0,209,11641,0,0,87,1939,0,0;QS=1,0;MQ0F=0 PL 0,12,115 17 1668 . A <*> 0 . DP=4;I16=1,3,0,0,153,5865,0,0,209,11641,0,0,86,1882,0,0;QS=1,0;MQ0F=0 PL 0,12,124 @@ -1699,7 +1698,7 @@ 17 1676 . G <*> 0 . DP=4;I16=1,3,0,0,107,3465,0,0,209,11641,0,0,78,1642,0,0;QS=1,0;MQ0F=0 PL 0,12,95 17 1677 . C <*> 0 . DP=4;I16=1,3,0,0,93,3133,0,0,209,11641,0,0,76,1588,0,0;QS=1,0;MQ0F=0 PL 0,12,74 17 1678 . C <*> 0 . DP=4;I16=1,3,0,0,110,3654,0,0,209,11641,0,0,74,1538,0,0;QS=1,0;MQ0F=0 PL 0,12,87 -17 1679 . A G,<*> 0 . DP=4;I16=1,2,0,1,125,5211,6,36,149,8041,60,3600,47,867,25,625;QS=0.94958,0.0504202,0;SGB=-0.379885;RPBZ=-0.447214;MQBZ=0.57735;MQSBZ=1.73205;BQBZ=-1.41421;NMBZ=1;SCBZ=1.41421;FS=0;MQ0F=0 PL 0,4,99,9,102,101 +17 1679 . A G,<*> 0 . DP=4;I16=1,2,0,1,125,5211,6,36,149,8041,60,3600,47,867,25,625;QS=0.94958,0.0504202,0;SGB=-0.379885;RPBZ=-0.447214;MQBZ=0.57735;MQSBZ=1.73205;BQBZ=-1.41421;SCBZ=1.41421;FS=0;MQ0F=0 PL 0,4,99,9,102,101 17 1680 . G <*> 0 . DP=4;I16=1,3,0,0,130,4382,0,0,209,11641,0,0,70,1450,0,0;QS=1,0;MQ0F=0 PL 0,12,104 17 1681 . C <*> 0 . DP=4;I16=1,3,0,0,95,2849,0,0,209,11641,0,0,68,1412,0,0;QS=1,0;MQ0F=0 PL 0,12,74 17 1682 . G <*> 0 . DP=4;I16=1,3,0,0,111,3081,0,0,209,11641,0,0,66,1378,0,0;QS=1,0;MQ0F=0 PL 0,12,98 @@ -1709,7 +1708,7 @@ 17 1686 . C <*> 0 . DP=4;I16=1,3,0,0,127,4127,0,0,209,11641,0,0,58,1282,0,0;QS=1,0;MQ0F=0 PL 0,12,103 17 1687 . C <*> 0 . DP=4;I16=1,3,0,0,129,4325,0,0,209,11641,0,0,56,1268,0,0;QS=1,0;MQ0F=0 PL 0,12,106 17 1688 . C <*> 0 . DP=4;I16=1,3,0,0,147,5445,0,0,209,11641,0,0,54,1258,0,0;QS=1,0;MQ0F=0 PL 0,12,120 -17 1689 . T A,<*> 0 . DP=4;I16=1,2,0,1,111,4185,33,1089,149,8041,60,3600,27,627,25,625;QS=0.744186,0.255814,0;SGB=-0.379885;RPBZ=-0.447214;MQBZ=0.57735;MQSBZ=1.73205;BQBZ=-0.447214;NMBZ=1;SCBZ=1;FS=0;MQ0F=0 PL 21,0,79,30,82,106 +17 1689 . T A,<*> 0 . DP=4;I16=1,2,0,1,111,4185,33,1089,149,8041,60,3600,27,627,25,625;QS=0.744186,0.255814,0;SGB=-0.379885;RPBZ=-0.447214;MQBZ=0.57735;MQSBZ=1.73205;BQBZ=-0.447214;SCBZ=1;FS=0;MQ0F=0 PL 21,0,79,30,82,106 17 1690 . C <*> 0 . DP=4;I16=1,3,0,0,120,3996,0,0,209,11641,0,0,50,1250,0,0;QS=1,0;MQ0F=0 PL 0,12,95 17 1691 . T <*> 0 . DP=2;I16=1,1,0,0,71,2633,0,0,89,4441,0,0,50,1250,0,0;QS=1,0;MQ0F=0 PL 0,6,57 17 1692 . G <*> 0 . DP=2;I16=1,1,0,0,73,2705,0,0,89,4441,0,0,50,1250,0,0;QS=1,0;MQ0F=0 PL 0,6,61 @@ -1756,7 +1755,7 @@ 17 1733 . C <*> 0 . DP=5;I16=4,1,0,0,170,5934,0,0,269,15241,0,0,99,2235,0,0;QS=1,0;MQ0F=0 PL 0,15,136 17 1734 . C <*> 0 . DP=5;I16=4,1,0,0,176,6536,0,0,269,15241,0,0,99,2213,0,0;QS=1,0;MQ0F=0 PL 0,15,141 17 1735 . T <*> 0 . DP=5;I16=4,1,0,0,193,7605,0,0,269,15241,0,0,99,2195,0,0;QS=1,0;MQ0F=0 PL 0,15,148 -17 1736 . G T,<*> 0 . DP=5;I16=3,1,1,0,142,5070,6,36,209,11641,60,3600,74,1556,25,625;QS=0.957143,0.0428571,0;SGB=-0.379885;RPBZ=-0.725476;MQBZ=0.5;MQSBZ=0.5;BQBZ=-1.41421;NMBZ=2;SCBZ=2;FS=0;MQ0F=0 PL 0,7,111,12,114,112 +17 1736 . G T,<*> 0 . DP=5;I16=3,1,1,0,142,5070,6,36,209,11641,60,3600,74,1556,25,625;QS=0.957143,0.0428571,0;SGB=-0.379885;RPBZ=-0.725476;MQBZ=0.5;MQSBZ=0.5;BQBZ=-1.41421;SCBZ=2;FS=0;MQ0F=0 PL 0,7,111,12,114,112 17 1737 . A <*> 0 . DP=5;I16=4,1,0,0,168,6138,0,0,269,15241,0,0,99,2171,0,0;QS=1,0;MQ0F=0 PL 0,15,131 17 1738 . C <*> 0 . DP=5;I16=4,1,0,0,164,5714,0,0,269,15241,0,0,99,2165,0,0;QS=1,0;MQ0F=0 PL 0,15,130 17 1739 . C <*> 0 . DP=5;I16=4,1,0,0,172,6730,0,0,269,15241,0,0,99,2163,0,0;QS=1,0;MQ0F=0 PL 0,15,138 @@ -1917,7 +1916,7 @@ 17 1894 . G <*> 0 . DP=2;I16=1,1,0,0,75,2817,0,0,120,7200,0,0,6,26,0,0;QS=1,0;MQ0F=0 PL 0,6,75 17 1895 . C <*> 0 . DP=2;I16=1,1,0,0,73,2665,0,0,120,7200,0,0,6,20,0,0;QS=1,0;MQ0F=0 PL 0,6,73 17 1896 . C <*> 0 . DP=2;I16=1,1,0,0,72,2600,0,0,120,7200,0,0,6,18,0,0;QS=1,0;MQ0F=0 PL 0,6,72 -17 1897 . G A,<*> 0 . DP=2;I16=1,0,0,1,27,729,37,1369,60,3600,60,3600,4,16,2,4;QS=0.421875,0.578125,0;SGB=-0.379885;RPBZ=1;MQBZ=0;MQSBZ=0;BQBZ=1;NMBZ=0;SCBZ=0;FS=0;MQ0F=0 PL 31,0,21,34,24,55 +17 1897 . G A,<*> 0 . DP=2;I16=1,0,0,1,27,729,37,1369,60,3600,60,3600,4,16,2,4;QS=0.421875,0.578125,0;SGB=-0.379885;RPBZ=1;MQBZ=0;MQSBZ=0;BQBZ=1;SCBZ=0;FS=0;MQ0F=0 PL 31,0,21,34,24,55 17 1898 . T <*> 0 . DP=3;I16=2,1,0,0,106,3790,0,0,180,10800,0,0,6,26,0,0;QS=1,0;MQ0F=0 PL 0,9,100 17 1899 . G <*> 0 . DP=3;I16=2,1,0,0,100,3334,0,0,180,10800,0,0,7,37,0,0;QS=1,0;MQ0F=0 PL 0,9,94 17 1900 . T <*> 0 . DP=2;I16=2,0,0,0,76,2890,0,0,120,7200,0,0,9,53,0,0;QS=1,0;MQ0F=0 PL 0,6,69 @@ -1959,7 +1958,7 @@ 17 1936 . C <*> 0 . DP=5;I16=2,3,0,0,181,6735,0,0,269,15241,0,0,93,2051,0,0;QS=1,0;MQ0F=0 PL 0,15,159 17 1937 . T <*> 0 . DP=5;I16=2,3,0,0,195,7741,0,0,269,15241,0,0,96,2140,0,0;QS=1,0;MQ0F=0 PL 0,15,170 17 1938 . G <*> 0 . DP=5;I16=2,3,0,0,176,6536,0,0,269,15241,0,0,99,2235,0,0;QS=1,0;MQ0F=0 PL 0,15,155 -17 1939 . T C,<*> 0 . DP=5;I16=2,2,0,1,158,6250,3,9,240,14400,29,841,82,1924,19,361;QS=0.975309,0.0246914,0;SGB=-0.379885;RPBZ=-0.707107;MQBZ=-2;MQSBZ=-0.816497;BQBZ=-1.49071;NMBZ=1.22474;SCBZ=-0.5;FS=0;MQ0F=0 PL 0,8,138,12,141,138 +17 1939 . T C,<*> 0 . DP=5;I16=2,2,0,1,158,6250,3,9,240,14400,29,841,82,1924,19,361;QS=0.975309,0.0246914,0;SGB=-0.379885;RPBZ=-0.707107;MQBZ=-2;MQSBZ=-0.816497;BQBZ=-1.49071;SCBZ=-0.5;FS=0;MQ0F=0 PL 0,8,138,12,141,138 17 1940 . G <*> 0 . DP=5;I16=2,3,0,0,177,6449,0,0,269,15241,0,0,103,2339,0,0;QS=1,0;MQ0F=0 PL 0,15,155 17 1941 . G <*> 0 . DP=5;I16=2,3,0,0,180,6620,0,0,269,15241,0,0,105,2397,0,0;QS=1,0;MQ0F=0 PL 0,15,156 17 1942 . C <*> 0 . DP=5;I16=2,3,0,0,161,5973,0,0,269,15241,0,0,107,2459,0,0;QS=1,0;MQ0F=0 PL 0,15,144 @@ -1968,16 +1967,16 @@ 17 1945 . T <*> 0 . DP=5;I16=2,3,0,0,200,8062,0,0,269,15241,0,0,113,2669,0,0;QS=1,0;MQ0F=0 PL 0,15,171 17 1946 . G <*> 0 . DP=5;I16=2,3,0,0,188,7132,0,0,269,15241,0,0,114,2696,0,0;QS=1,0;MQ0F=0 PL 0,15,162 17 1947 . A <*> 0 . DP=5;I16=2,3,0,0,181,6939,0,0,269,15241,0,0,115,2725,0,0;QS=1,0;MQ0F=0 PL 0,15,160 -17 1948 . G C,<*> 0 . DP=5;I16=2,2,0,1,150,5708,16,256,240,14400,29,841,91,2131,25,625;QS=0.903614,0.0963855,0;SGB=-0.379885;RPBZ=-0.707107;MQBZ=-2;MQSBZ=-0.816497;BQBZ=-1.41421;NMBZ=1.22474;SCBZ=-0.5;FS=0;MQ0F=0 PL 1,0,123,13,126,132 +17 1948 . G C,<*> 0 . DP=5;I16=2,2,0,1,150,5708,16,256,240,14400,29,841,91,2131,25,625;QS=0.903614,0.0963855,0;SGB=-0.379885;RPBZ=-0.707107;MQBZ=-2;MQSBZ=-0.816497;BQBZ=-1.41421;SCBZ=-0.5;FS=0;MQ0F=0 PL 1,0,123,13,126,132 17 1949 . A <*> 0 . DP=5;I16=2,3,0,0,181,6599,0,0,269,15241,0,0,117,2789,0,0;QS=1,0;MQ0F=0 PL 0,15,155 17 1950 . A <*> 0 . DP=6;I16=2,4,0,0,222,8392,0,0,329,18841,0,0,118,2824,0,0;QS=1,0;MQ0F=0 PL 0,18,178 17 1951 . G <*> 0 . DP=6;I16=2,4,0,0,225,8533,0,0,329,18841,0,0,120,2862,0,0;QS=1,0;MQ0F=0 PL 0,18,181 17 1952 . A <*> 0 . DP=6;I16=2,4,0,0,219,8221,0,0,329,18841,0,0,122,2904,0,0;QS=1,0;MQ0F=0 PL 0,18,182 17 1953 . A <*> 0 . DP=6;I16=2,4,0,0,201,7161,0,0,329,18841,0,0,124,2950,0,0;QS=1,0;MQ0F=0 PL 0,18,168 -17 1954 . A C,<*> 0 . DP=6;I16=2,3,0,1,166,5942,18,324,300,18000,29,841,101,2375,25,625;QS=0.902174,0.0978261,0;SGB=-0.379885;RPBZ=-0.29277;MQBZ=-2.23607;MQSBZ=-0.707107;BQBZ=-0.87831;NMBZ=1.41421;SCBZ=-0.447214;FS=0;MQ0F=0 PL 0,0,130,15,133,141 +17 1954 . A C,<*> 0 . DP=6;I16=2,3,0,1,166,5942,18,324,300,18000,29,841,101,2375,25,625;QS=0.902174,0.0978261,0;SGB=-0.379885;RPBZ=-0.29277;MQBZ=-2.23607;MQSBZ=-0.707107;BQBZ=-0.87831;SCBZ=-0.447214;FS=0;MQ0F=0 PL 0,0,130,15,133,141 17 1955 . C <*> 0 . DP=6;I16=2,4,0,0,200,7332,0,0,329,18841,0,0,128,3054,0,0;QS=1,0;MQ0F=0 PL 0,18,168 17 1956 . C <*> 0 . DP=6;I16=2,4,0,0,191,7215,0,0,329,18841,0,0,130,3112,0,0;QS=1,0;MQ0F=0 PL 0,18,164 -17 1957 . C G,<*> 0 . DP=6;I16=2,3,0,1,192,7426,7,49,300,18000,29,841,107,2549,25,625;QS=0.964824,0.0351759,0;SGB=-0.379885;RPBZ=-0.29277;MQBZ=-2.23607;MQSBZ=-0.707107;BQBZ=-1.48522;NMBZ=1.41421;SCBZ=-0.447214;FS=0;MQ0F=0 PL 0,9,159,15,162,161 +17 1957 . C G,<*> 0 . DP=6;I16=2,3,0,1,192,7426,7,49,300,18000,29,841,107,2549,25,625;QS=0.964824,0.0351759,0;SGB=-0.379885;RPBZ=-0.29277;MQBZ=-2.23607;MQSBZ=-0.707107;BQBZ=-1.48522;SCBZ=-0.447214;FS=0;MQ0F=0 PL 0,9,159,15,162,161 17 1958 . C <*> 0 . DP=6;I16=2,4,0,0,234,9220,0,0,329,18841,0,0,133,3189,0,0;QS=1,0;MQ0F=0 PL 0,18,190 17 1959 . T <*> 0 . DP=6;I16=2,4,0,0,233,9255,0,0,329,18841,0,0,134,3206,0,0;QS=1,0;MQ0F=0 PL 0,18,193 17 1960 . T <*> 0 . DP=6;I16=2,4,0,0,227,8703,0,0,329,18841,0,0,135,3225,0,0;QS=1,0;MQ0F=0 PL 0,18,186 @@ -2006,11 +2005,11 @@ 17 1983 . G <*> 0 . DP=9;I16=4,5,0,0,337,12781,0,0,509,29641,0,0,140,2974,0,0;QS=1,0;MQ0F=0 PL 0,27,249 17 1984 . A <*> 0 . DP=9;I16=4,5,0,0,355,14231,0,0,509,29641,0,0,141,2959,0,0;QS=1,0;MQ0F=0 PL 0,27,255 17 1985 . G <*> 0 . DP=9;I16=4,5,0,0,307,10921,0,0,509,29641,0,0,142,2954,0,0;QS=1,0;MQ0F=0 PL 0,27,231 -17 1986 . A T,<*> 0 . DP=9;I16=4,4,0,1,287,10695,12,144,480,28800,29,841,118,2334,25,625;QS=0.959866,0.0401338,0;SGB=-0.379885;RPBZ=0.387298;MQBZ=-2.82843;MQSBZ=-0.894427;BQBZ=-1.55569;NMBZ=1.15728;SCBZ=-0.53033;FS=0;MQ0F=0 PL 0,14,213,24,216,217 +17 1986 . A T,<*> 0 . DP=9;I16=4,4,0,1,287,10695,12,144,480,28800,29,841,118,2334,25,625;QS=0.959866,0.0401338,0;SGB=-0.379885;RPBZ=0.387298;MQBZ=-2.82843;MQSBZ=-0.894427;BQBZ=-1.55569;SCBZ=-0.53033;FS=0;MQ0F=0 PL 0,14,213,24,216,217 17 1987 . A <*> 0 . DP=9;I16=4,5,0,0,333,12731,0,0,509,29641,0,0,144,2974,0,0;QS=1,0;MQ0F=0 PL 0,27,247 17 1988 . G <*> 0 . DP=9;I16=4,5,0,0,324,12106,0,0,509,29641,0,0,145,2999,0,0;QS=1,0;MQ0F=0 PL 0,27,239 17 1989 . G <*> 0 . DP=9;I16=4,5,0,0,322,12030,0,0,509,29641,0,0,145,2985,0,0;QS=1,0;MQ0F=0 PL 0,27,237 -17 1990 . G T,<*> 0 . DP=9;I16=4,4,0,1,282,10212,33,1089,480,28800,29,841,120,2358,25,625;QS=0.906752,0.0932476,0;SGB=-0.379885;RPBZ=0.387298;MQBZ=-2.82843;MQSBZ=-0.894427;BQBZ=-0.58585;NMBZ=1.15728;SCBZ=-0.53033;FS=0;MQ0F=0 PL 2,0,195,26,198,215 +17 1990 . G T,<*> 0 . DP=9;I16=4,4,0,1,282,10212,33,1089,480,28800,29,841,120,2358,25,625;QS=0.906752,0.0932476,0;SGB=-0.379885;RPBZ=0.387298;MQBZ=-2.82843;MQSBZ=-0.894427;BQBZ=-0.58585;SCBZ=-0.53033;FS=0;MQ0F=0 PL 2,0,195,26,198,215 17 1991 . A <*> 0 . DP=9;I16=4,5,0,0,335,13049,0,0,509,29641,0,0,145,2993,0,0;QS=1,0;MQ0F=0 PL 0,27,250 17 1992 . G <*> 0 . DP=9;I16=4,5,0,0,307,11009,0,0,509,29641,0,0,145,3015,0,0;QS=1,0;MQ0F=0 PL 0,27,231 17 1993 . T <*> 0 . DP=9;I16=4,5,0,0,344,13332,0,0,509,29641,0,0,145,3049,0,0;QS=1,0;MQ0F=0 PL 0,27,248 @@ -2030,8 +2029,8 @@ 17 2007 . A <*> 0 . DP=7;I16=2,5,0,0,249,9041,0,0,389,22441,0,0,144,3330,0,0;QS=1,0;MQ0F=0 PL 0,21,193 17 2008 . C <*> 0 . DP=7;I16=2,5,0,0,232,8210,0,0,389,22441,0,0,141,3245,0,0;QS=1,0;MQ0F=0 PL 0,21,183 17 2009 . A <*> 0 . DP=7;I16=2,5,0,0,266,10628,0,0,389,22441,0,0,138,3166,0,0;QS=1,0;MQ0F=0 PL 0,21,210 -17 2010 . G C,<*> 0 . DP=7;I16=2,4,0,1,204,7382,10,100,360,21600,29,841,125,2993,10,100;QS=0.953271,0.046729,0;SGB=-0.379885;RPBZ=1;MQBZ=-2.44949;MQSBZ=-0.632456;BQBZ=-1.51357;NMBZ=0.83666;SCBZ=-0.62361;FS=0;MQ0F=0 PL 0,10,160,18,163,163 -17 2011 . C T,<*> 0 . DP=7;I16=2,4,0,1,211,7627,6,36,360,21600,29,841,123,2945,9,81;QS=0.97235,0.0276498,0;SGB=-0.379885;RPBZ=1;MQBZ=-2.44949;MQSBZ=-0.632456;BQBZ=-1.51357;NMBZ=0.83666;SCBZ=-0.62361;FS=0;MQ0F=0 PL 0,12,168,18,171,168 +17 2010 . G C,<*> 0 . DP=7;I16=2,4,0,1,204,7382,10,100,360,21600,29,841,125,2993,10,100;QS=0.953271,0.046729,0;SGB=-0.379885;RPBZ=1;MQBZ=-2.44949;MQSBZ=-0.632456;BQBZ=-1.51357;SCBZ=-0.62361;FS=0;MQ0F=0 PL 0,10,160,18,163,163 +17 2011 . C T,<*> 0 . DP=7;I16=2,4,0,1,211,7627,6,36,360,21600,29,841,123,2945,9,81;QS=0.97235,0.0276498,0;SGB=-0.379885;RPBZ=1;MQBZ=-2.44949;MQSBZ=-0.632456;BQBZ=-1.51357;SCBZ=-0.62361;FS=0;MQ0F=0 PL 0,12,168,18,171,168 17 2012 . A <*> 0 . DP=7;I16=2,5,0,0,239,8743,0,0,389,22441,0,0,129,2965,0,0;QS=1,0;MQ0F=0 PL 0,21,189 17 2013 . C <*> 0 . DP=7;I16=2,5,0,0,198,6510,0,0,389,22441,0,0,126,2910,0,0;QS=1,0;MQ0F=0 PL 0,21,159 17 2014 . G <*> 0 . DP=6;I16=2,4,0,0,195,6881,0,0,329,18841,0,0,124,2860,0,0;QS=1,0;MQ0F=0 PL 0,18,160 @@ -2080,7 +2079,7 @@ 17 2057 . T <*> 0 . DP=6;I16=4,2,0,0,219,8015,0,0,360,21600,0,0,138,3272,0,0;QS=1,0;MQ0F=0 PL 0,18,178 17 2058 . A <*> 0 . DP=6;I16=4,2,0,0,217,7929,0,0,360,21600,0,0,135,3149,0,0;QS=1,0;MQ0F=0 PL 0,18,179 17 2059 . A <*> 0 . DP=6;I16=4,2,0,0,224,8446,0,0,360,21600,0,0,132,3032,0,0;QS=1,0;MQ0F=0 PL 0,18,184 -17 2060 . C G,<*> 0 . DP=6;I16=3,2,1,0,162,5622,2,4,300,18000,60,3600,107,2437,22,484;QS=0.975904,0.0240964,0;SGB=-0.379885;RPBZ=1.48522;MQBZ=0;MQSBZ=0;BQBZ=-1.46385;NMBZ=1.73205;SCBZ=1.73205;FS=0;MQ0F=0 PL 0,10,137,15,140,137 +17 2060 . C G,<*> 0 . DP=6;I16=3,2,1,0,162,5622,2,4,300,18000,60,3600,107,2437,22,484;QS=0.975904,0.0240964,0;SGB=-0.379885;RPBZ=1.48522;MQBZ=0;MQSBZ=0;BQBZ=-1.46385;SCBZ=1.73205;FS=0;MQ0F=0 PL 0,10,137,15,140,137 17 2061 . A <*> 0 . DP=5;I16=3,2,0,0,187,7029,0,0,300,18000,0,0,105,2375,0,0;QS=1,0;MQ0F=0 PL 0,15,163 17 2062 . A <*> 0 . DP=5;I16=3,2,0,0,187,7195,0,0,300,18000,0,0,103,2317,0,0;QS=1,0;MQ0F=0 PL 0,15,164 17 2063 . C <*> 0 . DP=5;I16=3,2,0,0,182,6678,0,0,300,18000,0,0,101,2263,0,0;QS=1,0;MQ0F=0 PL 0,15,158 @@ -2096,7 +2095,7 @@ 17 2073 . C <*> 0 . DP=5;I16=4,1,0,0,161,5287,0,0,300,18000,0,0,91,2003,0,0;QS=1,0;MQ0F=0 PL 0,15,133 17 2074 . G <*> 0 . DP=5;I16=4,1,0,0,104,2430,0,0,300,18000,0,0,91,2005,0,0;QS=1,0;MQ0F=0 PL 0,15,87 17 2075 . C <*> 0 . DP=5;I16=4,1,0,0,138,3910,0,0,300,18000,0,0,91,2011,0,0;QS=1,0;MQ0F=0 PL 0,15,113 -17 2076 . A G,<*> 0 . DP=5;I16=3,1,1,0,130,4242,1,1,240,14400,60,3600,80,1900,11,121;QS=0.970149,0.0298507,0;SGB=-0.379885;RPBZ=-1.45095;MQBZ=0;MQSBZ=0;BQBZ=-1.45095;NMBZ=-0.5;SCBZ=-0.5;FS=0;MQ0F=0 PL 0,8,108,12,111,108 +17 2076 . A G,<*> 0 . DP=5;I16=3,1,1,0,130,4242,1,1,240,14400,60,3600,80,1900,11,121;QS=0.970149,0.0298507,0;SGB=-0.379885;RPBZ=-1.45095;MQBZ=0;MQSBZ=0;BQBZ=-1.45095;SCBZ=-0.5;FS=0;MQ0F=0 PL 0,8,108,12,111,108 17 2077 . C <*> 0 . DP=5;I16=4,1,0,0,150,4766,0,0,300,18000,0,0,91,2035,0,0;QS=1,0;MQ0F=0 PL 0,15,125 17 2078 . A <*> 0 . DP=5;I16=4,1,0,0,180,6606,0,0,300,18000,0,0,91,2053,0,0;QS=1,0;MQ0F=0 PL 0,15,148 17 2079 . G <*> 0 . DP=5;I16=4,1,0,0,160,5324,0,0,300,18000,0,0,91,2075,0,0;QS=1,0;MQ0F=0 PL 0,15,133 @@ -2187,7 +2186,7 @@ 17 2164 . G <*> 0 . DP=5;I16=3,2,0,0,179,6519,0,0,300,18000,0,0,95,2237,0,0;QS=1,0;MQ0F=0 PL 0,15,156 17 2165 . C <*> 0 . DP=5;I16=3,2,0,0,173,6199,0,0,300,18000,0,0,94,2226,0,0;QS=1,0;MQ0F=0 PL 0,15,151 17 2166 . T <*> 0 . DP=4;I16=2,2,0,0,152,5976,0,0,240,14400,0,0,94,2220,0,0;QS=1,0;MQ0F=0 PL 0,12,140 -17 2167 . A G,<*> 0 . DP=4;I16=2,1,0,1,117,4565,7,49,180,10800,60,3600,72,1734,22,484;QS=0.943548,0.0564516,0;SGB=-0.379885;RPBZ=-1.34164;MQBZ=0;MQSBZ=0;BQBZ=-1.34164;NMBZ=1.73205;SCBZ=1.73205;FS=0;MQ0F=0 PL 0,4,103,9,106,105 +17 2167 . A G,<*> 0 . DP=4;I16=2,1,0,1,117,4565,7,49,180,10800,60,3600,72,1734,22,484;QS=0.943548,0.0564516,0;SGB=-0.379885;RPBZ=-1.34164;MQBZ=0;MQSBZ=0;BQBZ=-1.34164;SCBZ=1.73205;FS=0;MQ0F=0 PL 0,4,103,9,106,105 17 2168 . C <*> 0 . DP=4;I16=2,2,0,0,135,4671,0,0,240,14400,0,0,93,2171,0,0;QS=1,0;MQ0F=0 PL 0,12,124 17 2169 . T <*> 0 . DP=4;I16=2,2,0,0,154,6034,0,0,240,14400,0,0,92,2130,0,0;QS=1,0;MQ0F=0 PL 0,12,142 17 2170 . C <*> 0 . DP=4;I16=2,2,0,0,147,5435,0,0,240,14400,0,0,91,2095,0,0;QS=1,0;MQ0F=0 PL 0,12,135 @@ -2334,7 +2333,7 @@ 17 2311 . A <*> 0 . DP=4;I16=2,2,0,0,149,5751,0,0,240,14400,0,0,75,1563,0,0;QS=1,0;MQ0F=0 PL 0,12,137 17 2312 . G <*> 0 . DP=4;I16=2,2,0,0,138,5634,0,0,240,14400,0,0,77,1615,0,0;QS=1,0;MQ0F=0 PL 0,12,128 17 2313 . C <*> 0 . DP=4;I16=2,2,0,0,141,5299,0,0,240,14400,0,0,79,1671,0,0;QS=1,0;MQ0F=0 PL 0,12,130 -17 2314 . A C,<*> 0 . DP=4;I16=2,1,0,1,122,4964,6,36,180,10800,60,3600,66,1506,15,225;QS=0.953125,0.046875,0;SGB=-0.379885;RPBZ=-1.34164;MQBZ=0;MQSBZ=0;BQBZ=-1.41421;NMBZ=1.73205;SCBZ=1.73205;FS=0;MQ0F=0 PL 0,4,107,9,110,109 +17 2314 . A C,<*> 0 . DP=4;I16=2,1,0,1,122,4964,6,36,180,10800,60,3600,66,1506,15,225;QS=0.953125,0.046875,0;SGB=-0.379885;RPBZ=-1.34164;MQBZ=0;MQSBZ=0;BQBZ=-1.41421;SCBZ=1.73205;FS=0;MQ0F=0 PL 0,4,107,9,110,109 17 2315 . C <*> 0 . DP=5;I16=2,3,0,0,149,5511,0,0,300,18000,0,0,91,1859,0,0;QS=1,0;MQ0F=0 PL 0,15,135 17 2316 . T <*> 0 . DP=5;I16=2,3,0,0,193,7565,0,0,300,18000,0,0,94,1944,0,0;QS=1,0;MQ0F=0 PL 0,15,168 17 2317 . T <*> 0 . DP=5;I16=2,3,0,0,196,7722,0,0,300,18000,0,0,97,2035,0,0;QS=1,0;MQ0F=0 PL 0,15,170 @@ -2382,7 +2381,7 @@ 17 2359 . G <*> 0 . DP=7;I16=2,5,0,0,275,10815,0,0,420,25200,0,0,150,3478,0,0;QS=1,0;MQ0F=0 PL 0,21,209 17 2360 . A <*> 0 . DP=7;I16=2,5,0,0,286,11734,0,0,420,25200,0,0,148,3430,0,0;QS=1,0;MQ0F=0 PL 0,21,220 17 2361 . G <*> 0 . DP=7;I16=2,5,0,0,211,7113,0,0,420,25200,0,0,146,3386,0,0;QS=1,0;MQ0F=0 PL 0,21,168 -17 2362 . A C,<*> 0 . DP=7;I16=2,4,0,1,189,6417,4,16,360,21600,60,3600,119,2721,25,625;QS=0.979275,0.0207254,0;SGB=-0.379885;RPBZ=0;MQBZ=0;MQSBZ=0;BQBZ=-1.5;NMBZ=1.24722;SCBZ=-0.408248;FS=0;MQ0F=0 PL 0,12,152,18,155,152 +17 2362 . A C,<*> 0 . DP=7;I16=2,4,0,1,189,6417,4,16,360,21600,60,3600,119,2721,25,625;QS=0.979275,0.0207254,0;SGB=-0.379885;RPBZ=0;MQBZ=0;MQSBZ=0;BQBZ=-1.5;SCBZ=-0.408248;FS=0;MQ0F=0 PL 0,12,152,18,155,152 17 2363 . C <*> 0 . DP=7;I16=2,5,0,0,236,8478,0,0,420,25200,0,0,142,3310,0,0;QS=1,0;MQ0F=0 PL 0,21,187 17 2364 . C <*> 0 . DP=7;I16=2,5,0,0,263,9923,0,0,420,25200,0,0,140,3278,0,0;QS=1,0;MQ0F=0 PL 0,21,201 17 2365 . A <*> 0 . DP=7;I16=2,5,0,0,286,11700,0,0,420,25200,0,0,138,3250,0,0;QS=1,0;MQ0F=0 PL 0,21,221 @@ -2562,7 +2561,7 @@ 17 2539 . C <*> 0 . DP=4;I16=2,2,0,0,125,3961,0,0,240,14400,0,0,76,1876,0,0;QS=1,0;MQ0F=0 PL 0,12,115 17 2540 . G <*> 0 . DP=4;I16=2,2,0,0,119,4027,0,0,240,14400,0,0,77,1879,0,0;QS=1,0;MQ0F=0 PL 0,12,110 17 2541 . G <*> 0 . DP=4;I16=2,2,0,0,153,5891,0,0,240,14400,0,0,78,1884,0,0;QS=1,0;MQ0F=0 PL 0,12,140 -17 2542 . T A,<*> 0 . DP=4;I16=1,2,1,0,116,4534,7,49,180,10800,60,3600,75,1875,4,16;QS=0.943089,0.0569106,0;SGB=-0.379885;RPBZ=-1.34164;MQBZ=0;MQSBZ=0;BQBZ=-1.34164;NMBZ=1.73205;SCBZ=0;FS=0;MQ0F=0 PL 0,4,101,9,104,104 +17 2542 . T A,<*> 0 . DP=4;I16=1,2,1,0,116,4534,7,49,180,10800,60,3600,75,1875,4,16;QS=0.943089,0.0569106,0;SGB=-0.379885;RPBZ=-1.34164;MQBZ=0;MQSBZ=0;BQBZ=-1.34164;SCBZ=0;FS=0;MQ0F=0 PL 0,4,101,9,104,104 17 2543 . G <*> 0 . DP=4;I16=2,2,0,0,127,4511,0,0,240,14400,0,0,80,1900,0,0;QS=1,0;MQ0F=0 PL 0,12,117 17 2544 . A <*> 0 . DP=4;I16=2,2,0,0,143,5367,0,0,240,14400,0,0,81,1911,0,0;QS=1,0;MQ0F=0 PL 0,12,132 17 2545 . C <*> 0 . DP=4;I16=2,2,0,0,142,5122,0,0,240,14400,0,0,82,1924,0,0;QS=1,0;MQ0F=0 PL 0,12,130 @@ -2607,7 +2606,7 @@ 17 2584 . A <*> 0 . DP=6;I16=4,2,0,0,227,8731,0,0,360,21600,0,0,99,2015,0,0;QS=1,0;MQ0F=0 PL 0,18,187 17 2585 . A <*> 0 . DP=6;I16=4,2,0,0,232,9042,0,0,360,21600,0,0,99,2005,0,0;QS=1,0;MQ0F=0 PL 0,18,190 17 2586 . G <*> 0 . DP=6;I16=4,2,0,0,213,7767,0,0,360,21600,0,0,99,2003,0,0;QS=1,0;MQ0F=0 PL 0,18,176 -17 2587 . A C,<*> 0 . DP=6;I16=3,2,1,0,157,5641,6,36,300,18000,60,3600,74,1384,25,625;QS=0.96319,0.0368098,0;SGB=-0.379885;RPBZ=0.29277;MQBZ=0;MQSBZ=0;BQBZ=-1.46385;NMBZ=1.03923;SCBZ=-0.447214;FS=0;MQ0F=0 PL 0,9,133,15,136,134 +17 2587 . A C,<*> 0 . DP=6;I16=3,2,1,0,157,5641,6,36,300,18000,60,3600,74,1384,25,625;QS=0.96319,0.0368098,0;SGB=-0.379885;RPBZ=0.29277;MQBZ=0;MQSBZ=0;BQBZ=-1.46385;SCBZ=-0.447214;FS=0;MQ0F=0 PL 0,9,133,15,136,134 17 2588 . A <*> 0 . DP=6;I16=4,2,0,0,197,6815,0,0,360,21600,0,0,99,2023,0,0;QS=1,0;MQ0F=0 PL 0,18,165 17 2589 . A <*> 0 . DP=6;I16=4,2,0,0,209,7591,0,0,360,21600,0,0,99,2045,0,0;QS=1,0;MQ0F=0 PL 0,18,174 17 2590 . A <*> 0 . DP=6;I16=4,2,0,0,193,6705,0,0,360,21600,0,0,99,2075,0,0;QS=1,0;MQ0F=0 PL 0,18,163 @@ -2733,11 +2732,11 @@ 17 2710 . C <*> 0 . DP=2;I16=1,1,0,0,47,1525,0,0,89,4441,0,0,43,949,0,0;QS=1,0;MQ0F=0 PL 0,6,47 17 2711 . T <*> 0 . DP=2;I16=1,1,0,0,78,3074,0,0,89,4441,0,0,42,914,0,0;QS=1,0;MQ0F=0 PL 0,6,72 17 2712 . A <*> 0 . DP=2;I16=1,1,0,0,66,2196,0,0,89,4441,0,0,41,881,0,0;QS=1,0;MQ0F=0 PL 0,6,65 -17 2713 . G T,<*> 0 . DP=2;I16=1,0,0,1,37,1369,14,196,60,3600,29,841,15,225,25,625;QS=0.72549,0.27451,0;SGB=-0.379885;RPBZ=-1;MQBZ=-1;MQSBZ=-1;BQBZ=-1;NMBZ=1;SCBZ=1;FS=0;MQ0F=0 PL 8,0,31,11,34,42 +17 2713 . G T,<*> 0 . DP=2;I16=1,0,0,1,37,1369,14,196,60,3600,29,841,15,225,25,625;QS=0.72549,0.27451,0;SGB=-0.379885;RPBZ=-1;MQBZ=-1;MQSBZ=-1;BQBZ=-1;SCBZ=1;FS=0;MQ0F=0 PL 8,0,31,11,34,42 17 2714 . G <*> 0 . DP=2;I16=1,1,0,0,65,2125,0,0,89,4441,0,0,39,821,0,0;QS=1,0;MQ0F=0 PL 0,6,64 17 2715 . A <*> 0 . DP=2;I16=1,1,0,0,63,2069,0,0,89,4441,0,0,38,794,0,0;QS=1,0;MQ0F=0 PL 0,6,63 17 2716 . T <*> 0 . DP=3;I16=1,2,0,0,95,3097,0,0,149,8041,0,0,37,769,0,0;QS=1,0;MQ0F=0 PL 0,9,90 -17 2717 . G T,<*> 0 . DP=3;I16=1,1,0,1,72,2592,9,81,120,7200,29,841,12,122,25,625;QS=0.888889,0.111111,0;SGB=-0.379885;RPBZ=0;MQBZ=-1.41421;MQSBZ=-0.707107;BQBZ=-1.41421;NMBZ=1.22474;SCBZ=1.22474;FS=0;MQ0F=0 PL 1,0,63,7,66,68 +17 2717 . G T,<*> 0 . DP=3;I16=1,1,0,1,72,2592,9,81,120,7200,29,841,12,122,25,625;QS=0.888889,0.111111,0;SGB=-0.379885;RPBZ=0;MQBZ=-1.41421;MQSBZ=-0.707107;BQBZ=-1.41421;SCBZ=1.22474;FS=0;MQ0F=0 PL 1,0,63,7,66,68 17 2718 . C <*> 0 . DP=3;I16=1,2,0,0,74,2234,0,0,149,8041,0,0,37,729,0,0;QS=1,0;MQ0F=0 PL 0,9,71 17 2719 . A <*> 0 . DP=3;I16=1,2,0,0,115,4427,0,0,149,8041,0,0,37,715,0,0;QS=1,0;MQ0F=0 PL 0,9,99 17 2720 . G <*> 0 . DP=3;I16=1,2,0,0,108,3902,0,0,149,8041,0,0,37,705,0,0;QS=1,0;MQ0F=0 PL 0,9,97 @@ -2753,7 +2752,7 @@ 17 2730 . G <*> 0 . DP=2;I16=0,2,0,0,52,1640,0,0,89,4441,0,0,39,821,0,0;QS=1,0;MQ0F=0 PL 0,6,49 17 2731 . C <*> 0 . DP=2;I16=0,2,0,0,57,1637,0,0,89,4441,0,0,40,850,0,0;QS=1,0;MQ0F=0 PL 0,6,52 17 2732 . C <*> 0 . DP=2;I16=0,2,0,0,41,881,0,0,89,4441,0,0,41,881,0,0;QS=1,0;MQ0F=0 PL 0,6,38 -17 2733 . C A,<*> 0 . DP=2;I16=0,1,0,1,24,576,13,169,60,3600,29,841,17,289,25,625;QS=0.648649,0.351351,0;SGB=-0.379885;RPBZ=1;MQBZ=-1;BQBZ=-1;NMBZ=1;SCBZ=1;FS=0;MQ0F=0 PL 7,0,18,10,21,28 +17 2733 . C A,<*> 0 . DP=2;I16=0,1,0,1,24,576,13,169,60,3600,29,841,17,289,25,625;QS=0.648649,0.351351,0;SGB=-0.379885;RPBZ=1;MQBZ=-1;BQBZ=-1;SCBZ=1;FS=0;MQ0F=0 PL 7,0,18,10,21,28 17 2734 . C <*> 0 . DP=2;I16=0,2,0,0,46,1570,0,0,89,4441,0,0,43,949,0,0;QS=1,0;MQ0F=0 PL 0,6,44 17 2735 . T <*> 0 . DP=2;I16=0,2,0,0,48,1730,0,0,89,4441,0,0,44,986,0,0;QS=1,0;MQ0F=0 PL 0,6,46 17 2736 . C <*> 0 . DP=2;I16=0,2,0,0,40,1138,0,0,89,4441,0,0,45,1025,0,0;QS=1,0;MQ0F=0 PL 0,6,38 @@ -2775,7 +2774,7 @@ 17 2752 . T <*> 0 . DP=4;I16=2,2,0,0,130,4356,0,0,209,11641,0,0,63,1327,0,0;QS=1,0;MQ0F=0 PL 0,12,119 17 2753 . G <*> 0 . DP=4;I16=2,2,0,0,126,4374,0,0,209,11641,0,0,64,1314,0,0;QS=1,0;MQ0F=0 PL 0,12,116 17 2754 . C <*> 0 . DP=4;I16=2,2,0,0,120,4208,0,0,209,11641,0,0,65,1307,0,0;QS=1,0;MQ0F=0 PL 0,12,111 -17 2755 . C G,<*> 0 . DP=4;I16=2,1,0,1,103,3709,7,49,180,10800,29,841,46,906,20,400;QS=0.936364,0.0636364,0;SGB=-0.379885;RPBZ=1.34164;MQBZ=-1.73205;MQSBZ=-1;BQBZ=-1.34164;NMBZ=1.41421;SCBZ=1.73205;FS=0;MQ0F=0 PL 0,4,89,9,92,91 +17 2755 . C G,<*> 0 . DP=4;I16=2,1,0,1,103,3709,7,49,180,10800,29,841,46,906,20,400;QS=0.936364,0.0636364,0;SGB=-0.379885;RPBZ=1.34164;MQBZ=-1.73205;MQSBZ=-1;BQBZ=-1.34164;SCBZ=1.73205;FS=0;MQ0F=0 PL 0,4,89,9,92,91 17 2756 . C <*> 0 . DP=4;I16=2,2,0,0,109,3745,0,0,209,11641,0,0,67,1311,0,0;QS=1,0;MQ0F=0 PL 0,12,100 17 2757 . T <*> 0 . DP=5;I16=3,2,0,0,168,6208,0,0,269,15241,0,0,68,1322,0,0;QS=1,0;MQ0F=0 PL 0,15,147 17 2758 . T <*> 0 . DP=5;I16=3,2,0,0,160,5916,0,0,269,15241,0,0,70,1340,0,0;QS=1,0;MQ0F=0 PL 0,15,140 @@ -2783,7 +2782,7 @@ 17 2760 . T <*> 0 . DP=5;I16=3,2,0,0,172,6448,0,0,269,15241,0,0,74,1400,0,0;QS=1,0;MQ0F=0 PL 0,15,150 17 2761 . T <*> 0 . DP=5;I16=3,2,0,0,170,6570,0,0,269,15241,0,0,76,1442,0,0;QS=1,0;MQ0F=0 PL 0,15,148 17 2762 . T <*> 0 . DP=6;I16=3,3,0,0,210,7698,0,0,329,18841,0,0,78,1492,0,0;QS=1,0;MQ0F=0 PL 0,18,177 -17 2763 . C A,<*> 0 . DP=6;I16=3,2,0,1,182,6872,13,169,300,18000,29,841,69,1407,12,144;QS=0.933333,0.0666667,0;SGB=-0.379885;RPBZ=1.46385;MQBZ=-2.23607;MQSBZ=-1;BQBZ=-1.46385;NMBZ=1.55543;SCBZ=1.73205;FS=0;MQ0F=0 PL 0,5,147,15,150,153 +17 2763 . C A,<*> 0 . DP=6;I16=3,2,0,1,182,6872,13,169,300,18000,29,841,69,1407,12,144;QS=0.933333,0.0666667,0;SGB=-0.379885;RPBZ=1.46385;MQBZ=-2.23607;MQSBZ=-1;BQBZ=-1.46385;SCBZ=1.73205;FS=0;MQ0F=0 PL 0,5,147,15,150,153 17 2764 . C <*> 0 . DP=6;I16=3,3,0,0,192,7040,0,0,329,18841,0,0,84,1620,0,0;QS=1,0;MQ0F=0 PL 0,18,165 17 2765 . T <*> 0 . DP=6;I16=3,3,0,0,223,8627,0,0,329,18841,0,0,86,1648,0,0;QS=1,0;MQ0F=0 PL 0,18,189 17 2766 . C <*> 0 . DP=7;I16=3,4,0,0,226,8350,0,0,389,22441,0,0,88,1684,0,0;QS=1,0;MQ0F=0 PL 0,21,186 @@ -2841,7 +2840,7 @@ 17 2818 . G <*> 0 . DP=7;I16=4,3,0,0,258,9646,0,0,420,25200,0,0,147,3567,0,0;QS=1,0;MQ0F=0 PL 0,21,208 17 2819 . G <*> 0 . DP=7;I16=4,3,0,0,243,8655,0,0,420,25200,0,0,147,3529,0,0;QS=1,0;MQ0F=0 PL 0,21,196 17 2820 . G <*> 0 . DP=7;I16=4,3,0,0,234,8150,0,0,420,25200,0,0,147,3495,0,0;QS=1,0;MQ0F=0 PL 0,21,188 -17 2821 . A G,<*> 0 . DP=8;I16=4,3,0,1,210,6834,2,4,420,25200,60,3600,147,3465,25,625;QS=0.981308,0.0186916,0;SGB=-0.379885;RPBZ=-1.5367;MQBZ=0;MQSBZ=0;BQBZ=-1.54604;NMBZ=1.75;SCBZ=1.75;FS=0;MQ0F=0 PL 0,15,164,21,167,164 +17 2821 . A G,<*> 0 . DP=8;I16=4,3,0,1,210,6834,2,4,420,25200,60,3600,147,3465,25,625;QS=0.981308,0.0186916,0;SGB=-0.379885;RPBZ=-1.5367;MQBZ=0;MQSBZ=0;BQBZ=-1.54604;SCBZ=1.75;FS=0;MQ0F=0 PL 0,15,164,21,167,164 17 2822 . C <*> 0 . DP=8;I16=4,4,0,0,216,6518,0,0,480,28800,0,0,172,4064,0,0;QS=1,0;MQ0F=0 PL 0,24,172 17 2823 . C <*> 0 . DP=8;I16=4,4,0,0,251,8419,0,0,480,28800,0,0,172,4042,0,0;QS=1,0;MQ0F=0 PL 0,24,197 17 2824 . C <*> 0 . DP=8;I16=4,4,0,0,276,10170,0,0,480,28800,0,0,172,4024,0,0;QS=1,0;MQ0F=0 PL 0,24,215 @@ -2886,7 +2885,7 @@ 17 2863 . G <*> 0 . DP=7;I16=2,5,0,0,250,9198,0,0,420,25200,0,0,118,2682,0,0;QS=1,0;MQ0F=0 PL 0,21,195 17 2864 . G <*> 0 . DP=7;I16=2,5,0,0,235,8639,0,0,420,25200,0,0,115,2649,0,0;QS=1,0;MQ0F=0 PL 0,21,188 17 2865 . G <*> 0 . DP=7;I16=2,5,0,0,238,8596,0,0,420,25200,0,0,112,2622,0,0;QS=1,0;MQ0F=0 PL 0,21,188 -17 2866 . T G,<*> 0 . DP=6;I16=1,4,1,0,179,6567,2,4,300,18000,60,3600,100,2500,10,100;QS=0.978142,0.0218579,0;SGB=-0.379885;RPBZ=0.87831;MQBZ=0;MQSBZ=0;BQBZ=-1.46385;NMBZ=-0.447214;SCBZ=-0.447214;FS=0;MQ0F=0 PL 0,10,141,15,144,141 +17 2866 . T G,<*> 0 . DP=6;I16=1,4,1,0,179,6567,2,4,300,18000,60,3600,100,2500,10,100;QS=0.978142,0.0218579,0;SGB=-0.379885;RPBZ=0.87831;MQBZ=0;MQSBZ=0;BQBZ=-1.46385;SCBZ=-0.447214;FS=0;MQ0F=0 PL 0,10,141,15,144,141 17 2867 . G <*> 0 . DP=5;I16=2,3,0,0,172,6102,0,0,300,18000,0,0,109,2581,0,0;QS=1,0;MQ0F=0 PL 0,15,150 17 2868 . T <*> 0 . DP=5;I16=2,3,0,0,179,6849,0,0,300,18000,0,0,108,2564,0,0;QS=1,0;MQ0F=0 PL 0,15,157 17 2869 . C <*> 0 . DP=5;I16=2,3,0,0,189,7277,0,0,300,18000,0,0,107,2549,0,0;QS=1,0;MQ0F=0 PL 0,15,165 @@ -3016,7 +3015,7 @@ 17 2993 . G <*> 0 . DP=4;I16=2,2,0,0,134,4698,0,0,240,14400,0,0,100,2500,0,0;QS=1,0;MQ0F=0 PL 0,12,123 17 2994 . G <*> 0 . DP=4;I16=2,2,0,0,127,4217,0,0,240,14400,0,0,99,2451,0,0;QS=1,0;MQ0F=0 PL 0,12,116 17 2995 . G <*> 0 . DP=4;I16=2,2,0,0,146,5388,0,0,240,14400,0,0,98,2404,0,0;QS=1,0;MQ0F=0 PL 0,12,134 -17 2996 . T G,<*> 0 . DP=4;I16=1,2,1,0,114,4428,1,1,180,10800,60,3600,75,1875,22,484;QS=0.966102,0.0338983,0;SGB=-0.379885;RPBZ=1.34164;MQBZ=0;MQSBZ=0;BQBZ=-1.41421;NMBZ=0;SCBZ=0;FS=0;MQ0F=0 PL 0,5,101,9,104,101 +17 2996 . T G,<*> 0 . DP=4;I16=1,2,1,0,114,4428,1,1,180,10800,60,3600,75,1875,22,484;QS=0.966102,0.0338983,0;SGB=-0.379885;RPBZ=1.34164;MQBZ=0;MQSBZ=0;BQBZ=-1.41421;SCBZ=0;FS=0;MQ0F=0 PL 0,5,101,9,104,101 17 2997 . C <*> 0 . DP=4;I16=2,2,0,0,125,4001,0,0,240,14400,0,0,96,2316,0,0;QS=1,0;MQ0F=0 PL 0,12,115 17 2998 . C <*> 0 . DP=4;I16=2,2,0,0,134,4610,0,0,240,14400,0,0,95,2275,0,0;QS=1,0;MQ0F=0 PL 0,12,123 17 2999 . A <*> 0 . DP=4;I16=2,2,0,0,148,5574,0,0,240,14400,0,0,94,2236,0,0;QS=1,0;MQ0F=0 PL 0,12,136 @@ -3080,7 +3079,7 @@ 17 3057 . C <*> 0 . DP=4;I16=2,2,0,0,105,3419,0,0,240,14400,0,0,65,1303,0,0;QS=1,0;MQ0F=0 PL 0,12,99 17 3058 . C <*> 0 . DP=4;I16=2,2,0,0,125,4207,0,0,240,14400,0,0,64,1318,0,0;QS=1,0;MQ0F=0 PL 0,12,116 17 3059 . T <*> 0 . DP=4;I16=2,2,0,0,109,3705,0,0,240,14400,0,0,63,1339,0,0;QS=1,0;MQ0F=0 PL 0,12,103 -17 3060 . G C,<*> 0 . DP=5;I16=2,2,0,1,126,4164,2,4,240,14400,60,3600,61,1315,25,625;QS=0.969231,0.0307692,0;SGB=-0.379885;RPBZ=-1.41421;MQBZ=0;MQSBZ=0;BQBZ=-1.41421;NMBZ=1.22474;SCBZ=1.22474;FS=0;MQ0F=0 PL 0,8,110,12,113,110 +17 3060 . G C,<*> 0 . DP=5;I16=2,2,0,1,126,4164,2,4,240,14400,60,3600,61,1315,25,625;QS=0.969231,0.0307692,0;SGB=-0.379885;RPBZ=-1.41421;MQBZ=0;MQSBZ=0;BQBZ=-1.41421;SCBZ=1.22474;FS=0;MQ0F=0 PL 0,8,110,12,113,110 17 3061 . C <*> 0 . DP=5;I16=2,3,0,0,164,5458,0,0,300,18000,0,0,84,1920,0,0;QS=1,0;MQ0F=0 PL 0,15,143 17 3062 . C <*> 0 . DP=5;I16=2,3,0,0,153,4913,0,0,300,18000,0,0,82,1904,0,0;QS=1,0;MQ0F=0 PL 0,15,134 17 3063 . C <*> 0 . DP=5;I16=2,3,0,0,149,4995,0,0,300,18000,0,0,80,1892,0,0;QS=1,0;MQ0F=0 PL 0,15,133 @@ -3089,7 +3088,7 @@ 17 3066 . A <*> 0 . DP=4;I16=1,3,0,0,115,3749,0,0,240,14400,0,0,76,1876,0,0;QS=1,0;MQ0F=0 PL 0,12,104 17 3067 . T <*> 0 . DP=4;I16=1,3,0,0,114,3570,0,0,240,14400,0,0,75,1875,0,0;QS=1,0;MQ0F=0 PL 0,12,103 17 3068 . G <*> 0 . DP=3;I16=1,2,0,0,88,2790,0,0,180,10800,0,0,75,1875,0,0;QS=1,0;MQ0F=0 PL 0,9,84 -17 3069 . G C,<*> 0 . DP=3;I16=1,1,0,1,57,1889,1,1,120,7200,60,3600,50,1250,25,625;QS=0.934426,0.0655738,0;SGB=-0.379885;RPBZ=-1.22474;MQBZ=0;MQSBZ=0;BQBZ=-1.22474;NMBZ=0.707107;SCBZ=1.22474;FS=0;MQ0F=0 PL 0,3,51,6,54,52 +17 3069 . G C,<*> 0 . DP=3;I16=1,1,0,1,57,1889,1,1,120,7200,60,3600,50,1250,25,625;QS=0.934426,0.0655738,0;SGB=-0.379885;RPBZ=-1.22474;MQBZ=0;MQSBZ=0;BQBZ=-1.22474;SCBZ=1.22474;FS=0;MQ0F=0 PL 0,3,51,6,54,52 17 3070 . C <*> 0 . DP=3;I16=1,2,0,0,100,3454,0,0,180,10800,0,0,75,1875,0,0;QS=1,0;MQ0F=0 PL 0,9,95 17 3071 . C <*> 0 . DP=3;I16=1,2,0,0,104,3656,0,0,180,10800,0,0,75,1875,0,0;QS=1,0;MQ0F=0 PL 0,9,98 17 3072 . C <*> 0 . DP=3;I16=1,2,0,0,112,4230,0,0,180,10800,0,0,75,1875,0,0;QS=1,0;MQ0F=0 PL 0,9,106 @@ -3124,7 +3123,7 @@ 17 3101 . C <*> 0 . DP=5;I16=2,3,0,0,186,6930,0,0,300,18000,0,0,78,1546,0,0;QS=1,0;MQ0F=0 PL 0,15,161 17 3102 . A <*> 0 . DP=6;I16=3,3,0,0,226,8548,0,0,360,21600,0,0,78,1560,0,0;QS=1,0;MQ0F=0 PL 0,18,189 17 3103 . T <*> 0 . DP=6;I16=3,3,0,0,223,8347,0,0,360,21600,0,0,79,1583,0,0;QS=1,0;MQ0F=0 PL 0,18,187 -17 3104 . C T,<*> 0 . DP=5;I16=1,2,2,0,114,4334,80,3202,180,10800,120,7200,41,765,40,850;QS=0.587629,0.412371,0;VDB=0.78;SGB=-0.453602;RPBZ=0.296174;MQBZ=0;MQSBZ=0;BQBZ=1.48087;NMBZ=-0.816497;SCBZ=-0.816497;FS=0;MQ0F=0 PL 59,0,93,68,99,157 +17 3104 . C T,<*> 0 . DP=5;I16=1,2,2,0,114,4334,80,3202,180,10800,120,7200,41,765,40,850;QS=0.587629,0.412371,0;VDB=0.78;SGB=-0.453602;RPBZ=0.296174;MQBZ=0;MQSBZ=0;BQBZ=1.48087;SCBZ=-0.816497;FS=0;MQ0F=0 PL 59,0,93,68,99,157 17 3105 . T <*> 0 . DP=5;I16=3,2,0,0,195,7621,0,0,300,18000,0,0,83,1655,0,0;QS=1,0;MQ0F=0 PL 0,15,169 17 3106 . G <*> 0 . DP=5;I16=3,2,0,0,193,7461,0,0,300,18000,0,0,85,1703,0,0;QS=1,0;MQ0F=0 PL 0,15,167 17 3107 . T <*> 0 . DP=6;I16=3,3,0,0,233,9067,0,0,360,21600,0,0,87,1759,0,0;QS=1,0;MQ0F=0 PL 0,18,195 @@ -3286,11 +3285,11 @@ 17 3263 . G <*> 0 . DP=4;I16=2,2,0,0,160,6442,0,0,240,14400,0,0,67,1291,0,0;QS=1,0;MQ0F=0 PL 0,12,146 17 3264 . G <*> 0 . DP=4;I16=2,2,0,0,156,6120,0,0,240,14400,0,0,68,1330,0,0;QS=1,0;MQ0F=0 PL 0,12,143 17 3265 . G <*> 0 . DP=4;I16=2,2,0,0,148,5530,0,0,240,14400,0,0,69,1375,0,0;QS=1,0;MQ0F=0 PL 0,12,136 -17 3266 . T G,<*> 0 . DP=4;I16=1,2,1,0,120,4802,2,4,180,10800,60,3600,61,1345,9,81;QS=0.967742,0.0322581,0;SGB=-0.379885;RPBZ=1.34164;MQBZ=0;MQSBZ=0;BQBZ=-1.34164;NMBZ=1.73205;SCBZ=1.73205;FS=0;MQ0F=0 PL 0,5,107,9,110,107 +17 3266 . T G,<*> 0 . DP=4;I16=1,2,1,0,120,4802,2,4,180,10800,60,3600,61,1345,9,81;QS=0.967742,0.0322581,0;SGB=-0.379885;RPBZ=1.34164;MQBZ=0;MQSBZ=0;BQBZ=-1.34164;SCBZ=1.73205;FS=0;MQ0F=0 PL 0,5,107,9,110,107 17 3267 . G <*> 0 . DP=4;I16=2,2,0,0,144,5394,0,0,240,14400,0,0,71,1483,0,0;QS=1,0;MQ0F=0 PL 0,12,133 17 3268 . G <*> 0 . DP=4;I16=2,2,0,0,154,6010,0,0,240,14400,0,0,71,1495,0,0;QS=1,0;MQ0F=0 PL 0,12,142 17 3269 . G <*> 0 . DP=4;I16=2,2,0,0,149,5625,0,0,240,14400,0,0,71,1511,0,0;QS=1,0;MQ0F=0 PL 0,12,137 -17 3270 . T G,<*> 0 . DP=5;I16=2,2,1,0,148,5560,2,4,240,14400,60,3600,65,1457,5,25;QS=0.973684,0.0263158,0;SGB=-0.379885;RPBZ=1.41421;MQBZ=0;MQSBZ=0;BQBZ=-1.41421;NMBZ=1.58114;SCBZ=2;FS=0;MQ0F=0 PL 0,8,129,12,132,129 +17 3270 . T G,<*> 0 . DP=5;I16=2,2,1,0,148,5560,2,4,240,14400,60,3600,65,1457,5,25;QS=0.973684,0.0263158,0;SGB=-0.379885;RPBZ=1.41421;MQBZ=0;MQSBZ=0;BQBZ=-1.41421;SCBZ=2;FS=0;MQ0F=0 PL 0,8,129,12,132,129 17 3271 . G <*> 0 . DP=4;I16=2,2,0,0,157,6181,0,0,240,14400,0,0,66,1444,0,0;QS=1,0;MQ0F=0 PL 0,12,143 17 3272 . G <*> 0 . DP=4;I16=2,2,0,0,153,5881,0,0,240,14400,0,0,67,1437,0,0;QS=1,0;MQ0F=0 PL 0,12,140 17 3273 . A <*> 0 . DP=4;I16=2,2,0,0,161,6485,0,0,240,14400,0,0,68,1436,0,0;QS=1,0;MQ0F=0 PL 0,12,147 @@ -3336,7 +3335,7 @@ 17 3313 . T <*> 0 . DP=5;I16=4,1,0,0,198,7856,0,0,300,18000,0,0,111,2621,0,0;QS=1,0;MQ0F=0 PL 0,15,161 17 3314 . G <*> 0 . DP=5;I16=4,1,0,0,197,7831,0,0,300,18000,0,0,112,2644,0,0;QS=1,0;MQ0F=0 PL 0,15,161 17 3315 . G <*> 0 . DP=5;I16=4,1,0,0,189,7205,0,0,300,18000,0,0,113,2669,0,0;QS=1,0;MQ0F=0 PL 0,15,155 -17 3316 . T G,<*> 0 . DP=5;I16=3,1,1,0,139,4903,4,16,240,14400,60,3600,89,2071,25,625;QS=0.972028,0.027972,0;SGB=-0.379885;RPBZ=0;MQBZ=0;MQSBZ=0;BQBZ=-1.45095;NMBZ=0;SCBZ=0;FS=0;MQ0F=0 PL 0,8,116,12,119,116 +17 3316 . T G,<*> 0 . DP=5;I16=3,1,1,0,139,4903,4,16,240,14400,60,3600,89,2071,25,625;QS=0.972028,0.027972,0;SGB=-0.379885;RPBZ=0;MQBZ=0;MQSBZ=0;BQBZ=-1.45095;SCBZ=0;FS=0;MQ0F=0 PL 0,8,116,12,119,116 17 3317 . G <*> 0 . DP=6;I16=4,2,0,0,203,7051,0,0,360,21600,0,0,115,2725,0,0;QS=1,0;MQ0F=0 PL 0,18,168 17 3318 . A <*> 0 . DP=6;I16=4,2,0,0,225,8557,0,0,360,21600,0,0,116,2708,0,0;QS=1,0;MQ0F=0 PL 0,18,185 17 3319 . A <*> 0 . DP=6;I16=4,2,0,0,230,9112,0,0,360,21600,0,0,117,2697,0,0;QS=1,0;MQ0F=0 PL 0,18,188 @@ -3379,7 +3378,7 @@ 17 3356 . T <*> 0 . DP=6;I16=4,2,0,0,241,9683,0,0,360,21600,0,0,137,3225,0,0;QS=1,0;MQ0F=0 PL 0,18,195 17 3357 . G <*> 0 . DP=6;I16=4,2,0,0,235,9245,0,0,360,21600,0,0,137,3245,0,0;QS=1,0;MQ0F=0 PL 0,18,192 17 3358 . G <*> 0 . DP=6;I16=4,2,0,0,228,8744,0,0,360,21600,0,0,137,3269,0,0;QS=1,0;MQ0F=0 PL 0,18,187 -17 3359 . T G,<*> 0 . DP=6;I16=3,2,1,0,185,6969,2,4,300,18000,60,3600,125,3125,11,121;QS=0.978836,0.021164,0;SGB=-0.379885;RPBZ=1.46385;MQBZ=0;MQSBZ=0;BQBZ=-1.46385;NMBZ=0;SCBZ=0;FS=0;MQ0F=0 PL 0,10,155,15,158,155 +17 3359 . T G,<*> 0 . DP=6;I16=3,2,1,0,185,6969,2,4,300,18000,60,3600,125,3125,11,121;QS=0.978836,0.021164,0;SGB=-0.379885;RPBZ=1.46385;MQBZ=0;MQSBZ=0;BQBZ=-1.46385;SCBZ=0;FS=0;MQ0F=0 PL 0,10,155,15,158,155 17 3360 . G <*> 0 . DP=6;I16=4,2,0,0,211,7669,0,0,360,21600,0,0,135,3225,0,0;QS=1,0;MQ0F=0 PL 0,18,175 17 3361 . G <*> 0 . DP=6;I16=4,2,0,0,211,7655,0,0,360,21600,0,0,134,3206,0,0;QS=1,0;MQ0F=0 PL 0,18,175 17 3362 . C <*> 0 . DP=6;I16=4,2,0,0,210,7526,0,0,360,21600,0,0,133,3189,0,0;QS=1,0;MQ0F=0 PL 0,18,173 @@ -3528,7 +3527,7 @@ 17 3505 . A <*> 0 . DP=6;I16=1,5,0,0,217,8043,0,0,329,18841,0,0,104,2160,0,0;QS=1,0;MQ0F=0 PL 0,18,163 17 3506 . A <*> 0 . DP=6;I16=1,5,0,0,221,8287,0,0,329,18841,0,0,105,2181,0,0;QS=1,0;MQ0F=0 PL 0,18,168 17 3507 . T <*> 0 . DP=6;I16=1,5,0,0,201,7061,0,0,329,18841,0,0,106,2208,0,0;QS=1,0;MQ0F=0 PL 0,18,153 -17 3508 . C A,<*> 0 . DP=6;I16=0,5,1,0,164,5506,2,4,300,18000,29,841,82,1616,25,625;QS=0.97619,0.0238095,0;SGB=-0.379885;RPBZ=1.46385;MQBZ=-2.23607;MQSBZ=2.23607;BQBZ=-1.46385;NMBZ=1.41421;SCBZ=1.73205;FS=0;MQ0F=0 PL 0,10,113,15,116,114 +17 3508 . C A,<*> 0 . DP=6;I16=0,5,1,0,164,5506,2,4,300,18000,29,841,82,1616,25,625;QS=0.97619,0.0238095,0;SGB=-0.379885;RPBZ=1.46385;MQBZ=-2.23607;MQSBZ=2.23607;BQBZ=-1.46385;SCBZ=1.73205;FS=0;MQ0F=0 PL 0,10,113,15,116,114 17 3509 . A <*> 0 . DP=5;I16=0,5,0,0,171,6123,0,0,300,18000,0,0,83,1655,0,0;QS=1,0;MQ0F=0 PL 0,15,125 17 3510 . C <*> 0 . DP=5;I16=0,5,0,0,163,5573,0,0,300,18000,0,0,84,1700,0,0;QS=1,0;MQ0F=0 PL 0,15,119 17 3511 . A <*> 0 . DP=5;I16=0,5,0,0,153,5207,0,0,300,18000,0,0,85,1751,0,0;QS=1,0;MQ0F=0 PL 0,15,115 @@ -3630,7 +3629,7 @@ 17 3607 . A <*> 0 . DP=9;I16=6,3,0,0,321,11705,0,0,540,32400,0,0,142,3018,0,0;QS=1,0;MQ0F=0 PL 0,27,232 17 3608 . A <*> 0 . DP=9;I16=6,3,0,0,316,11960,0,0,540,32400,0,0,145,3081,0,0;QS=1,0;MQ0F=0 PL 0,27,233 17 3609 . A <*> 0 . DP=9;I16=6,3,0,0,328,12274,0,0,540,32400,0,0,147,3107,0,0;QS=1,0;MQ0F=0 PL 0,27,238 -17 3610 . C A,<*> 0 . DP=9;I16=5,3,1,0,292,10792,8,64,480,28800,60,3600,124,2520,25,625;QS=0.973333,0.0266667,0;SGB=-0.379885;RPBZ=-0.387298;MQBZ=0;MQSBZ=0;BQBZ=-1.62549;NMBZ=0.920358;SCBZ=-0.53033;FS=0;MQ0F=0 PL 0,17,213,24,216,214 +17 3610 . C A,<*> 0 . DP=9;I16=5,3,1,0,292,10792,8,64,480,28800,60,3600,124,2520,25,625;QS=0.973333,0.0266667,0;SGB=-0.379885;RPBZ=-0.387298;MQBZ=0;MQSBZ=0;BQBZ=-1.62549;SCBZ=-0.53033;FS=0;MQ0F=0 PL 0,17,213,24,216,214 17 3611 . C <*> 0 . DP=9;I16=6,3,0,0,316,12098,0,0,540,32400,0,0,150,3144,0,0;QS=1,0;MQ0F=0 PL 0,27,234 17 3612 . A <*> 0 . DP=9;I16=6,3,0,0,341,13619,0,0,540,32400,0,0,151,3153,0,0;QS=1,0;MQ0F=0 PL 0,27,251 17 3613 . G <*> 0 . DP=9;I16=6,3,0,0,306,11050,0,0,540,32400,0,0,152,3172,0,0;QS=1,0;MQ0F=0 PL 0,27,226 @@ -3662,12 +3661,12 @@ 17 3639 . G <*> 0 . DP=9;I16=6,3,0,0,308,10662,0,0,540,32400,0,0,175,4019,0,0;QS=1,0;MQ0F=0 PL 0,27,221 17 3640 . T <*> 0 . DP=9;I16=6,3,0,0,315,11283,0,0,540,32400,0,0,175,3975,0,0;QS=1,0;MQ0F=0 PL 0,27,229 17 3641 . G <*> 0 . DP=9;I16=6,3,0,0,309,10867,0,0,540,32400,0,0,175,3939,0,0;QS=1,0;MQ0F=0 PL 0,27,224 -17 3642 . T G,<*> 0 . DP=9;I16=5,3,1,0,293,11005,3,9,480,28800,60,3600,150,3286,25,625;QS=0.986532,0.013468,0;SGB=-0.379885;RPBZ=0.387298;MQBZ=0;MQSBZ=0;BQBZ=-1.55569;NMBZ=0.920358;SCBZ=-0.53033;FS=0;MQ0F=0 PL 0,18,219,24,222,219 +17 3642 . T G,<*> 0 . DP=9;I16=5,3,1,0,293,11005,3,9,480,28800,60,3600,150,3286,25,625;QS=0.986532,0.013468,0;SGB=-0.379885;RPBZ=0.387298;MQBZ=0;MQSBZ=0;BQBZ=-1.55569;SCBZ=-0.53033;FS=0;MQ0F=0 PL 0,18,219,24,222,219 17 3643 . T <*> 0 . DP=9;I16=6,3,0,0,312,11318,0,0,540,32400,0,0,175,3891,0,0;QS=1,0;MQ0F=0 PL 0,27,230 17 3644 . T <*> 0 . DP=9;I16=6,3,0,0,316,12098,0,0,540,32400,0,0,175,3879,0,0;QS=1,0;MQ0F=0 PL 0,27,237 17 3645 . T <*> 0 . DP=9;I16=6,3,0,0,326,12228,0,0,540,32400,0,0,175,3875,0,0;QS=1,0;MQ0F=0 PL 0,27,239 17 3646 . C <*> 0 . DP=9;I16=6,3,0,0,252,7724,0,0,540,32400,0,0,175,3879,0,0;QS=1,0;MQ0F=0 PL 0,27,188 -17 3647 . G T,<*> 0 . DP=9;I16=5,3,1,0,214,7092,12,144,480,28800,60,3600,150,3266,25,625;QS=0.947368,0.0526316,0;SGB=-0.379885;RPBZ=0.387298;MQBZ=0;MQSBZ=0;BQBZ=-1.1619;NMBZ=0.920358;SCBZ=-0.53033;FS=0;MQ0F=0 PL 0,14,162,24,165,165 +17 3647 . G T,<*> 0 . DP=9;I16=5,3,1,0,214,7092,12,144,480,28800,60,3600,150,3266,25,625;QS=0.947368,0.0526316,0;SGB=-0.379885;RPBZ=0.387298;MQBZ=0;MQSBZ=0;BQBZ=-1.1619;SCBZ=-0.53033;FS=0;MQ0F=0 PL 0,14,162,24,165,165 17 3648 . A <*> 0 . DP=9;I16=6,3,0,0,304,11112,0,0,540,32400,0,0,175,3911,0,0;QS=1,0;MQ0F=0 PL 0,27,227 17 3649 . C <*> 0 . DP=9;I16=6,3,0,0,309,10981,0,0,540,32400,0,0,175,3939,0,0;QS=1,0;MQ0F=0 PL 0,27,226 17 3650 . A <*> 0 . DP=9;I16=6,3,0,0,335,12925,0,0,540,32400,0,0,175,3975,0,0;QS=1,0;MQ0F=0 PL 0,27,246 @@ -3682,7 +3681,7 @@ 17 3659 . T <*> 0 . DP=7;I16=5,2,0,0,235,8387,0,0,420,25200,0,0,169,4101,0,0;QS=1,0;MQ0F=0 PL 0,21,186 17 3660 . G <*> 0 . DP=7;I16=5,2,0,0,215,7415,0,0,420,25200,0,0,169,4095,0,0;QS=1,0;MQ0F=0 PL 0,21,174 17 3661 . T <*> 0 . DP=7;I16=5,2,0,0,234,8550,0,0,420,25200,0,0,168,4044,0,0;QS=1,0;MQ0F=0 PL 0,21,188 -17 3662 . T G,<*> 0 . DP=7;I16=4,2,1,0,222,8532,10,100,360,21600,60,3600,146,3558,21,441;QS=0.956897,0.0431034,0;SGB=-0.379885;RPBZ=1;MQBZ=0;MQSBZ=0;BQBZ=-1.51357;NMBZ=1.24722;SCBZ=-0.408248;FS=0;MQ0F=0 PL 0,10,175,18,178,178 +17 3662 . T G,<*> 0 . DP=7;I16=4,2,1,0,222,8532,10,100,360,21600,60,3600,146,3558,21,441;QS=0.956897,0.0431034,0;SGB=-0.379885;RPBZ=1;MQBZ=0;MQSBZ=0;BQBZ=-1.51357;SCBZ=-0.408248;FS=0;MQ0F=0 PL 0,10,175,18,178,178 17 3663 . A <*> 0 . DP=7;I16=5,2,0,0,231,8235,0,0,420,25200,0,0,166,3960,0,0;QS=1,0;MQ0F=0 PL 0,21,183 17 3664 . T <*> 0 . DP=7;I16=5,2,0,0,250,9272,0,0,420,25200,0,0,165,3927,0,0;QS=1,0;MQ0F=0 PL 0,21,196 17 3665 . A <*> 0 . DP=7;I16=5,2,0,0,271,10551,0,0,420,25200,0,0,163,3849,0,0;QS=1,0;MQ0F=0 PL 0,21,208 @@ -3739,11 +3738,11 @@ 17 3716 . T <*> 0 . DP=6;I16=5,1,0,0,218,8322,0,0,337,19369,0,0,124,2760,0,0;QS=1,0;MQ0F=0 PL 0,18,164 17 3717 . C <*> 0 . DP=6;I16=5,1,0,0,222,8600,0,0,337,19369,0,0,123,2729,0,0;QS=1,0;MQ0F=0 PL 0,18,168 17 3718 . T <*> 0 . DP=6;I16=5,1,0,0,223,9053,0,0,337,19369,0,0,122,2704,0,0;QS=1,0;MQ0F=0 PL 0,18,165 -17 3719 . A T,<*> 0 . DP=6;I16=5,0,0,1,200,8050,12,144,300,18000,37,1369,96,2060,25,625;QS=0.943396,0.0566038,0;SGB=-0.379885;RPBZ=-0.87831;MQBZ=-2.23607;MQSBZ=-2.23607;BQBZ=-1.46385;NMBZ=2.23607;SCBZ=0;FS=0;MQ0F=0 PL 0,5,133,15,136,137 +17 3719 . A T,<*> 0 . DP=6;I16=5,0,0,1,200,8050,12,144,300,18000,37,1369,96,2060,25,625;QS=0.943396,0.0566038,0;SGB=-0.379885;RPBZ=-0.87831;MQBZ=-2.23607;MQSBZ=-2.23607;BQBZ=-1.46385;SCBZ=0;FS=0;MQ0F=0 PL 0,5,133,15,136,137 17 3720 . C <*> 0 . DP=6;I16=5,1,0,0,212,7920,0,0,337,19369,0,0,120,2672,0,0;QS=1,0;MQ0F=0 PL 0,18,158 -17 3721 . A C,<*> 0 . DP=6;I16=5,0,0,1,205,8415,4,16,300,18000,37,1369,94,2040,25,625;QS=0.980861,0.0191388,0;SGB=-0.379885;RPBZ=-0.87831;MQBZ=-2.23607;MQSBZ=-2.23607;BQBZ=-1.46385;NMBZ=2.23607;SCBZ=0;FS=0;MQ0F=0 PL 0,10,140,15,143,140 +17 3721 . A C,<*> 0 . DP=6;I16=5,0,0,1,205,8415,4,16,300,18000,37,1369,94,2040,25,625;QS=0.980861,0.0191388,0;SGB=-0.379885;RPBZ=-0.87831;MQBZ=-2.23607;MQSBZ=-2.23607;BQBZ=-1.46385;SCBZ=0;FS=0;MQ0F=0 PL 0,10,140,15,143,140 17 3722 . C <*> 0 . DP=6;I16=5,1,0,0,220,8352,0,0,337,19369,0,0,118,2664,0,0;QS=1,0;MQ0F=0 PL 0,18,165 -17 3723 . A G,<*> 0 . DP=6;I16=5,0,0,1,205,8419,8,64,300,18000,37,1369,92,2044,25,625;QS=0.962441,0.0375587,0;SGB=-0.379885;RPBZ=-0.87831;MQBZ=-2.23607;MQSBZ=-2.23607;BQBZ=-1.50756;NMBZ=2.23607;SCBZ=0;FS=0;MQ0F=0 PL 0,8,138,15,141,140 +17 3723 . A G,<*> 0 . DP=6;I16=5,0,0,1,205,8419,8,64,300,18000,37,1369,92,2044,25,625;QS=0.962441,0.0375587,0;SGB=-0.379885;RPBZ=-0.87831;MQBZ=-2.23607;MQSBZ=-2.23607;BQBZ=-1.50756;SCBZ=0;FS=0;MQ0F=0 PL 0,8,138,15,141,140 17 3724 . C <*> 0 . DP=6;I16=5,1,0,0,222,8374,0,0,337,19369,0,0,116,2680,0,0;QS=1,0;MQ0F=0 PL 0,18,169 17 3725 . T <*> 0 . DP=6;I16=5,1,0,0,249,10441,0,0,337,19369,0,0,115,2697,0,0;QS=1,0;MQ0F=0 PL 0,18,190 17 3726 . G <*> 0 . DP=6;I16=5,1,0,0,215,8133,0,0,337,19369,0,0,113,2669,0,0;QS=1,0;MQ0F=0 PL 0,18,166 @@ -3784,7 +3783,7 @@ 17 3761 . A <*> 0 . DP=6;I16=4,2,0,0,230,9010,0,0,337,19369,0,0,97,2101,0,0;QS=1,0;MQ0F=0 PL 0,18,188 17 3762 . C <*> 0 . DP=6;I16=4,2,0,0,198,7636,0,0,337,19369,0,0,96,2064,0,0;QS=1,0;MQ0F=0 PL 0,18,161 17 3763 . C <*> 0 . DP=6;I16=4,2,0,0,226,8912,0,0,337,19369,0,0,94,1984,0,0;QS=1,0;MQ0F=0 PL 0,18,186 -17 3764 . A C,<*> 0 . DP=6;I16=4,1,0,1,204,8328,8,64,300,18000,37,1369,69,1383,23,529;QS=0.962264,0.0377358,0;SGB=-0.379885;RPBZ=0.29277;MQBZ=-2.23607;MQSBZ=-1.41421;BQBZ=-1.55543;NMBZ=2.23607;SCBZ=0;FS=0;MQ0F=0 PL 0,8,159,15,162,161 +17 3764 . A C,<*> 0 . DP=6;I16=4,1,0,1,204,8328,8,64,300,18000,37,1369,69,1383,23,529;QS=0.962264,0.0377358,0;SGB=-0.379885;RPBZ=0.29277;MQBZ=-2.23607;MQSBZ=-1.41421;BQBZ=-1.55543;SCBZ=0;FS=0;MQ0F=0 PL 0,8,159,15,162,161 17 3765 . C <*> 0 . DP=6;I16=4,2,0,0,231,8935,0,0,337,19369,0,0,90,1848,0,0;QS=1,0;MQ0F=0 PL 0,18,189 17 3766 . A <*> 0 . DP=6;I16=4,2,0,0,234,9192,0,0,337,19369,0,0,88,1792,0,0;QS=1,0;MQ0F=0 PL 0,18,191 17 3767 . A <*> 0 . DP=6;I16=4,2,0,0,232,9038,0,0,337,19369,0,0,86,1744,0,0;QS=1,0;MQ0F=0 PL 0,18,191 @@ -3923,7 +3922,7 @@ 17 3900 . T <*> 0 . DP=10;I16=2,8,0,0,377,14437,0,0,554,31538,0,0,187,4177,0,0;QS=1,0;MQ0F=0 PL 0,30,240 17 3901 . G <*> 0 . DP=10;I16=2,8,0,0,332,11724,0,0,554,31538,0,0,189,4219,0,0;QS=1,0;MQ0F=0 PL 0,30,218 17 3902 . C <*> 0 . DP=10;I16=2,8,0,0,352,12592,0,0,554,31538,0,0,191,4269,0,0;QS=1,0;MQ0F=0 PL 0,30,217 -17 3903 . A C,<*> 0 . DP=11;I16=2,8,0,1,318,10522,2,4,554,31538,60,3600,193,4327,2,4;QS=0.987421,0.0125786,0;SGB=-0.379885;RPBZ=-1.58114;MQBZ=0.471405;MQSBZ=3.16228;BQBZ=-1.58474;NMBZ=1.2066;SCBZ=2.011;FS=0;MQ0F=0 PL 0,23,198,30,201,198 +17 3903 . A C,<*> 0 . DP=11;I16=2,8,0,1,318,10522,2,4,554,31538,60,3600,193,4327,2,4;QS=0.987421,0.0125786,0;SGB=-0.379885;RPBZ=-1.58114;MQBZ=0.471405;MQSBZ=3.16228;BQBZ=-1.58474;SCBZ=2.011;FS=0;MQ0F=0 PL 0,23,198,30,201,198 17 3904 . C <*> 0 . DP=11;I16=2,9,0,0,390,14732,0,0,614,35138,0,0,198,4402,0,0;QS=1,0;MQ0F=0 PL 0,33,243 17 3905 . C <*> 0 . DP=11;I16=2,9,0,0,429,16811,0,0,614,35138,0,0,201,4483,0,0;QS=1,0;MQ0F=0 PL 0,33,255 17 3906 . T <*> 0 . DP=11;I16=2,9,0,0,440,17690,0,0,614,35138,0,0,204,4574,0,0;QS=1,0;MQ0F=0 PL 0,33,253 @@ -3932,7 +3931,7 @@ 17 3909 . T <*> 0 . DP=11;I16=2,9,0,0,395,14975,0,0,614,35138,0,0,211,4811,0,0;QS=1,0;MQ0F=0 PL 0,33,237 17 3910 . A <*> 0 . DP=10;I16=2,8,0,0,351,12613,0,0,554,31538,0,0,213,4845,0,0;QS=1,0;MQ0F=0 PL 0,30,224 17 3911 . C <*> 0 . DP=10;I16=2,8,0,0,338,11622,0,0,554,31538,0,0,215,4887,0,0;QS=1,0;MQ0F=0 PL 0,30,214 -17 3912 . A C,<*> 0 . DP=10;I16=2,7,0,1,319,11431,16,256,494,27938,60,3600,205,4767,11,121;QS=0.951807,0.0481928,0;SGB=-0.379885;RPBZ=-1.5667;MQBZ=0.5;MQSBZ=3;BQBZ=-1.59599;NMBZ=1.07088;SCBZ=1.07088;FS=0;MQ0F=0 PL 0,14,202,27,205,208 +17 3912 . A C,<*> 0 . DP=10;I16=2,7,0,1,319,11431,16,256,494,27938,60,3600,205,4767,11,121;QS=0.951807,0.0481928,0;SGB=-0.379885;RPBZ=-1.5667;MQBZ=0.5;MQSBZ=3;BQBZ=-1.59599;SCBZ=1.07088;FS=0;MQ0F=0 PL 0,14,202,27,205,208 17 3913 . C <*> 0 . DP=10;I16=2,8,0,0,369,14053,0,0,554,31538,0,0,217,4899,0,0;QS=1,0;MQ0F=0 PL 0,30,234 17 3914 . T <*> 0 . DP=10;I16=2,8,0,0,364,13634,0,0,554,31538,0,0,218,4920,0,0;QS=1,0;MQ0F=0 PL 0,30,228 17 3915 . C <*> 0 . DP=10;I16=2,8,0,0,360,13176,0,0,554,31538,0,0,219,4951,0,0;QS=1,0;MQ0F=0 PL 0,30,229 @@ -3960,7 +3959,7 @@ 17 3937 . C <*> 0 . DP=8;I16=1,7,0,0,238,7390,0,0,457,26569,0,0,160,3616,0,0;QS=1,0;MQ0F=0 PL 0,24,156 17 3938 . G <*> 0 . DP=8;I16=1,7,0,0,256,8698,0,0,457,26569,0,0,156,3500,0,0;QS=1,0;MQ0F=0 PL 0,24,176 17 3939 . C <*> 0 . DP=8;I16=1,7,0,0,258,8868,0,0,457,26569,0,0,152,3392,0,0;QS=1,0;MQ0F=0 PL 0,24,176 -17 3940 . A C,<*> 0 . DP=8;I16=1,6,0,1,224,7816,4,16,397,22969,60,3600,123,2667,25,625;QS=0.982143,0.0178571,0;SGB=-0.379885;RPBZ=-1.52753;MQBZ=0.377964;MQSBZ=2.64575;BQBZ=-1.52753;NMBZ=1.42857;SCBZ=-0.377964;FS=0;MQ0F=0 PL 0,15,157,21,160,157 +17 3940 . A C,<*> 0 . DP=8;I16=1,6,0,1,224,7816,4,16,397,22969,60,3600,123,2667,25,625;QS=0.982143,0.0178571,0;SGB=-0.379885;RPBZ=-1.52753;MQBZ=0.377964;MQSBZ=2.64575;BQBZ=-1.52753;SCBZ=-0.377964;FS=0;MQ0F=0 PL 0,15,157,21,160,157 17 3941 . C <*> 0 . DP=8;I16=1,7,0,0,264,9696,0,0,457,26569,0,0,144,3200,0,0;QS=1,0;MQ0F=0 PL 0,24,181 17 3942 . C <*> 0 . DP=8;I16=1,7,0,0,295,11227,0,0,457,26569,0,0,140,3116,0,0;QS=1,0;MQ0F=0 PL 0,24,195 17 3943 . T <*> 0 . DP=8;I16=1,7,0,0,292,10930,0,0,457,26569,0,0,136,3040,0,0;QS=1,0;MQ0F=0 PL 0,24,195 @@ -3969,7 +3968,7 @@ 17 3946 . T <*> 0 . DP=7;I16=1,6,0,0,221,7929,0,0,397,22969,0,0,126,2856,0,0;QS=1,0;MQ0F=0 PL 0,21,160 17 3947 . A <*> 0 . DP=6;I16=1,5,0,0,193,6675,0,0,337,19369,0,0,124,2806,0,0;QS=1,0;MQ0F=0 PL 0,18,149 17 3948 . C <*> 0 . DP=6;I16=1,5,0,0,202,7182,0,0,337,19369,0,0,122,2760,0,0;QS=1,0;MQ0F=0 PL 0,18,155 -17 3949 . A C,<*> 0 . DP=6;I16=1,4,0,1,152,5110,24,576,277,15769,60,3600,95,2093,25,625;QS=0.861272,0.138728,0;SGB=-0.379885;RPBZ=-1.46385;MQBZ=0.447214;MQSBZ=2.23607;BQBZ=-0.87831;NMBZ=1.03923;SCBZ=-0.447214;FS=0;MQ0F=0 PL 6,0,110,21,113,126 +17 3949 . A C,<*> 0 . DP=6;I16=1,4,0,1,152,5110,24,576,277,15769,60,3600,95,2093,25,625;QS=0.861272,0.138728,0;SGB=-0.379885;RPBZ=-1.46385;MQBZ=0.447214;MQSBZ=2.23607;BQBZ=-0.87831;SCBZ=-0.447214;FS=0;MQ0F=0 PL 6,0,110,21,113,126 17 3950 . C <*> 0 . DP=6;I16=1,5,0,0,217,8159,0,0,337,19369,0,0,118,2680,0,0;QS=1,0;MQ0F=0 PL 0,18,168 17 3951 . T <*> 0 . DP=6;I16=1,5,0,0,194,7366,0,0,337,19369,0,0,116,2646,0,0;QS=1,0;MQ0F=0 PL 0,18,154 17 3952 . C <*> 0 . DP=6;I16=1,5,0,0,183,6271,0,0,337,19369,0,0,114,2616,0,0;QS=1,0;MQ0F=0 PL 0,18,146 diff --git a/test/mpileup/mpileup.2.out b/test/mpileup/mpileup.2.out index 082fa9d57..30de883c1 100644 --- a/test/mpileup/mpileup.2.out +++ b/test/mpileup/mpileup.2.out @@ -11,7 +11,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -25,29 +24,29 @@ 17 100 . C <*> 0 . DP=18;I16=16,1,0,0,672,27586,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,189:9:0 0,9,118:3:0 0,15,134:5:0 17 101 . C <*> 0 . DP=18;I16=16,1,0,0,630,24730,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,182:9:0 0,9,108:3:0 0,15,132:5:0 17 102 . C <*> 0 . DP=18;I16=16,1,0,0,676,27812,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,188:9:0 0,9,121:3:0 0,15,139:5:0 -17 103 . T C,<*> 0 . DP=18;I16=15,1,1,0,668,28542,6,36,929,54841,29,841,323,7035,6,36;QS=2.98256,0.0174419,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64924;NMBZ=2.45514;SCBZ=4;FS=0;MQ0F=0 PL:DP:DV 0,17,184,24,187,185:9:1 0,9,118,9,118,118:3:0 0,15,147,15,147,147:5:0 -17 104 . G C,<*> 0 . DP=18;I16=15,1,1,0,601,24163,3,9,929,54841,29,841,320,6884,7,49;QS=2.98726,0.0127389,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64309;NMBZ=2.45514;SCBZ=4;FS=0;MQ0F=0 PL:DP:DV 0,18,173,24,176,173:9:1 0,9,101,9,101,101:3:0 0,15,133,15,133,133:5:0 +17 103 . T C,<*> 0 . DP=18;I16=15,1,1,0,668,28542,6,36,929,54841,29,841,323,7035,6,36;QS=2.98256,0.0174419,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64924;SCBZ=4;FS=0;MQ0F=0 PL:DP:DV 0,17,184,24,187,185:9:1 0,9,118,9,118,118:3:0 0,15,147,15,147,147:5:0 +17 104 . G C,<*> 0 . DP=18;I16=15,1,1,0,601,24163,3,9,929,54841,29,841,320,6884,7,49;QS=2.98726,0.0127389,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64309;SCBZ=4;FS=0;MQ0F=0 PL:DP:DV 0,18,173,24,176,173:9:1 0,9,101,9,101,101:3:0 0,15,133,15,133,133:5:0 17 105 . G <*> 0 . DP=19;I16=17,1,0,0,603,22351,0,0,1018,59282,0,0,325,6815,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,171:10:0 0,9,106:3:0 0,15,125:5:0 17 106 . G <*> 0 . DP=19;I16=17,1,0,0,636,25058,0,0,1018,59282,0,0,324,6718,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,190:10:0 0,9,92:3:0 0,15,124:5:0 17 107 . C <*> 0 . DP=19;I16=17,1,0,0,686,27952,0,0,1018,59282,0,0,323,6643,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,192:10:0 0,9,119:3:0 0,15,136:5:0 17 108 . C <*> 0 . DP=19;I16=17,1,0,0,681,27429,0,0,1018,59282,0,0,322,6590,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,190:10:0 0,9,119:3:0 0,15,135:5:0 -17 109 . T C,<*> 0 . DP=19;I16=16,1,1,0,716,30648,2,4,989,58441,29,841,309,6415,12,144;QS=2.98922,0.0107817,0;SGB=-0.556633;RPBZ=-0.674966;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.6661;NMBZ=2.52179;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV 0,20,191,27,194,191:10:1 0,9,120,9,120,120:3:0 0,15,150,15,150,150:5:0 +17 109 . T C,<*> 0 . DP=19;I16=16,1,1,0,716,30648,2,4,989,58441,29,841,309,6415,12,144;QS=2.98922,0.0107817,0;SGB=-0.556633;RPBZ=-0.674966;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.6661;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV 0,20,191,27,194,191:10:1 0,9,120,9,120,120:3:0 0,15,150,15,150,150:5:0 17 110 . G <*> 0 . DP=19;I16=17,1,0,0,688,28036,0,0,1018,59282,0,0,320,6550,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,194:10:0 0,9,113:3:0 0,15,136:5:0 17 111 . G <*> 0 . DP=19;I16=17,1,0,0,573,21453,0,0,1018,59282,0,0,318,6514,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,167:10:0 0,9,95:3:0 0,15,119:5:0 -17 112 . C G,<*> 0 . DP=19;I16=16,1,1,0,657,26565,2,4,989,58441,29,841,301,6277,15,225;QS=2.98907,0.010929,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65292;NMBZ=2.52179;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV 0,20,187,27,190,187:10:1 0,9,103,9,103,103:3:0 0,15,135,15,135,135:5:0 -17 113 . A G,<*> 0 . DP=19;I16=16,1,1,0,635,25055,4,16,989,58441,29,841,297,6207,16,256;QS=2.98817,0.0118343,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65205;NMBZ=2.52179;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV 0,20,172,27,175,172:10:1 0,9,102,9,102,102:3:0 0,15,139,15,139,139:5:0 +17 112 . C G,<*> 0 . DP=19;I16=16,1,1,0,657,26565,2,4,989,58441,29,841,301,6277,15,225;QS=2.98907,0.010929,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65292;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV 0,20,187,27,190,187:10:1 0,9,103,9,103,103:3:0 0,15,135,15,135,135:5:0 +17 113 . A G,<*> 0 . DP=19;I16=16,1,1,0,635,25055,4,16,989,58441,29,841,297,6207,16,256;QS=2.98817,0.0118343,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65205;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV 0,20,172,27,175,172:10:1 0,9,102,9,102,102:3:0 0,15,139,15,139,139:5:0 17 114 . C <*> 0 . DP=19;I16=17,1,0,0,660,25876,0,0,1018,59282,0,0,310,6446,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,181:10:0 0,9,113:3:0 0,15,133:5:0 -17 115 . C A,<*> 0 . DP=21;I16=17,2,1,0,688,27426,12,144,1078,62882,29,841,283,5827,25,625;QS=2.88785,0.11215,0;SGB=-0.556633;RPBZ=0.260329;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.47798;NMBZ=2.3712;SCBZ=-0.418446;FS=0;MQ0F=0 PL:DP:DV 0,30,189,30,189,189:10:0 3,0,86,9,89,93:3:1 0,21,153,21,153,153:7:0 -17 116 . A C,<*> 0 . DP=21;I16=17,2,1,0,705,27791,2,4,1078,62882,29,841,287,6073,19,361;QS=2.98873,0.0112676,0;SGB=-0.556633;RPBZ=0.0867763;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.65814;NMBZ=2.65016;SCBZ=2.65016;FS=0;MQ0F=0 PL:DP:DV 0,20,179,27,182,179:10:1 0,9,102,9,102,102:3:0 0,21,175,21,175,175:7:0 +17 115 . C A,<*> 0 . DP=21;I16=17,2,1,0,688,27426,12,144,1078,62882,29,841,283,5827,25,625;QS=2.88785,0.11215,0;SGB=-0.556633;RPBZ=0.260329;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.47798;SCBZ=-0.418446;FS=0;MQ0F=0 PL:DP:DV 0,30,189,30,189,189:10:0 3,0,86,9,89,93:3:1 0,21,153,21,153,153:7:0 +17 116 . A C,<*> 0 . DP=21;I16=17,2,1,0,705,27791,2,4,1078,62882,29,841,287,6073,19,361;QS=2.98873,0.0112676,0;SGB=-0.556633;RPBZ=0.0867763;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.65814;SCBZ=2.65016;FS=0;MQ0F=0 PL:DP:DV 0,20,179,27,182,179:10:1 0,9,102,9,102,102:3:0 0,21,175,21,175,175:7:0 17 117 . G <*> 0 . DP=21;I16=18,2,0,0,715,28045,0,0,1107,63723,0,0,304,6444,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,185:10:0 0,9,97:3:0 0,21,177:7:0 17 118 . G <*> 0 . DP=20;I16=17,2,0,0,620,23470,0,0,1047,60123,0,0,303,6481,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,175:9:0 0,9,65:3:0 0,21,162:7:0 17 119 . G <*> 0 . DP=19;I16=16,2,0,0,619,23459,0,0,987,56523,0,0,301,6493,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,176:9:0 0,6,76:2:0 0,21,160:7:0 -17 120 . A G,<*> 0 . DP=19;I16=15,2,1,0,646,25392,4,16,958,55682,29,841,277,5999,23,529;QS=2.9873,0.0126984,0;SGB=-0.556633;RPBZ=0.28942;MQBZ=-2.23607;MQSBZ=-1.30384;BQBZ=-1.6486;NMBZ=3;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV 0,18,171,24,174,171:9:1 0,6,88,6,88,88:2:0 0,21,171,21,171,171:7:0 +17 120 . A G,<*> 0 . DP=19;I16=15,2,1,0,646,25392,4,16,958,55682,29,841,277,5999,23,529;QS=2.9873,0.0126984,0;SGB=-0.556633;RPBZ=0.28942;MQBZ=-2.23607;MQSBZ=-1.30384;BQBZ=-1.6486;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV 0,18,171,24,174,171:9:1 0,6,88,6,88,88:2:0 0,21,171,21,171,171:7:0 17 121 . G <*> 0 . DP=19;I16=16,2,0,0,650,25148,0,0,987,56523,0,0,298,6534,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,181:9:0 0,6,84:2:0 0,21,168:7:0 17 122 . C <*> 0 . DP=20;I16=17,2,0,0,696,27784,0,0,1047,60123,0,0,296,6560,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,180:9:0 0,9,107:3:0 0,21,178:7:0 17 123 . T <*> 0 . DP=18;I16=15,2,0,0,647,26145,0,0,927,52923,0,0,296,6554,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,170:8:0 0,9,123:3:0 0,18,166:6:0 17 124 . T <*> 0 . DP=19;I16=16,2,0,0,606,22002,0,0,987,56523,0,0,296,6564,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,154:9:0 0,9,114:3:0 0,18,154:6:0 -17 125 . A T,<*> 0 . DP=18;I16=14,2,1,0,589,22565,4,16,898,52082,29,841,272,5916,25,625;QS=2.98444,0.0155642,0;SGB=-0.556633;RPBZ=1.02125;MQBZ=-2.16025;MQSBZ=-1.23956;BQBZ=-1.64106;NMBZ=2.91548;SCBZ=2.91548;FS=0;MQ0F=0 PL:DP:DV 0,15,149,21,152,149:8:1 0,9,114,9,114,114:3:0 0,18,162,18,162,162:6:0 +17 125 . A T,<*> 0 . DP=18;I16=14,2,1,0,589,22565,4,16,898,52082,29,841,272,5916,25,625;QS=2.98444,0.0155642,0;SGB=-0.556633;RPBZ=1.02125;MQBZ=-2.16025;MQSBZ=-1.23956;BQBZ=-1.64106;SCBZ=2.91548;FS=0;MQ0F=0 PL:DP:DV 0,15,149,21,152,149:8:1 0,9,114,9,114,114:3:0 0,18,162,18,162,162:6:0 17 126 . A <*> 0 . DP=18;I16=15,2,0,0,629,24725,0,0,927,52923,0,0,298,6536,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,162:8:0 0,9,117:3:0 0,18,174:6:0 17 127 . C <*> 0 . DP=18;I16=15,2,0,0,627,24331,0,0,927,52923,0,0,299,6549,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,163:8:0 0,9,119:3:0 0,18,160:6:0 17 128 . A <*> 0 . DP=18;I16=15,2,0,0,660,26364,0,0,927,52923,0,0,300,6580,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,169:8:0 0,9,121:3:0 0,18,168:6:0 @@ -81,7 +80,7 @@ 17 156 . C <*> 0 . DP=14;I16=12,2,0,0,536,20884,0,0,809,47641,0,0,266,5934,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,163:7:0 0,6,84:2:0 0,15,150:5:0 17 157 . C <*> 0 . DP=14;I16=12,2,0,0,555,22081,0,0,809,47641,0,0,264,5904,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,169:7:0 0,6,85:2:0 0,15,149:5:0 17 158 . T <*> 0 . DP=14;I16=12,2,0,0,568,23154,0,0,809,47641,0,0,262,5886,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,170:7:0 0,6,84:2:0 0,15,159:5:0 -17 159 . A G,<*> 0 . DP=15;I16=12,2,1,0,519,19467,5,25,809,47641,60,3600,260,5880,0,0;QS=2.97076,0.0292398,0;SGB=-0.556633;RPBZ=-1.62019;MQBZ=0.267261;MQSBZ=-2.54951;BQBZ=-1.63041;NMBZ=0;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,21,157,21,157,157:7:0 0,6,83,6,83,83:2:0 0,10,129,15,132,129:6:1 +17 159 . A G,<*> 0 . DP=15;I16=12,2,1,0,519,19467,5,25,809,47641,60,3600,260,5880,0,0;QS=2.97076,0.0292398,0;SGB=-0.556633;RPBZ=-1.62019;MQBZ=0.267261;MQSBZ=-2.54951;BQBZ=-1.63041;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,21,157,21,157,157:7:0 0,6,83,6,83,83:2:0 0,10,129,15,132,129:6:1 17 160 . G <*> 0 . DP=15;I16=13,2,0,0,547,20633,0,0,869,51241,0,0,259,5887,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,165:7:0 0,6,85:2:0 0,18,139:6:0 17 161 . A <*> 0 . DP=15;I16=13,2,0,0,568,21610,0,0,869,51241,0,0,258,5908,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,157:7:0 0,6,83:2:0 0,18,162:6:0 17 162 . A <*> 0 . DP=15;I16=13,2,0,0,558,21206,0,0,869,51241,0,0,255,5843,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,147:7:0 0,6,87:2:0 0,18,167:6:0 @@ -112,7 +111,7 @@ 17 187 . C <*> 0 . DP=14;I16=13,1,0,0,511,18979,0,0,809,47641,0,0,266,5952,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,18,147:6:0 0,3,38:1:0 0,21,172:7:0 17 188 . C <*> 0 . DP=14;I16=13,1,0,0,496,18042,0,0,809,47641,0,0,267,5989,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,18,147:6:0 0,3,37:1:0 0,21,162:7:0 17 189 . C <*> 0 . DP=15;I16=13,2,0,0,552,20504,0,0,838,48482,0,0,268,6040,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,18,152:6:0 0,6,67:2:0 0,21,167:7:0 -17 190 . A C,<*> 0 . DP=15;I16=12,2,1,0,500,18230,5,25,778,44882,60,3600,243,5381,25,625;QS=2.97664,0.0233645,0;SGB=-0.556633;RPBZ=0;MQBZ=0.392232;MQSBZ=-3.74166;BQBZ=-1.63041;NMBZ=-0.267261;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,18,138,18,138,138:6:0 0,6,68,6,68,68:2:0 0,12,153,18,156,153:7:1 +17 190 . A C,<*> 0 . DP=15;I16=12,2,1,0,500,18230,5,25,778,44882,60,3600,243,5381,25,625;QS=2.97664,0.0233645,0;SGB=-0.556633;RPBZ=0;MQBZ=0.392232;MQSBZ=-3.74166;BQBZ=-1.63041;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,18,138,18,138,138:6:0 0,6,68,6,68,68:2:0 0,12,153,18,156,153:7:1 17 191 . T <*> 0 . DP=15;I16=13,2,0,0,534,19276,0,0,838,48482,0,0,267,5939,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,18,143:6:0 0,6,67:2:0 0,21,169:7:0 17 192 . G <*> 0 . DP=15;I16=13,2,0,0,499,17439,0,0,838,48482,0,0,266,5890,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,18,143:6:0 0,6,67:2:0 0,21,151:7:0 17 193 . T <*> 0 . DP=15;I16=13,2,0,0,505,17811,0,0,838,48482,0,0,265,5859,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,18,140:6:0 0,6,63:2:0 0,21,157:7:0 @@ -145,10 +144,10 @@ 17 220 . G <*> 0 . DP=14;I16=11,3,0,0,495,18407,0,0,747,42123,0,0,267,6079,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,188:7:0 0,9,88:3:0 0,12,84:4:0 17 221 . A <*> 0 . DP=14;I16=11,3,0,0,488,17688,0,0,747,42123,0,0,267,6135,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,176:7:0 0,9,89:3:0 0,12,101:4:0 17 222 . A <*> 0 . DP=14;I16=11,3,0,0,479,17747,0,0,747,42123,0,0,267,6203,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,186:7:0 0,9,89:3:0 0,12,73:4:0 -17 223 . G T,<*> 0 . DP=13;I16=9,3,1,0,412,14782,8,64,627,34923,60,3600,243,5657,25,625;QS=2.96596,0.0340426,0;SGB=-0.556633;RPBZ=1.07052;MQBZ=0.547723;MQSBZ=-3.4641;BQBZ=-1.60577;NMBZ=-0.288675;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,11,166,18,169,167:7:1 0,6,53,6,53,53:2:0 0,12,81,12,81,81:4:0 +17 223 . G T,<*> 0 . DP=13;I16=9,3,1,0,412,14782,8,64,627,34923,60,3600,243,5657,25,625;QS=2.96596,0.0340426,0;SGB=-0.556633;RPBZ=1.07052;MQBZ=0.547723;MQSBZ=-3.4641;BQBZ=-1.60577;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,11,166,18,169,167:7:1 0,6,53,6,53,53:2:0 0,12,81,12,81,81:4:0 17 224 . G <*> 0 . DP=12;I16=9,3,0,0,379,12759,0,0,627,34923,0,0,270,6370,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,18,168:6:0 0,6,50:2:0 0,12,70:4:0 17 225 . C <*> 0 . DP=12;I16=9,3,0,0,390,13960,0,0,627,34923,0,0,272,6466,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,18,165:6:0 0,6,48:2:0 0,12,86:4:0 -17 226 . A G,C,<*> 0 . DP=13;I16=8,3,1,1,381,13669,6,18,567,31323,89,4441,248,5894,44,986;QS=2.94293,0.0392157,0.0178571,0;VDB=0.84;SGB=-2.62246;RPBZ=-0.592157;MQBZ=-0.615457;MQSBZ=-3.4641;BQBZ=-2.17723;NMBZ=2.34521;SCBZ=2.34521;FS=0;MQ0F=0 PL:DP:DV 0,18,159,12,162,159,18,159,162,159:7:1 0,6,53,6,53,53,6,53,53,53:2:0 0,5,79,9,82,80,9,82,80,80:4:1 +17 226 . A G,C,<*> 0 . DP=13;I16=8,3,1,1,381,13669,6,18,567,31323,89,4441,248,5894,44,986;QS=2.94293,0.0392157,0.0178571,0;VDB=0.84;SGB=-2.62246;RPBZ=-0.592157;MQBZ=-0.615457;MQSBZ=-3.4641;BQBZ=-2.17723;SCBZ=2.34521;FS=0;MQ0F=0 PL:DP:DV 0,18,159,12,162,159,18,159,162,159:7:1 0,6,53,6,53,53,6,53,53,53:2:0 0,5,79,9,82,80,9,82,80,80:4:1 17 227 . C <*> 0 . DP=13;I16=9,4,0,0,412,14342,0,0,656,35764,0,0,292,6878,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,190:7:0 0,6,53:2:0 0,12,75:4:0 17 228 . C <*> 0 . DP=13;I16=9,4,0,0,417,14381,0,0,656,35764,0,0,292,6884,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,187:7:0 0,6,45:2:0 0,12,96:4:0 17 229 . G <*> 0 . DP=13;I16=9,4,0,0,368,11524,0,0,656,35764,0,0,292,6898,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,145:7:0 0,6,53:2:0 0,12,70:4:0 @@ -159,7 +158,7 @@ 17 234 . A <*> 0 . DP=14;I16=10,4,0,0,502,18390,0,0,716,39364,0,0,292,6988,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,185:7:0 0,6,53:2:0 0,15,123:5:0 17 235 . A <*> 0 . DP=14;I16=10,4,0,0,488,17796,0,0,716,39364,0,0,291,6951,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,186:7:0 0,6,53:2:0 0,15,115:5:0 17 236 . G <*> 0 . DP=15;I16=11,4,0,0,501,17481,0,0,776,42964,0,0,290,6924,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,206:8:0 0,6,53:2:0 0,15,103:5:0 -17 237 . A C,<*> 0 . DP=14;I16=9,4,1,0,465,16877,8,64,656,35764,60,3600,266,6282,25,625;QS=2.93162,0.0683761,0;SGB=-0.556633;RPBZ=1.11754;MQBZ=0.632456;MQSBZ=-3.60555;BQBZ=-1.61959;NMBZ=-0.27735;SCBZ=-0.27735;FS=0;MQ0F=0 PL:DP:DV 0,24,206,24,206,206:8:0 0,6,53,6,53,53:2:0 0,3,84,9,87,87:4:1 +17 237 . A C,<*> 0 . DP=14;I16=9,4,1,0,465,16877,8,64,656,35764,60,3600,266,6282,25,625;QS=2.93162,0.0683761,0;SGB=-0.556633;RPBZ=1.11754;MQBZ=0.632456;MQSBZ=-3.60555;BQBZ=-1.61959;SCBZ=-0.27735;FS=0;MQ0F=0 PL:DP:DV 0,24,206,24,206,206:8:0 0,6,53,6,53,53:2:0 0,3,84,9,87,87:4:1 17 238 . C <*> 0 . DP=14;I16=10,4,0,0,482,17238,0,0,716,39364,0,0,292,6900,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,211:8:0 0,6,53:2:0 0,12,82:4:0 17 239 . A <*> 0 . DP=15;I16=10,5,0,0,525,19155,0,0,776,42964,0,0,292,6852,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,223:9:0 0,6,50:2:0 0,12,108:4:0 17 240 . C <*> 0 . DP=15;I16=10,5,0,0,512,17930,0,0,776,42964,0,0,292,6764,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,220:9:0 0,6,53:2:0 0,12,106:4:0 @@ -189,18 +188,18 @@ 17 264 . C <*> 0 . DP=22;I16=10,12,0,0,821,31325,0,0,1049,54897,0,0,386,8326,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,15,104:5:0 0,18,172:6:0 17 265 . A <*> 0 . DP=21;I16=9,12,0,0,800,31906,0,0,989,51297,0,0,390,8380,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,15,114:5:0 0,15,129:5:0 17 266 . G <*> 0 . DP=21;I16=9,12,0,0,754,28204,0,0,989,51297,0,0,394,8458,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,15,99:5:0 0,15,138:5:0 -17 267 . T G,<*> 0 . DP=21;I16=9,11,0,1,739,27465,8,64,960,50456,29,841,373,7935,25,625;QS=2.94203,0.057971,0;SGB=-0.556633;RPBZ=-0.330396;MQBZ=-1.23153;MQSBZ=-3.3021;BQBZ=-1.66282;NMBZ=2.4409;SCBZ=2.91633;FS=0;MQ0F=0 PL:DP:DV 0,33,254,33,254,254:11:0 0,6,93,12,96,96:5:1 0,15,149,15,149,149:5:0 +17 267 . T G,<*> 0 . DP=21;I16=9,11,0,1,739,27465,8,64,960,50456,29,841,373,7935,25,625;QS=2.94203,0.057971,0;SGB=-0.556633;RPBZ=-0.330396;MQBZ=-1.23153;MQSBZ=-3.3021;BQBZ=-1.66282;SCBZ=2.91633;FS=0;MQ0F=0 PL:DP:DV 0,33,254,33,254,254:11:0 0,6,93,12,96,96:5:1 0,15,149,15,149,149:5:0 17 268 . T <*> 0 . DP=21;I16=9,12,0,0,748,27708,0,0,989,51297,0,0,402,8686,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,238:11:0 0,15,110:5:0 0,15,156:5:0 17 269 . C <*> 0 . DP=22;I16=9,13,0,0,767,28641,0,0,1018,52138,0,0,406,8836,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,15,91:5:0 0,15,154:5:0 17 270 . C <*> 0 . DP=22;I16=9,13,0,0,766,28210,0,0,1018,52138,0,0,410,8962,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,15,98:5:0 0,15,143:5:0 17 271 . T <*> 0 . DP=22;I16=9,13,0,0,847,32935,0,0,1018,52138,0,0,413,9065,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,15,113:5:0 0,15,152:5:0 17 272 . C <*> 0 . DP=22;I16=9,13,0,0,815,31449,0,0,1018,52138,0,0,415,9143,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,15,97:5:0 0,15,149:5:0 -17 273 . T C,<*> 0 . DP=22;I16=9,12,0,1,798,30664,5,25,989,51297,29,841,392,8620,25,625;QS=2.96094,0.0390625,0;SGB=-0.556633;RPBZ=-0.236567;MQBZ=-1.16701;MQSBZ=-3.42286;BQBZ=-1.66779;NMBZ=2.50862;SCBZ=3.00076;FS=0;MQ0F=0 PL:DP:DV 0,36,255,36,255,255:12:0 0,7,89,12,92,90:5:1 0,15,161,15,161,161:5:0 +17 273 . T C,<*> 0 . DP=22;I16=9,12,0,1,798,30664,5,25,989,51297,29,841,392,8620,25,625;QS=2.96094,0.0390625,0;SGB=-0.556633;RPBZ=-0.236567;MQBZ=-1.16701;MQSBZ=-3.42286;BQBZ=-1.66779;SCBZ=3.00076;FS=0;MQ0F=0 PL:DP:DV 0,36,255,36,255,255:12:0 0,7,89,12,92,90:5:1 0,15,161,15,161,161:5:0 17 274 . C <*> 0 . DP=22;I16=9,13,0,0,767,28193,0,0,1018,52138,0,0,419,9371,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,15,101:5:0 0,15,144:5:0 17 275 . C <*> 0 . DP=20;I16=7,13,0,0,768,29994,0,0,898,44938,0,0,423,9519,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,15,114:5:0 0,12,122:4:0 17 276 . A <*> 0 . DP=20;I16=7,13,0,0,805,32931,0,0,898,44938,0,0,424,9538,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,253:11:0 0,15,122:5:0 0,12,124:4:0 17 277 . G <*> 0 . DP=20;I16=7,13,0,0,764,29732,0,0,898,44938,0,0,425,9579,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,15,114:5:0 0,12,121:4:0 -17 278 . A C,<*> 0 . DP=21;I16=6,14,1,0,722,26452,7,49,867,42179,60,3600,415,9521,11,121;QS=2.97935,0.020649,0;SGB=-0.556633;RPBZ=1.65198;MQBZ=1.0247;MQSBZ=-3.24037;BQBZ=-1.66667;NMBZ=-0.406816;SCBZ=-0.324037;FS=0;MQ0F=0 PL:DP:DV 0,22,231,30,234,231:11:1 0,18,123,18,123,123:6:0 0,12,121,12,121,121:4:0 +17 278 . A C,<*> 0 . DP=21;I16=6,14,1,0,722,26452,7,49,867,42179,60,3600,415,9521,11,121;QS=2.97935,0.020649,0;SGB=-0.556633;RPBZ=1.65198;MQBZ=1.0247;MQSBZ=-3.24037;BQBZ=-1.66667;SCBZ=-0.324037;FS=0;MQ0F=0 PL:DP:DV 0,22,231,30,234,231:11:1 0,18,123,18,123,123:6:0 0,12,121,12,121,121:4:0 17 279 . A <*> 0 . DP=22;I16=7,15,0,0,786,28694,0,0,956,46620,0,0,427,9677,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,18,123:6:0 0,12,122:4:0 17 280 . A <*> 0 . DP=22;I16=7,15,0,0,815,31561,0,0,956,46620,0,0,428,9684,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,253:12:0 0,18,130:6:0 0,12,129:4:0 17 281 . G <*> 0 . DP=22;I16=7,15,0,0,820,31416,0,0,956,46620,0,0,428,9662,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,18,122:6:0 0,12,123:4:0 @@ -219,13 +218,13 @@ 17 294 . A <*> 0 . DP=26;I16=10,16,0,0,931,33937,0,0,1227,63779,0,0,443,9785,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,252:12:0 0,24,201:8:0 0,18,161:6:0 17 295 . C <*> 0 . DP=25;I16=10,15,0,0,909,34117,0,0,1198,62938,0,0,447,9833,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,183:8:0 0,18,159:6:0 17 296 . A <*> 0 . DP=25;I16=10,15,0,0,874,31846,0,0,1198,62938,0,0,451,9905,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,169:8:0 0,18,169:6:0 -17 297 . C G,<*> 0 . DP=25;I16=9,15,1,0,901,34305,4,16,1138,59338,60,3600,445,9901,10,100;QS=2.98261,0.0173913,0;SGB=-0.556633;RPBZ=-1.24856;MQBZ=0.806872;MQSBZ=-3.22749;BQBZ=-1.67542;NMBZ=-0.434372;SCBZ=-0.368383;FS=0;MQ0F=0 PL:DP:DV 0,33,255,33,255,255:11:0 0,15,168,21,171,168:8:1 0,18,161,18,161,161:6:0 +17 297 . C G,<*> 0 . DP=25;I16=9,15,1,0,901,34305,4,16,1138,59338,60,3600,445,9901,10,100;QS=2.98261,0.0173913,0;SGB=-0.556633;RPBZ=-1.24856;MQBZ=0.806872;MQSBZ=-3.22749;BQBZ=-1.67542;SCBZ=-0.368383;FS=0;MQ0F=0 PL:DP:DV 0,33,255,33,255,255:11:0 0,15,168,21,171,168:8:1 0,18,161,18,161,161:6:0 17 298 . A <*> 0 . DP=26;I16=11,15,0,0,936,34652,0,0,1258,66538,0,0,459,10121,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,184:8:0 0,21,191:7:0 17 299 . C <*> 0 . DP=27;I16=11,15,0,0,971,36863,0,0,1258,66538,0,0,464,10266,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,193:8:0 0,21,189:7:0 17 300 . A <*> 0 . DP=27;I16=11,15,0,0,1001,39455,0,0,1258,66538,0,0,469,10437,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,204:8:0 0,21,210:7:0 17 301 . G <*> 0 . DP=25;I16=10,14,0,0,928,36116,0,0,1169,62097,0,0,476,10632,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,255:10:0 0,21,195:7:0 0,21,196:7:0 17 302 . T <*> 0 . DP=25;I16=10,14,0,0,879,32885,0,0,1169,62097,0,0,483,10849,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,231:10:0 0,21,172:7:0 0,21,202:7:0 -17 302 . T TA 0 . INDEL;IDV=7;IMF=1;DP=25;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.539485,2.46052;VDB=0.241622;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.22749;BQBZ=-1.67542;NMBZ=-0.199304;SCBZ=-0.268121;FS=0;MQ0F=0 PL:DP:DV 161,0,99:11:6 158,0,14:7:6 201,21,0:7:7 +17 302 . T TA 0 . INDEL;IDV=7;IMF=1;DP=25;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.539485,2.46052;VDB=0.241622;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.22749;BQBZ=-1.67542;SCBZ=-0.268121;FS=0;MQ0F=0 PL:DP:DV 161,0,99:11:6 158,0,14:7:6 201,21,0:7:7 17 303 . G <*> 0 . DP=25;I16=10,15,0,0,968,37972,0,0,1229,65697,0,0,497,11181,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,21,197:7:0 0,21,195:7:0 17 304 . C <*> 0 . DP=27;I16=11,16,0,0,991,37005,0,0,1318,70138,0,0,503,11359,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,206:8:0 0,24,200:8:0 17 305 . C <*> 0 . DP=27;I16=11,16,0,0,1057,41761,0,0,1318,70138,0,0,510,11508,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,213:8:0 0,24,211:8:0 @@ -258,9 +257,9 @@ 17 332 . A <*> 0 . DP=32;I16=14,18,0,0,1156,42666,0,0,1649,90897,0,0,560,12178,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,27,214:9:0 0,33,255:11:0 17 333 . A <*> 0 . DP=32;I16=14,18,0,0,1141,41987,0,0,1649,90897,0,0,558,12064,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,27,223:9:0 0,33,255:11:0 17 334 . A <*> 0 . DP=32;I16=14,18,0,0,1162,43328,0,0,1649,90897,0,0,556,11986,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,27,221:9:0 0,33,255:11:0 -17 335 . A G,<*> 0 . DP=32;I16=13,18,1,0,1084,40336,4,16,1589,87297,60,3600,555,11943,0,0;QS=2.98919,0.0108108,0;SGB=-0.556633;RPBZ=-1.67936;MQBZ=0.622171;MQSBZ=-2.25492;BQBZ=-1.68602;NMBZ=-0.428353;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV 0,33,252,33,252,252:11:0 0,27,219,27,219,219:9:0 0,25,245,33,248,245:12:1 +17 335 . A G,<*> 0 . DP=32;I16=13,18,1,0,1084,40336,4,16,1589,87297,60,3600,555,11943,0,0;QS=2.98919,0.0108108,0;SGB=-0.556633;RPBZ=-1.67936;MQBZ=0.622171;MQSBZ=-2.25492;BQBZ=-1.68602;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV 0,33,252,33,252,252:11:0 0,27,219,27,219,219:9:0 0,25,245,33,248,245:12:1 17 336 . A <*> 0 . DP=32;I16=14,18,0,0,1094,39794,0,0,1649,90897,0,0,555,11935,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,27,212:9:0 0,36,255:12:0 -17 337 . C A,<*> 0 . DP=32;I16=14,17,0,1,1125,42481,5,25,1612,89528,37,1369,536,11590,18,324;QS=2.98113,0.0188679,0;SGB=-0.556633;RPBZ=0.812593;MQBZ=-1.03695;MQSBZ=-2.25492;BQBZ=-1.68353;NMBZ=-0.376914;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV 0,33,255,33,255,255:11:0 0,17,195,24,198,195:9:1 0,36,255,36,255,255:12:0 +17 337 . C A,<*> 0 . DP=32;I16=14,17,0,1,1125,42481,5,25,1612,89528,37,1369,536,11590,18,324;QS=2.98113,0.0188679,0;SGB=-0.556633;RPBZ=0.812593;MQBZ=-1.03695;MQSBZ=-2.25492;BQBZ=-1.68353;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV 0,33,255,33,255,255:11:0 0,17,195,24,198,195:9:1 0,36,255,36,255,255:12:0 17 338 . T <*> 0 . DP=30;I16=14,16,0,0,1190,47898,0,0,1560,86456,0,0,554,11878,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,255:10:0 0,24,226:8:0 0,36,255:12:0 17 339 . C <*> 0 . DP=31;I16=14,17,0,0,1130,43210,0,0,1589,87297,0,0,554,11874,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,185:8:0 0,36,255:12:0 17 340 . C <*> 0 . DP=31;I16=14,17,0,0,1196,47044,0,0,1589,87297,0,0,554,11852,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,221:8:0 0,36,255:12:0 @@ -278,11 +277,11 @@ 17 352 . A <*> 0 . DP=31;I16=16,15,0,0,1162,45664,0,0,1651,92815,0,0,569,13029,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,27,230:9:0 0,33,255:11:0 17 353 . G <*> 0 . DP=29;I16=15,14,0,0,1109,43095,0,0,1562,88374,0,0,570,13064,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,255:10:0 0,27,231:9:0 0,30,255:10:0 17 354 . A <*> 0 . DP=28;I16=14,14,0,0,1078,42938,0,0,1502,84774,0,0,571,13075,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,225:9:0 0,27,244:9:0 0,30,255:10:0 -17 355 . G T,<*> 0 . DP=28;I16=14,13,0,1,1001,37907,41,1681,1442,81174,60,3600,547,12487,25,625;QS=2.875,0.125,0;SGB=-0.556633;RPBZ=0.185772;MQBZ=0.520126;MQSBZ=-1.7696;BQBZ=0.683978;NMBZ=2.33874;SCBZ=-0.27735;FS=0;MQ0F=0 PL:DP:DV 14,0,200,38,203,231:9:1 0,27,222,27,222,222:9:0 0,30,255,30,255,255:10:0 +17 355 . G T,<*> 0 . DP=28;I16=14,13,0,1,1001,37907,41,1681,1442,81174,60,3600,547,12487,25,625;QS=2.875,0.125,0;SGB=-0.556633;RPBZ=0.185772;MQBZ=0.520126;MQSBZ=-1.7696;BQBZ=0.683978;SCBZ=-0.27735;FS=0;MQ0F=0 PL:DP:DV 14,0,200,38,203,231:9:1 0,27,222,27,222,222:9:0 0,30,255,30,255,255:10:0 17 356 . G <*> 0 . DP=27;I16=14,13,0,0,993,37481,0,0,1465,83405,0,0,574,13174,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,228:9:0 0,24,201:8:0 0,30,255:10:0 17 357 . C <*> 0 . DP=28;I16=15,13,0,0,1026,39496,0,0,1525,87005,0,0,575,13209,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,255:10:0 0,24,205:8:0 0,30,252:10:0 17 358 . A <*> 0 . DP=28;I16=15,13,0,0,1050,40518,0,0,1525,87005,0,0,576,13216,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,254:10:0 0,24,197:8:0 0,30,255:10:0 -17 359 . G T,<*> 0 . DP=29;I16=15,13,0,1,1085,42761,10,100,1525,87005,60,3600,552,12620,25,625;QS=2.96032,0.0396825,0;SGB=-0.556633;RPBZ=-0.119611;MQBZ=0.456435;MQSBZ=-1.53333;BQBZ=-1.68246;NMBZ=3.0531;SCBZ=5.2915;FS=0;MQ0F=0 PL:DP:DV 0,30,255,30,255,255:10:0 0,13,178,21,181,180:8:1 0,33,255,33,255,255:11:0 +17 359 . G T,<*> 0 . DP=29;I16=15,13,0,1,1085,42761,10,100,1525,87005,60,3600,552,12620,25,625;QS=2.96032,0.0396825,0;SGB=-0.556633;RPBZ=-0.119611;MQBZ=0.456435;MQSBZ=-1.53333;BQBZ=-1.68246;SCBZ=5.2915;FS=0;MQ0F=0 PL:DP:DV 0,30,255,30,255,255:10:0 0,13,178,21,181,180:8:1 0,33,255,33,255,255:11:0 17 360 . A <*> 0 . DP=29;I16=15,14,0,0,1111,43259,0,0,1585,90605,0,0,579,13297,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,252:10:0 0,24,220:8:0 0,33,255:11:0 17 361 . A <*> 0 . DP=29;I16=15,14,0,0,1116,43442,0,0,1585,90605,0,0,579,13273,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,252:10:0 0,24,219:8:0 0,33,255:11:0 17 362 . A <*> 0 . DP=29;I16=16,13,0,0,1104,42700,0,0,1585,90605,0,0,580,13272,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,218:8:0 0,30,255:10:0 @@ -292,13 +291,13 @@ 17 366 . A <*> 0 . DP=29;I16=16,13,0,0,1090,41562,0,0,1585,90605,0,0,581,13167,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,211:8:0 0,30,255:10:0 17 367 . T <*> 0 . DP=29;I16=16,13,0,0,1055,39149,0,0,1585,90605,0,0,579,13093,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,204:8:0 0,30,255:10:0 17 368 . A <*> 0 . DP=29;I16=16,13,0,0,1054,39632,0,0,1585,90605,0,0,576,12998,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,208:8:0 0,30,255:10:0 -17 369 . T G,<*> 0 . DP=28;I16=16,11,0,1,1037,40275,6,36,1496,86164,60,3600,548,12256,25,625;QS=2.97683,0.023166,0;SGB=-0.556633;RPBZ=0.12395;MQBZ=0.408248;MQSBZ=-1.37784;BQBZ=-1.68703;NMBZ=2.99794;SCBZ=5.19615;FS=0;MQ0F=0 PL:DP:DV 0,30,250,30,250,250:10:0 0,15,189,21,192,190:8:1 0,30,255,30,255,255:10:0 +17 369 . T G,<*> 0 . DP=28;I16=16,11,0,1,1037,40275,6,36,1496,86164,60,3600,548,12256,25,625;QS=2.97683,0.023166,0;SGB=-0.556633;RPBZ=0.12395;MQBZ=0.408248;MQSBZ=-1.37784;BQBZ=-1.68703;SCBZ=5.19615;FS=0;MQ0F=0 PL:DP:DV 0,30,250,30,250,250:10:0 0,15,189,21,192,190:8:1 0,30,255,30,255,255:10:0 17 370 . C <*> 0 . DP=28;I16=16,12,0,0,1045,40219,0,0,1556,89764,0,0,570,12790,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,255:10:0 0,24,201:8:0 0,30,255:10:0 17 371 . T <*> 0 . DP=29;I16=16,13,0,0,1155,46591,0,0,1616,93364,0,0,567,12725,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,255:10:0 0,24,227:8:0 0,33,255:11:0 17 372 . C <*> 0 . DP=30;I16=16,14,0,0,1139,44019,0,0,1676,96964,0,0,564,12636,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,215:8:0 0,33,255:11:0 17 373 . A <*> 0 . DP=30;I16=16,14,0,0,1142,44118,0,0,1676,96964,0,0,561,12525,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,220:8:0 0,33,255:11:0 17 374 . T <*> 0 . DP=30;I16=16,14,0,0,1098,41180,0,0,1676,96964,0,0,556,12344,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,221:8:0 0,33,255:11:0 -17 375 . A T,<*> 0 . DP=31;I16=17,13,0,1,1138,43798,14,196,1676,96964,60,3600,547,12177,4,16;QS=2.9661,0.0338983,0;SGB=-0.556633;RPBZ=-1.45432;MQBZ=0.3849;MQSBZ=-1.26404;BQBZ=-1.68488;NMBZ=2.30253;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,36,255,36,255,255:12:0 0,24,218,24,218,218:8:0 0,18,255,30,255,255:11:1 +17 375 . A T,<*> 0 . DP=31;I16=17,13,0,1,1138,43798,14,196,1676,96964,60,3600,547,12177,4,16;QS=2.9661,0.0338983,0;SGB=-0.556633;RPBZ=-1.45432;MQBZ=0.3849;MQSBZ=-1.26404;BQBZ=-1.68488;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,36,255,36,255,255:12:0 0,24,218,24,218,218:8:0 0,18,255,30,255,255:11:1 17 376 . G <*> 0 . DP=31;I16=17,14,0,0,1131,42581,0,0,1736,100564,0,0,547,12073,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,24,220:8:0 0,33,255:11:0 17 377 . T <*> 0 . DP=31;I16=17,14,0,0,1116,41750,0,0,1736,100564,0,0,543,11985,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,24,211:8:0 0,33,255:11:0 17 378 . T <*> 0 . DP=30;I16=18,12,0,0,1098,41066,0,0,1707,99723,0,0,541,11927,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,39,255:13:0 0,21,186:7:0 0,30,255:10:0 @@ -307,7 +306,7 @@ 17 381 . T <*> 0 . DP=29;I16=18,11,0,0,1167,47337,0,0,1678,98882,0,0,537,11729,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,21,211:7:0 0,30,255:10:0 17 382 . T <*> 0 . DP=29;I16=18,11,0,0,1062,40514,0,0,1678,98882,0,0,535,11693,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,21,182:7:0 0,30,255:10:0 17 383 . T <*> 0 . DP=29;I16=18,11,0,0,1059,39847,0,0,1678,98882,0,0,532,11638,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,21,172:7:0 0,30,255:10:0 -17 384 . A C,<*> 0 . DP=31;I16=19,11,0,1,1077,39885,4,16,1738,102482,60,3600,504,10988,25,625;QS=2.98419,0.0158103,0;SGB=-0.556633;RPBZ=0.615229;MQBZ=0.262613;MQSBZ=-0.333409;BQBZ=-1.68746;NMBZ=3.26825;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,39,255,39,255,255:13:0 0,15,171,21,174,171:8:1 0,30,255,30,255,255:10:0 +17 384 . A C,<*> 0 . DP=31;I16=19,11,0,1,1077,39885,4,16,1738,102482,60,3600,504,10988,25,625;QS=2.98419,0.0158103,0;SGB=-0.556633;RPBZ=0.615229;MQBZ=0.262613;MQSBZ=-0.333409;BQBZ=-1.68746;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,39,255,39,255,255:13:0 0,15,171,21,174,171:8:1 0,30,255,30,255,255:10:0 17 385 . C <*> 0 . DP=31;I16=19,12,0,0,1118,41180,0,0,1798,106082,0,0,527,11569,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,39,255:13:0 0,24,186:8:0 0,30,255:10:0 17 386 . T <*> 0 . DP=30;I16=18,12,0,0,1158,45592,0,0,1738,102482,0,0,526,11556,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,39,255:13:0 0,21,191:7:0 0,30,255:10:0 17 387 . T <*> 0 . DP=30;I16=18,12,0,0,1105,41821,0,0,1738,102482,0,0,525,11573,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,39,255:13:0 0,21,187:7:0 0,30,255:10:0 @@ -324,7 +323,7 @@ 17 398 . A <*> 0 . DP=28;I16=17,11,0,0,1025,38361,0,0,1587,92523,0,0,524,11850,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,39,255:13:0 0,15,144:5:0 0,30,255:10:0 17 399 . A <*> 0 . DP=28;I16=17,11,0,0,1023,38949,0,0,1587,92523,0,0,526,11900,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,39,255:13:0 0,15,140:5:0 0,30,255:10:0 17 400 . A <*> 0 . DP=29;I16=17,12,0,0,1070,40554,0,0,1647,96123,0,0,526,11828,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,39,255:13:0 0,15,159:5:0 0,33,255:11:0 -17 401 . A C,<*> 0 . DP=29;I16=17,11,0,1,1063,41001,8,64,1587,92523,60,3600,501,11113,25,625;QS=2.97985,0.0201511,0;SGB=-0.556633;RPBZ=-0.478622;MQBZ=0.339683;MQSBZ=0.29364;BQBZ=-1.68267;NMBZ=3.53589;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,39,255,39,255,255:13:0 0,15,160,15,160,160:5:0 0,22,255,30,255,255:11:1 +17 401 . A C,<*> 0 . DP=29;I16=17,11,0,1,1063,41001,8,64,1587,92523,60,3600,501,11113,25,625;QS=2.97985,0.0201511,0;SGB=-0.556633;RPBZ=-0.478622;MQBZ=0.339683;MQSBZ=0.29364;BQBZ=-1.68267;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,39,255,39,255,255:13:0 0,15,160,15,160,160:5:0 0,22,255,30,255,255:11:1 17 402 . T <*> 0 . DP=29;I16=17,12,0,0,1076,40740,0,0,1647,96123,0,0,526,11680,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,39,255:13:0 0,15,149:5:0 0,33,255:11:0 17 403 . T <*> 0 . DP=29;I16=17,12,0,0,1085,40985,0,0,1647,96123,0,0,526,11654,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,39,255:13:0 0,15,148:5:0 0,33,255:11:0 17 404 . G <*> 0 . DP=29;I16=17,12,0,0,1074,40524,0,0,1647,96123,0,0,525,11609,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,39,255:13:0 0,15,131:5:0 0,33,255:11:0 @@ -335,7 +334,7 @@ 17 409 . T <*> 0 . DP=29;I16=17,12,0,0,1100,42734,0,0,1678,98882,0,0,525,11503,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,42,255:14:0 0,12,131:4:0 0,33,255:11:0 17 410 . T <*> 0 . DP=29;I16=17,12,0,0,1035,38325,0,0,1678,98882,0,0,524,11432,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,42,255:14:0 0,12,125:4:0 0,33,255:11:0 17 411 . T <*> 0 . DP=29;I16=17,12,0,0,1022,37928,0,0,1678,98882,0,0,522,11342,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,42,255:14:0 0,12,111:4:0 0,33,255:11:0 -17 412 . C T,<*> 0 . DP=30;I16=17,12,1,0,1094,42458,14,196,1678,98882,60,3600,495,10659,25,625;QS=2.97455,0.0254545,0;SGB=-0.556633;RPBZ=-0.40473;MQBZ=0.267261;MQSBZ=-0.293785;BQBZ=-1.6942;NMBZ=-0.267102;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,30,255,42,255,255:15:1 0,12,124,12,124,124:4:0 0,33,255,33,255,255:11:0 +17 412 . C T,<*> 0 . DP=30;I16=17,12,1,0,1094,42458,14,196,1678,98882,60,3600,495,10659,25,625;QS=2.97455,0.0254545,0;SGB=-0.556633;RPBZ=-0.40473;MQBZ=0.267261;MQSBZ=-0.293785;BQBZ=-1.6942;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,30,255,42,255,255:15:1 0,12,124,12,124,124:4:0 0,33,255,33,255,255:11:0 17 413 . A <*> 0 . DP=31;I16=18,13,0,0,1189,45985,0,0,1798,106082,0,0,520,11258,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,9,102:3:0 0,33,255:11:0 17 414 . T <*> 0 . DP=30;I16=18,12,0,0,1151,44355,0,0,1738,102482,0,0,523,11265,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,9,109:3:0 0,33,255:11:0 17 415 . G <*> 0 . DP=30;I16=18,12,0,0,1131,43175,0,0,1738,102482,0,0,526,11306,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,9,110:3:0 0,33,255:11:0 @@ -360,7 +359,7 @@ 17 434 . T <*> 0 . DP=29;I16=15,14,0,0,1036,37654,0,0,1647,96123,0,0,561,12567,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,9,98:3:0 0,30,243:10:0 17 435 . A <*> 0 . DP=29;I16=15,14,0,0,1035,38091,0,0,1647,96123,0,0,562,12596,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,9,103:3:0 0,30,237:10:0 17 436 . T <*> 0 . DP=28;I16=14,14,0,0,998,36220,0,0,1587,92523,0,0,564,12654,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,9,110:3:0 0,27,223:9:0 -17 437 . T G,<*> 0 . DP=28;I16=13,14,1,0,990,36832,6,36,1558,91682,29,841,549,12435,16,256;QS=2.9781,0.0218978,0;SGB=-0.556633;RPBZ=-1.36214;MQBZ=-2.88675;MQSBZ=0.6;BQBZ=-1.67909;NMBZ=-0.19245;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,48,255,48,255,255:16:0 0,9,109,9,109,109:3:0 0,17,200,24,203,201:9:1 +17 437 . T G,<*> 0 . DP=28;I16=13,14,1,0,990,36832,6,36,1558,91682,29,841,549,12435,16,256;QS=2.9781,0.0218978,0;SGB=-0.556633;RPBZ=-1.36214;MQBZ=-2.88675;MQSBZ=0.6;BQBZ=-1.67909;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,48,255,48,255,255:16:0 0,9,109,9,109,109:3:0 0,17,200,24,203,201:9:1 17 438 . A <*> 0 . DP=28;I16=14,14,0,0,984,35784,0,0,1587,92523,0,0,565,12707,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,9,107:3:0 0,27,220:9:0 17 439 . C <*> 0 . DP=28;I16=14,14,0,0,1055,40273,0,0,1587,92523,0,0,563,12649,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,9,107:3:0 0,27,224:9:0 17 440 . A <*> 0 . DP=28;I16=14,14,0,0,1095,43251,0,0,1587,92523,0,0,561,12615,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,9,115:3:0 0,27,247:9:0 @@ -388,13 +387,13 @@ 17 462 . G <*> 0 . DP=32;I16=18,13,0,0,1169,46001,0,0,1775,103851,0,0,577,12669,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,12,131:4:0 0,30,241:10:0 17 463 . G <*> 0 . DP=32;I16=18,13,0,0,1095,41573,0,0,1775,103851,0,0,583,12729,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,12,126:4:0 0,30,221:10:0 17 464 . A <*> 0 . DP=32;I16=18,13,0,0,1100,41724,0,0,1775,103851,0,0,589,12821,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,12,148:4:0 0,30,217:10:0 -17 465 . C T,<*> 0 . DP=33;I16=19,12,0,1,1173,45601,4,16,1775,103851,60,3600,589,12909,6,36;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.67982;MQBZ=0.321288;MQSBZ=0.341466;BQBZ=-1.68493;NMBZ=3.21288;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,51,255,51,255,255:17:0 0,15,158,15,158,158:5:0 0,20,224,27,227,224:10:1 +17 465 . C T,<*> 0 . DP=33;I16=19,12,0,1,1173,45601,4,16,1775,103851,60,3600,589,12909,6,36;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.67982;MQBZ=0.321288;MQSBZ=0.341466;BQBZ=-1.68493;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,51,255,51,255,255:17:0 0,15,158,15,158,158:5:0 0,20,224,27,227,224:10:1 17 466 . A <*> 0 . DP=34;I16=20,13,0,0,1268,49686,0,0,1895,111051,0,0,602,13102,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,15,173:5:0 0,30,255:10:0 17 467 . A <*> 0 . DP=34;I16=20,13,0,0,1246,48610,0,0,1895,111051,0,0,608,13194,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,15,177:5:0 0,30,251:10:0 17 468 . A <*> 0 . DP=35;I16=21,13,0,0,1253,48095,0,0,1955,114651,0,0,613,13273,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,15,174:5:0 0,30,251:10:0 17 469 . A <*> 0 . DP=35;I16=21,13,0,0,1260,49028,0,0,1955,114651,0,0,618,13340,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,15,165:5:0 0,30,255:10:0 17 470 . G <*> 0 . DP=35;I16=21,13,0,0,1265,48879,0,0,1955,114651,0,0,623,13445,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,15,167:5:0 0,30,238:10:0 -17 471 . T G,C,<*> 0 . DP=36;I16=21,12,0,2,1220,46380,18,162,1918,113282,97,4969,611,13281,16,256;QS=2.94529,0.0273556,0.0273556,0;VDB=0.96;SGB=0.346553;RPBZ=0.497712;MQBZ=-1.9761;MQSBZ=0.312094;BQBZ=-2.35032;NMBZ=2.19566;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,57,255,57,255,255,57,255,255,255:19:0 0,15,169,15,169,169,15,169,169,169:5:0 0,19,219,19,221,219,27,222,222,221:11:2 +17 471 . T G,C,<*> 0 . DP=36;I16=21,12,0,2,1220,46380,18,162,1918,113282,97,4969,611,13281,16,256;QS=2.94529,0.0273556,0.0273556,0;VDB=0.96;SGB=0.346553;RPBZ=0.497712;MQBZ=-1.9761;MQSBZ=0.312094;BQBZ=-2.35032;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,57,255,57,255,255,57,255,255,255:19:0 0,15,169,15,169,169,15,169,169,169:5:0 0,19,219,19,221,219,27,222,222,221:11:2 17 472 . T <*> 0 . DP=35;I16=21,13,0,0,1234,46640,0,0,1955,114651,0,0,633,13665,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,15,172:5:0 0,30,241:10:0 17 473 . G <*> 0 . DP=35;I16=21,13,0,0,1303,51953,0,0,1955,114651,0,0,638,13780,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,15,159:5:0 0,30,250:10:0 17 474 . G <*> 0 . DP=36;I16=22,13,0,0,1279,49235,0,0,2015,118251,0,0,642,13884,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,15,146:5:0 0,33,255:11:0 @@ -411,7 +410,7 @@ 17 485 . G <*> 0 . DP=35;I16=23,12,0,0,1329,51411,0,0,2015,118251,0,0,669,14931,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,18,160:6:0 0,33,255:11:0 17 486 . A <*> 0 . DP=34;I16=22,12,0,0,1313,51667,0,0,1955,114651,0,0,671,14989,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,18,173:6:0 0,33,255:11:0 17 487 . G <*> 0 . DP=34;I16=22,12,0,0,1300,50304,0,0,1955,114651,0,0,672,15030,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,18,169:6:0 0,33,255:11:0 -17 488 . A G,<*> 0 . DP=35;I16=22,12,1,0,1278,48412,4,16,1986,117410,29,841,646,14380,25,625;QS=2.98947,0.0105263,0;SGB=-0.556633;RPBZ=0.594463;MQBZ=-3.36505;MQSBZ=0.10737;BQBZ=-1.69552;NMBZ=-0.171499;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,54,255,54,255,255:18:0 0,18,177,18,177,177:6:0 0,23,255,30,255,255:11:1 +17 488 . A G,<*> 0 . DP=35;I16=22,12,1,0,1278,48412,4,16,1986,117410,29,841,646,14380,25,625;QS=2.98947,0.0105263,0;SGB=-0.556633;RPBZ=0.594463;MQBZ=-3.36505;MQSBZ=0.10737;BQBZ=-1.69552;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,54,255,54,255,255:18:0 0,18,177,18,177,177:6:0 0,23,255,30,255,255:11:1 17 489 . A <*> 0 . DP=35;I16=23,12,0,0,1264,46916,0,0,2015,118251,0,0,671,15015,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,18,175:6:0 0,33,255:11:0 17 490 . A <*> 0 . DP=36;I16=24,12,0,0,1332,50280,0,0,2075,121851,0,0,671,15061,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,188:7:0 0,33,255:11:0 17 491 . T <*> 0 . DP=36;I16=24,12,0,0,1284,46802,0,0,2075,121851,0,0,671,15093,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,178:7:0 0,33,255:11:0 @@ -435,9 +434,9 @@ 17 509 . C <*> 0 . DP=34;I16=24,10,0,0,1272,48272,0,0,1986,117410,0,0,640,14430,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,186:7:0 0,27,241:9:0 17 510 . A <*> 0 . DP=34;I16=23,11,0,0,1211,44827,0,0,1986,117410,0,0,638,14398,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,21,187:7:0 0,24,221:8:0 17 511 . A <*> 0 . DP=34;I16=23,11,0,0,1238,46516,0,0,1986,117410,0,0,637,14395,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,21,195:7:0 0,24,233:8:0 -17 512 . A C,<*> 0 . DP=33;I16=22,10,0,1,1133,41513,13,169,1866,110210,60,3600,628,14340,9,81;QS=2.97766,0.0223368,0;SGB=-0.556633;RPBZ=-1.47079;MQBZ=0.253876;MQSBZ=-0.461593;BQBZ=-1.68442;NMBZ=2.68627;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,39,255,51,255,255:18:1 0,21,183,21,183,183:7:0 0,24,231,24,231,231:8:0 -17 513 . A T,<*> 0 . DP=32;I16=21,10,1,0,1125,42283,12,144,1806,106610,60,3600,623,14249,15,225;QS=2.97966,0.020339,0;SGB=-0.556633;RPBZ=-1.24609;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.57376;NMBZ=2.63913;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,37,255,48,255,255:17:1 0,21,177,21,177,177:7:0 0,24,233,24,233,233:8:0 -17 514 . A T,<*> 0 . DP=32;I16=22,9,0,1,1086,40204,16,256,1806,106610,60,3600,627,14381,11,121;QS=2.97127,0.0287253,0;SGB=-0.556633;RPBZ=-1.4628;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.46657;NMBZ=2.63913;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,34,255,48,255,255:17:1 0,21,172,21,172,172:7:0 0,24,235,24,235,235:8:0 +17 512 . A C,<*> 0 . DP=33;I16=22,10,0,1,1133,41513,13,169,1866,110210,60,3600,628,14340,9,81;QS=2.97766,0.0223368,0;SGB=-0.556633;RPBZ=-1.47079;MQBZ=0.253876;MQSBZ=-0.461593;BQBZ=-1.68442;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,39,255,51,255,255:18:1 0,21,183,21,183,183:7:0 0,24,231,24,231,231:8:0 +17 513 . A T,<*> 0 . DP=32;I16=21,10,1,0,1125,42283,12,144,1806,106610,60,3600,623,14249,15,225;QS=2.97966,0.020339,0;SGB=-0.556633;RPBZ=-1.24609;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.57376;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,37,255,48,255,255:17:1 0,21,177,21,177,177:7:0 0,24,233,24,233,233:8:0 +17 514 . A T,<*> 0 . DP=32;I16=22,9,0,1,1086,40204,16,256,1806,106610,60,3600,627,14381,11,121;QS=2.97127,0.0287253,0;SGB=-0.556633;RPBZ=-1.4628;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.46657;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,34,255,48,255,255:17:1 0,21,172,21,172,172:7:0 0,24,235,24,235,235:8:0 17 515 . C <*> 0 . DP=32;I16=22,10,0,0,1050,37704,0,0,1866,110210,0,0,638,14554,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,21,169:7:0 0,24,211:8:0 17 516 . C <*> 0 . DP=32;I16=22,10,0,0,1109,40651,0,0,1866,110210,0,0,637,14579,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,21,187:7:0 0,24,215:8:0 17 517 . T <*> 0 . DP=33;I16=23,10,0,0,1269,49995,0,0,1926,113810,0,0,636,14626,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,201:7:0 0,24,242:8:0 @@ -446,7 +445,7 @@ 17 520 . T <*> 0 . DP=36;I16=25,11,0,0,1243,45051,0,0,2106,124610,0,0,638,14818,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,63,255:21:0 0,21,180:7:0 0,24,223:8:0 17 521 . C <*> 0 . DP=34;I16=25,9,0,0,1281,49527,0,0,1986,117410,0,0,641,14875,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,60,255:20:0 0,21,191:7:0 0,21,204:7:0 17 522 . A <*> 0 . DP=32;I16=24,8,0,0,1158,43228,0,0,1897,112969,0,0,646,14960,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,60,255:20:0 0,21,185:7:0 0,15,170:5:0 -17 523 . T G,<*> 0 . DP=32;I16=23,8,1,0,1184,45708,15,225,1837,109369,60,3600,626,14446,25,625;QS=2.9794,0.0206044,0;SGB=-0.556633;RPBZ=1.13742;MQBZ=0.179605;MQSBZ=-1.73205;BQBZ=-1.68805;NMBZ=2.89159;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,44,255,57,255,255:20:1 0,21,191,21,191,191:7:0 0,15,166,15,166,166:5:0 +17 523 . T G,<*> 0 . DP=32;I16=23,8,1,0,1184,45708,15,225,1837,109369,60,3600,626,14446,25,625;QS=2.9794,0.0206044,0;SGB=-0.556633;RPBZ=1.13742;MQBZ=0.179605;MQSBZ=-1.73205;BQBZ=-1.68805;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,44,255,57,255,255:20:1 0,21,191,21,191,191:7:0 0,15,166,15,166,166:5:0 17 524 . T <*> 0 . DP=32;I16=24,8,0,0,1096,39618,0,0,1897,112969,0,0,654,15108,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,60,255:20:0 0,21,194:7:0 0,15,150:5:0 17 525 . G <*> 0 . DP=32;I16=24,8,0,0,1188,45718,0,0,1897,112969,0,0,656,15120,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,60,255:20:0 0,21,188:7:0 0,15,133:5:0 17 526 . C <*> 0 . DP=32;I16=24,8,0,0,1154,44014,0,0,1897,112969,0,0,658,15156,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,60,255:20:0 0,21,185:7:0 0,15,137:5:0 @@ -458,7 +457,7 @@ 17 532 . T <*> 0 . DP=32;I16=25,7,0,0,1161,43607,0,0,1897,112969,0,0,649,14477,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,21,181:7:0 0,18,192:6:0 17 533 . C <*> 0 . DP=32;I16=25,7,0,0,1154,44084,0,0,1897,112969,0,0,644,14274,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,21,178:7:0 0,18,180:6:0 17 534 . T <*> 0 . DP=31;I16=24,7,0,0,1222,49526,0,0,1837,109369,0,0,640,14104,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,205:7:0 0,18,205:6:0 -17 535 . A G,<*> 0 . DP=31;I16=24,6,0,1,1080,39870,8,64,1777,105769,60,3600,611,13341,25,625;QS=2.98623,0.0137694,0;SGB=-0.556633;RPBZ=-0.894788;MQBZ=0.182574;MQSBZ=-1.85164;BQBZ=-1.6854;NMBZ=2.94255;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,21,194,21,194,194:7:0 0,18,189,18,189,189:6:0 +17 535 . A G,<*> 0 . DP=31;I16=24,6,0,1,1080,39870,8,64,1777,105769,60,3600,611,13341,25,625;QS=2.98623,0.0137694,0;SGB=-0.556633;RPBZ=-0.894788;MQBZ=0.182574;MQSBZ=-1.85164;BQBZ=-1.6854;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,21,194,21,194,194:7:0 0,18,189,18,189,189:6:0 17 536 . C <*> 0 . DP=31;I16=24,7,0,0,1095,40551,0,0,1837,109369,0,0,631,13809,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,184:7:0 0,18,157:6:0 17 537 . C <*> 0 . DP=31;I16=24,7,0,0,1049,38677,0,0,1837,109369,0,0,626,13682,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,172:7:0 0,18,183:6:0 17 538 . A <*> 0 . DP=31;I16=24,7,0,0,1138,42478,0,0,1837,109369,0,0,620,13536,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,189:7:0 0,18,181:6:0 @@ -471,8 +470,8 @@ 17 545 . A <*> 0 . DP=33;I16=25,8,0,0,1197,44795,0,0,1926,113810,0,0,587,12951,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,24,196:8:0 0,18,184:6:0 17 546 . A <*> 0 . DP=32;I16=24,8,0,0,1136,41758,0,0,1866,110210,0,0,580,12802,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,21,166:7:0 0,18,193:6:0 17 547 . A <*> 0 . DP=32;I16=24,8,0,0,1159,43539,0,0,1866,110210,0,0,572,12634,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,21,180:7:0 0,18,195:6:0 -17 548 . A C,<*> 0 . DP=33;I16=23,9,1,0,1153,42673,9,81,1866,110210,60,3600,561,12489,3,9;QS=2.98607,0.0139319,0;SGB=-0.556633;RPBZ=1.57584;MQBZ=0.253876;MQSBZ=-2.34521;BQBZ=-1.68939;NMBZ=2.40838;SCBZ=3.80814;FS=0;MQ0F=0 PL:DP:DV 0,44,255,54,255,255:19:1 0,21,181,21,181,181:7:0 0,21,211,21,211,211:7:0 -17 549 . T G,<*> 0 . DP=32;I16=23,8,0,1,1135,42143,20,400,1806,106610,60,3600,532,11720,25,625;QS=2.96918,0.0308166,0;SGB=-0.556633;RPBZ=-0.487556;MQBZ=0.258065;MQSBZ=-2.29695;BQBZ=-1.68602;NMBZ=2.45062;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV 0,34,255,51,255,255:18:1 0,21,168,21,168,168:7:0 0,21,208,21,208,208:7:0 +17 548 . A C,<*> 0 . DP=33;I16=23,9,1,0,1153,42673,9,81,1866,110210,60,3600,561,12489,3,9;QS=2.98607,0.0139319,0;SGB=-0.556633;RPBZ=1.57584;MQBZ=0.253876;MQSBZ=-2.34521;BQBZ=-1.68939;SCBZ=3.80814;FS=0;MQ0F=0 PL:DP:DV 0,44,255,54,255,255:19:1 0,21,181,21,181,181:7:0 0,21,211,21,211,211:7:0 +17 549 . T G,<*> 0 . DP=32;I16=23,8,0,1,1135,42143,20,400,1806,106610,60,3600,532,11720,25,625;QS=2.96918,0.0308166,0;SGB=-0.556633;RPBZ=-0.487556;MQBZ=0.258065;MQSBZ=-2.29695;BQBZ=-1.68602;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV 0,34,255,51,255,255:18:1 0,21,168,21,168,168:7:0 0,21,208,21,208,208:7:0 17 550 . T <*> 0 . DP=32;I16=23,9,0,0,1056,37314,0,0,1866,110210,0,0,549,12177,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,150:7:0 0,21,220:7:0 17 551 . G <*> 0 . DP=31;I16=22,9,0,0,1121,41639,0,0,1806,106610,0,0,541,12045,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,21,172:7:0 0,21,208:7:0 17 552 . C <*> 0 . DP=30;I16=21,9,0,0,1093,41365,0,0,1746,103010,0,0,535,11947,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,21,167:7:0 0,21,208:7:0 @@ -482,14 +481,14 @@ 17 556 . C <*> 0 . DP=29;I16=20,9,0,0,1055,39195,0,0,1709,101641,0,0,509,11219,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,18,158:6:0 0,18,186:6:0 17 557 . A <*> 0 . DP=27;I16=18,9,0,0,987,36749,0,0,1589,94441,0,0,506,11074,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,45,255:15:0 0,18,157:6:0 0,18,186:6:0 17 558 . A <*> 0 . DP=27;I16=18,9,0,0,956,35872,0,0,1589,94441,0,0,502,10906,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,45,255:15:0 0,18,153:6:0 0,18,177:6:0 -17 559 . C A,<*> 0 . DP=27;I16=18,8,0,1,915,33775,14,196,1560,93600,29,841,473,10141,25,625;QS=2.92708,0.0729167,0;SGB=-0.556633;RPBZ=-1.02726;MQBZ=-5.09902;MQSBZ=-1.41421;BQBZ=-1.54776;NMBZ=3.05941;SCBZ=5.09902;FS=0;MQ0F=0 PL:DP:DV 0,45,255,45,255,255:15:0 0,4,116,15,119,123:6:1 0,18,169,18,169,169:6:0 +17 559 . C A,<*> 0 . DP=27;I16=18,8,0,1,915,33775,14,196,1560,93600,29,841,473,10141,25,625;QS=2.92708,0.0729167,0;SGB=-0.556633;RPBZ=-1.02726;MQBZ=-5.09902;MQSBZ=-1.41421;BQBZ=-1.54776;SCBZ=5.09902;FS=0;MQ0F=0 PL:DP:DV 0,45,255,45,255,255:15:0 0,4,116,15,119,123:6:1 0,18,169,18,169,169:6:0 17 560 . C <*> 0 . DP=28;I16=19,9,0,0,992,36552,0,0,1649,98041,0,0,494,10654,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,45,255:15:0 0,18,160:6:0 0,21,181:7:0 17 561 . A <*> 0 . DP=28;I16=19,9,0,0,973,35555,0,0,1649,98041,0,0,491,10571,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,45,255:15:0 0,18,158:6:0 0,21,194:7:0 17 562 . C <*> 0 . DP=28;I16=19,9,0,0,1014,38392,0,0,1649,98041,0,0,488,10518,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,45,255:15:0 0,18,153:6:0 0,21,187:7:0 17 563 . A <*> 0 . DP=27;I16=18,9,0,0,903,32513,0,0,1589,94441,0,0,485,10445,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,45,255:15:0 0,15,149:5:0 0,21,179:7:0 17 564 . C <*> 0 . DP=27;I16=18,9,0,0,859,28747,0,0,1589,94441,0,0,482,10402,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,45,255:15:0 0,15,121:5:0 0,21,182:7:0 17 565 . G <*> 0 . DP=30;I16=18,12,0,0,842,27104,0,0,1769,105241,0,0,479,10389,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,18,100:6:0 0,21,154:7:0 -17 566 . C A,<*> 0 . DP=29;I16=16,12,1,0,920,33998,9,81,1649,98041,60,3600,454,9734,25,625;QS=2.98321,0.016791,0;SGB=-0.556633;RPBZ=0.239193;MQBZ=0.188982;MQSBZ=-1.19024;BQBZ=-1.43942;NMBZ=-0.339233;SCBZ=-0.188982;FS=0;MQ0F=0 PL:DP:DV 0,38,255,48,255,255:17:1 0,15,155,15,155,155:5:0 0,21,170,21,170,170:7:0 +17 566 . C A,<*> 0 . DP=29;I16=16,12,1,0,920,33998,9,81,1649,98041,60,3600,454,9734,25,625;QS=2.98321,0.016791,0;SGB=-0.556633;RPBZ=0.239193;MQBZ=0.188982;MQSBZ=-1.19024;BQBZ=-1.43942;SCBZ=-0.188982;FS=0;MQ0F=0 PL:DP:DV 0,38,255,48,255,255:17:1 0,15,155,15,155,155:5:0 0,21,170,21,170,170:7:0 17 567 . C <*> 0 . DP=30;I16=17,13,0,0,956,34312,0,0,1769,105241,0,0,496,10638,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,18,156:6:0 0,21,194:7:0 17 568 . C <*> 0 . DP=29;I16=16,13,0,0,1060,40304,0,0,1709,101641,0,0,497,10663,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,18,179:6:0 0,21,193:7:0 17 569 . T <*> 0 . DP=30;I16=16,13,0,0,1061,41321,0,0,1709,101641,0,0,497,10671,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,18,190:6:0 0,21,213:7:0 @@ -497,15 +496,15 @@ 17 571 . C <*> 0 . DP=31;I16=17,13,0,0,1069,40739,0,0,1769,105241,0,0,497,10783,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,18,159:6:0 0,21,193:7:0 17 572 . A <*> 0 . DP=31;I16=18,12,0,0,1092,41268,0,0,1769,105241,0,0,499,10887,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,21,204:7:0 0,18,175:6:0 17 573 . A <*> 0 . DP=31;I16=18,12,0,0,1060,38698,0,0,1769,105241,0,0,501,10975,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,21,201:7:0 0,18,178:6:0 -17 574 . C A,<*> 0 . DP=31;I16=18,11,0,1,1088,41328,15,225,1740,104400,29,841,478,10422,25,625;QS=2.94071,0.0592885,0;SGB=-0.556633;RPBZ=-0.173514;MQBZ=-5.38516;MQSBZ=-1.22474;BQBZ=-1.68578;NMBZ=2.63996;SCBZ=3.60588;FS=0;MQ0F=0 PL:DP:DV 0,48,255,48,255,255:16:0 0,9,170,21,173,177:8:1 0,18,173,18,173,173:6:0 -17 575 . T C,<*> 0 . DP=30;I16=17,11,0,1,1048,41548,9,81,1680,100800,29,841,480,10426,25,625;QS=2.96786,0.0321429,0;SGB=-0.556633;RPBZ=-0.119685;MQBZ=-5.2915;MQSBZ=-1.19024;BQBZ=-1.68121;NMBZ=2.59197;SCBZ=3.53589;FS=0;MQ0F=0 PL:DP:DV 0,48,255,48,255,255:16:0 0,13,200,21,203,202:8:1 0,15,163,15,163,163:5:0 +17 574 . C A,<*> 0 . DP=31;I16=18,11,0,1,1088,41328,15,225,1740,104400,29,841,478,10422,25,625;QS=2.94071,0.0592885,0;SGB=-0.556633;RPBZ=-0.173514;MQBZ=-5.38516;MQSBZ=-1.22474;BQBZ=-1.68578;SCBZ=3.60588;FS=0;MQ0F=0 PL:DP:DV 0,48,255,48,255,255:16:0 0,9,170,21,173,177:8:1 0,18,173,18,173,173:6:0 +17 575 . T C,<*> 0 . DP=30;I16=17,11,0,1,1048,41548,9,81,1680,100800,29,841,480,10426,25,625;QS=2.96786,0.0321429,0;SGB=-0.556633;RPBZ=-0.119685;MQBZ=-5.2915;MQSBZ=-1.19024;BQBZ=-1.68121;SCBZ=3.53589;FS=0;MQ0F=0 PL:DP:DV 0,48,255,48,255,255:16:0 0,13,200,21,203,202:8:1 0,15,163,15,163,163:5:0 17 576 . G <*> 0 . DP=30;I16=17,12,0,0,1043,39581,0,0,1709,101641,0,0,507,11087,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,24,208:8:0 0,15,151:5:0 17 577 . G <*> 0 . DP=30;I16=17,12,0,0,997,37255,0,0,1709,101641,0,0,509,11155,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,24,204:8:0 0,15,146:5:0 17 578 . G <*> 0 . DP=29;I16=16,13,0,0,975,34803,0,0,1709,101641,0,0,520,11286,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,24,198:8:0 0,15,151:5:0 17 579 . G <*> 0 . DP=30;I16=16,14,0,0,1038,38820,0,0,1769,105241,0,0,523,11335,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,24,224:8:0 0,15,144:5:0 -17 580 . A C,<*> 0 . DP=30;I16=15,14,1,0,1060,39178,16,256,1709,101641,60,3600,510,11078,17,289;QS=2.97338,0.0266223,0;SGB=-0.556633;RPBZ=1.32953;MQBZ=0.185695;MQSBZ=-1.06904;BQBZ=-1.69093;NMBZ=1.86885;SCBZ=-0.267102;FS=0;MQ0F=0 PL:DP:DV 0,34,255,48,255,255:17:1 0,24,221,24,221,221:8:0 0,15,155,15,155,155:5:0 +17 580 . A C,<*> 0 . DP=30;I16=15,14,1,0,1060,39178,16,256,1709,101641,60,3600,510,11078,17,289;QS=2.97338,0.0266223,0;SGB=-0.556633;RPBZ=1.32953;MQBZ=0.185695;MQSBZ=-1.06904;BQBZ=-1.69093;SCBZ=-0.267102;FS=0;MQ0F=0 PL:DP:DV 0,34,255,48,255,255:17:1 0,24,221,24,221,221:8:0 0,15,155,15,155,155:5:0 17 581 . A <*> 0 . DP=31;I16=16,15,0,0,1083,39215,0,0,1829,108841,0,0,530,11384,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,24,223:8:0 0,15,153:5:0 -17 582 . C G,<*> 0 . DP=31;I16=15,15,1,0,1080,39870,8,64,1769,105241,60,3600,519,11211,15,225;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.34259;MQBZ=0.182574;MQSBZ=-1.0328;BQBZ=-1.68266;NMBZ=1.92049;SCBZ=-0.262467;FS=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,24,207,24,207,207:8:0 0,15,151,15,151,151:5:0 +17 582 . C G,<*> 0 . DP=31;I16=15,15,1,0,1080,39870,8,64,1769,105241,60,3600,519,11211,15,225;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.34259;MQBZ=0.182574;MQSBZ=-1.0328;BQBZ=-1.68266;SCBZ=-0.262467;FS=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,24,207,24,207,207:8:0 0,15,151,15,151,151:5:0 17 583 . T <*> 0 . DP=30;I16=16,14,0,0,1135,43913,0,0,1769,105241,0,0,539,11523,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,24,238:8:0 0,15,163:5:0 17 584 . C <*> 0 . DP=31;I16=17,14,0,0,1069,39521,0,0,1798,106082,0,0,544,11644,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,24,209:8:0 0,15,157:5:0 17 585 . A <*> 0 . DP=31;I16=17,14,0,0,1096,39866,0,0,1798,106082,0,0,549,11751,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,24,211:8:0 0,15,157:5:0 @@ -516,10 +515,10 @@ 17 590 . C <*> 0 . DP=32;I16=17,15,0,0,1103,41355,0,0,1858,109682,0,0,574,12576,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,24,194:8:0 0,18,175:6:0 17 591 . A <*> 0 . DP=31;I16=16,15,0,0,1164,44088,0,0,1798,106082,0,0,579,12695,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,209:7:0 0,18,188:6:0 17 592 . A <*> 0 . DP=31;I16=16,15,0,0,1121,42193,0,0,1798,106082,0,0,583,12795,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,215:7:0 0,18,182:6:0 -17 593 . C A,<*> 0 . DP=31;I16=16,14,0,1,1071,39925,7,49,1769,105241,29,841,561,12253,25,625;QS=2.97021,0.0297872,0;SGB=-0.556633;RPBZ=0.559355;MQBZ=-3.80789;MQSBZ=-0.0464238;BQBZ=-1.57464;NMBZ=2.13779;SCBZ=3.67454;FS=0;MQ0F=0 PL:DP:DV 0,54,255,54,255,255:18:0 0,12,184,18,187,185:7:1 0,18,174,18,174,174:6:0 -17 594 . A G,<*> 0 . DP=33;I16=16,16,1,0,1161,42757,4,16,1858,109682,60,3600,572,12672,15,225;QS=2.99359,0.00641026,0;SGB=-0.556633;RPBZ=-0.998367;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68954;NMBZ=1.76408;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:DV 0,42,255,51,255,255:18:1 0,21,205,21,205,205:7:0 0,24,213,24,213,213:8:0 +17 593 . C A,<*> 0 . DP=31;I16=16,14,0,1,1071,39925,7,49,1769,105241,29,841,561,12253,25,625;QS=2.97021,0.0297872,0;SGB=-0.556633;RPBZ=0.559355;MQBZ=-3.80789;MQSBZ=-0.0464238;BQBZ=-1.57464;SCBZ=3.67454;FS=0;MQ0F=0 PL:DP:DV 0,54,255,54,255,255:18:0 0,12,184,18,187,185:7:1 0,18,174,18,174,174:6:0 +17 594 . A G,<*> 0 . DP=33;I16=16,16,1,0,1161,42757,4,16,1858,109682,60,3600,572,12672,15,225;QS=2.99359,0.00641026,0;SGB=-0.556633;RPBZ=-0.998367;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68954;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:DV 0,42,255,51,255,255:18:1 0,21,205,21,205,205:7:0 0,24,213,24,213,213:8:0 17 595 . A <*> 0 . DP=33;I16=17,16,0,0,1136,40412,0,0,1918,113282,0,0,589,12905,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,198:7:0 0,24,218:8:0 -17 596 . A G,<*> 0 . DP=33;I16=16,16,1,0,1061,37187,8,64,1858,109682,60,3600,590,12952,1,1;QS=2.98564,0.0143627,0;SGB=-0.556633;RPBZ=1.68146;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68357;NMBZ=1.61602;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,21,169,21,169,169:7:0 0,24,231,24,231,231:8:0 +17 596 . A G,<*> 0 . DP=33;I16=16,16,1,0,1061,37187,8,64,1858,109682,60,3600,590,12952,1,1;QS=2.98564,0.0143627,0;SGB=-0.556633;RPBZ=1.68146;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68357;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,21,169,21,169,169:7:0 0,24,231,24,231,231:8:0 17 597 . C <*> 0 . DP=33;I16=17,16,0,0,1196,44890,0,0,1918,113282,0,0,592,12990,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,204:7:0 0,24,220:8:0 17 598 . T <*> 0 . DP=33;I16=16,17,0,0,1219,47333,0,0,1918,113282,0,0,597,13029,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,21,217:7:0 0,27,242:9:0 17 599 . T <*> 0 . DP=33;I16=16,17,0,0,1182,43598,0,0,1918,113282,0,0,599,13095,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,21,197:7:0 0,27,247:9:0 diff --git a/test/mpileup/mpileup.3.out b/test/mpileup/mpileup.3.out index a3c30a6f4..89c6c0607 100644 --- a/test/mpileup/mpileup.3.out +++ b/test/mpileup/mpileup.3.out @@ -11,7 +11,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= diff --git a/test/mpileup/mpileup.4.out b/test/mpileup/mpileup.4.out index 8e0c16766..061f8975f 100644 --- a/test/mpileup/mpileup.4.out +++ b/test/mpileup/mpileup.4.out @@ -11,7 +11,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -29,29 +28,29 @@ 17 100 . C <*> 0 . DP=18;DPR=17,0;I16=16,1,0,0,672,27586,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,189:9:0:0:9,0,0,0:9,0 0,9,118:3:0:0:2,1,0,0:3,0 0,15,134:5:0:0:5,0,0,0:5,0 17 101 . C <*> 0 . DP=18;DPR=17,0;I16=16,1,0,0,630,24730,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,182:9:0:0:9,0,0,0:9,0 0,9,108:3:0:0:2,1,0,0:3,0 0,15,132:5:0:0:5,0,0,0:5,0 17 102 . C <*> 0 . DP=18;DPR=17,0;I16=16,1,0,0,676,27812,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,188:9:0:0:9,0,0,0:9,0 0,9,121:3:0:0:2,1,0,0:3,0 0,15,139:5:0:0:5,0,0,0:5,0 -17 103 . T C,<*> 0 . DP=18;DPR=16,1,0;I16=15,1,1,0,668,28542,6,36,929,54841,29,841,323,7035,6,36;QS=2.98256,0.0174419,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64924;NMBZ=2.45514;SCBZ=4;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,17,184,24,187,185:9:1:0:8,0,1,0:8,1,0 0,9,118,9,118,118:3:0:0:2,1,0,0:3,0,0 0,15,147,15,147,147:5:0:0:5,0,0,0:5,0,0 -17 104 . G C,<*> 0 . DP=18;DPR=16,1,0;I16=15,1,1,0,601,24163,3,9,929,54841,29,841,320,6884,7,49;QS=2.98726,0.0127389,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64309;NMBZ=2.45514;SCBZ=4;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,173,24,176,173:9:1:0:8,0,1,0:8,1,0 0,9,101,9,101,101:3:0:0:2,1,0,0:3,0,0 0,15,133,15,133,133:5:0:0:5,0,0,0:5,0,0 +17 103 . T C,<*> 0 . DP=18;DPR=16,1,0;I16=15,1,1,0,668,28542,6,36,929,54841,29,841,323,7035,6,36;QS=2.98256,0.0174419,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64924;SCBZ=4;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,17,184,24,187,185:9:1:0:8,0,1,0:8,1,0 0,9,118,9,118,118:3:0:0:2,1,0,0:3,0,0 0,15,147,15,147,147:5:0:0:5,0,0,0:5,0,0 +17 104 . G C,<*> 0 . DP=18;DPR=16,1,0;I16=15,1,1,0,601,24163,3,9,929,54841,29,841,320,6884,7,49;QS=2.98726,0.0127389,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64309;SCBZ=4;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,173,24,176,173:9:1:0:8,0,1,0:8,1,0 0,9,101,9,101,101:3:0:0:2,1,0,0:3,0,0 0,15,133,15,133,133:5:0:0:5,0,0,0:5,0,0 17 105 . G <*> 0 . DP=19;DPR=18,0;I16=17,1,0,0,603,22351,0,0,1018,59282,0,0,325,6815,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,171:10:0:0:10,0,0,0:10,0 0,9,106:3:0:0:2,1,0,0:3,0 0,15,125:5:0:0:5,0,0,0:5,0 17 106 . G <*> 0 . DP=19;DPR=18,0;I16=17,1,0,0,636,25058,0,0,1018,59282,0,0,324,6718,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,190:10:0:0:10,0,0,0:10,0 0,9,92:3:0:0:2,1,0,0:3,0 0,15,124:5:0:0:5,0,0,0:5,0 17 107 . C <*> 0 . DP=19;DPR=18,0;I16=17,1,0,0,686,27952,0,0,1018,59282,0,0,323,6643,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,192:10:0:0:10,0,0,0:10,0 0,9,119:3:0:0:2,1,0,0:3,0 0,15,136:5:0:0:5,0,0,0:5,0 17 108 . C <*> 0 . DP=19;DPR=18,0;I16=17,1,0,0,681,27429,0,0,1018,59282,0,0,322,6590,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,190:10:0:0:10,0,0,0:10,0 0,9,119:3:0:0:2,1,0,0:3,0 0,15,135:5:0:0:5,0,0,0:5,0 -17 109 . T C,<*> 0 . DP=19;DPR=17,1,0;I16=16,1,1,0,716,30648,2,4,989,58441,29,841,309,6415,12,144;QS=2.98922,0.0107817,0;SGB=-0.556633;RPBZ=-0.674966;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.6661;NMBZ=2.52179;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,20,191,27,194,191:10:1:0:9,0,1,0:9,1,0 0,9,120,9,120,120:3:0:0:2,1,0,0:3,0,0 0,15,150,15,150,150:5:0:0:5,0,0,0:5,0,0 +17 109 . T C,<*> 0 . DP=19;DPR=17,1,0;I16=16,1,1,0,716,30648,2,4,989,58441,29,841,309,6415,12,144;QS=2.98922,0.0107817,0;SGB=-0.556633;RPBZ=-0.674966;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.6661;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,20,191,27,194,191:10:1:0:9,0,1,0:9,1,0 0,9,120,9,120,120:3:0:0:2,1,0,0:3,0,0 0,15,150,15,150,150:5:0:0:5,0,0,0:5,0,0 17 110 . G <*> 0 . DP=19;DPR=18,0;I16=17,1,0,0,688,28036,0,0,1018,59282,0,0,320,6550,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,194:10:0:0:10,0,0,0:10,0 0,9,113:3:0:0:2,1,0,0:3,0 0,15,136:5:0:0:5,0,0,0:5,0 17 111 . G <*> 0 . DP=19;DPR=18,0;I16=17,1,0,0,573,21453,0,0,1018,59282,0,0,318,6514,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,167:10:0:0:10,0,0,0:10,0 0,9,95:3:0:0:2,1,0,0:3,0 0,15,119:5:0:0:5,0,0,0:5,0 -17 112 . C G,<*> 0 . DP=19;DPR=17,1,0;I16=16,1,1,0,657,26565,2,4,989,58441,29,841,301,6277,15,225;QS=2.98907,0.010929,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65292;NMBZ=2.52179;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,20,187,27,190,187:10:1:0:9,0,1,0:9,1,0 0,9,103,9,103,103:3:0:0:2,1,0,0:3,0,0 0,15,135,15,135,135:5:0:0:5,0,0,0:5,0,0 -17 113 . A G,<*> 0 . DP=19;DPR=17,1,0;I16=16,1,1,0,635,25055,4,16,989,58441,29,841,297,6207,16,256;QS=2.98817,0.0118343,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65205;NMBZ=2.52179;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,20,172,27,175,172:10:1:0:9,0,1,0:9,1,0 0,9,102,9,102,102:3:0:0:2,1,0,0:3,0,0 0,15,139,15,139,139:5:0:0:5,0,0,0:5,0,0 +17 112 . C G,<*> 0 . DP=19;DPR=17,1,0;I16=16,1,1,0,657,26565,2,4,989,58441,29,841,301,6277,15,225;QS=2.98907,0.010929,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65292;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,20,187,27,190,187:10:1:0:9,0,1,0:9,1,0 0,9,103,9,103,103:3:0:0:2,1,0,0:3,0,0 0,15,135,15,135,135:5:0:0:5,0,0,0:5,0,0 +17 113 . A G,<*> 0 . DP=19;DPR=17,1,0;I16=16,1,1,0,635,25055,4,16,989,58441,29,841,297,6207,16,256;QS=2.98817,0.0118343,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65205;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,20,172,27,175,172:10:1:0:9,0,1,0:9,1,0 0,9,102,9,102,102:3:0:0:2,1,0,0:3,0,0 0,15,139,15,139,139:5:0:0:5,0,0,0:5,0,0 17 114 . C <*> 0 . DP=19;DPR=18,0;I16=17,1,0,0,660,25876,0,0,1018,59282,0,0,310,6446,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,181:10:0:0:10,0,0,0:10,0 0,9,113:3:0:0:2,1,0,0:3,0 0,15,133:5:0:0:5,0,0,0:5,0 -17 115 . C A,<*> 0 . DP=21;DPR=19,1,0;I16=17,2,1,0,688,27426,12,144,1078,62882,29,841,283,5827,25,625;QS=2.88785,0.11215,0;SGB=-0.556633;RPBZ=0.260329;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.47798;NMBZ=2.3712;SCBZ=-0.418446;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,189,30,189,189:10:0:0:10,0,0,0:10,0,0 3,0,86,9,89,93:3:1:0:1,1,1,0:2,1,0 0,21,153,21,153,153:7:0:0:6,1,0,0:7,0,0 -17 116 . A C,<*> 0 . DP=21;DPR=19,1,0;I16=17,2,1,0,705,27791,2,4,1078,62882,29,841,287,6073,19,361;QS=2.98873,0.0112676,0;SGB=-0.556633;RPBZ=0.0867763;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.65814;NMBZ=2.65016;SCBZ=2.65016;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,20,179,27,182,179:10:1:0:9,0,1,0:9,1,0 0,9,102,9,102,102:3:0:0:2,1,0,0:3,0,0 0,21,175,21,175,175:7:0:0:6,1,0,0:7,0,0 +17 115 . C A,<*> 0 . DP=21;DPR=19,1,0;I16=17,2,1,0,688,27426,12,144,1078,62882,29,841,283,5827,25,625;QS=2.88785,0.11215,0;SGB=-0.556633;RPBZ=0.260329;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.47798;SCBZ=-0.418446;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,189,30,189,189:10:0:0:10,0,0,0:10,0,0 3,0,86,9,89,93:3:1:0:1,1,1,0:2,1,0 0,21,153,21,153,153:7:0:0:6,1,0,0:7,0,0 +17 116 . A C,<*> 0 . DP=21;DPR=19,1,0;I16=17,2,1,0,705,27791,2,4,1078,62882,29,841,287,6073,19,361;QS=2.98873,0.0112676,0;SGB=-0.556633;RPBZ=0.0867763;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.65814;SCBZ=2.65016;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,20,179,27,182,179:10:1:0:9,0,1,0:9,1,0 0,9,102,9,102,102:3:0:0:2,1,0,0:3,0,0 0,21,175,21,175,175:7:0:0:6,1,0,0:7,0,0 17 117 . G <*> 0 . DP=21;DPR=20,0;I16=18,2,0,0,715,28045,0,0,1107,63723,0,0,304,6444,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,185:10:0:0:10,0,0,0:10,0 0,9,97:3:0:0:2,1,0,0:3,0 0,21,177:7:0:0:6,1,0,0:7,0 17 118 . G <*> 0 . DP=20;DPR=19,0;I16=17,2,0,0,620,23470,0,0,1047,60123,0,0,303,6481,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,175:9:0:0:9,0,0,0:9,0 0,9,65:3:0:0:2,1,0,0:3,0 0,21,162:7:0:0:6,1,0,0:7,0 17 119 . G <*> 0 . DP=19;DPR=18,0;I16=16,2,0,0,619,23459,0,0,987,56523,0,0,301,6493,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,176:9:0:0:9,0,0,0:9,0 0,6,76:2:0:0:1,1,0,0:2,0 0,21,160:7:0:0:6,1,0,0:7,0 -17 120 . A G,<*> 0 . DP=19;DPR=17,1,0;I16=15,2,1,0,646,25392,4,16,958,55682,29,841,277,5999,23,529;QS=2.9873,0.0126984,0;SGB=-0.556633;RPBZ=0.28942;MQBZ=-2.23607;MQSBZ=-1.30384;BQBZ=-1.6486;NMBZ=3;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,171,24,174,171:9:1:0:8,0,1,0:8,1,0 0,6,88,6,88,88:2:0:0:1,1,0,0:2,0,0 0,21,171,21,171,171:7:0:0:6,1,0,0:7,0,0 +17 120 . A G,<*> 0 . DP=19;DPR=17,1,0;I16=15,2,1,0,646,25392,4,16,958,55682,29,841,277,5999,23,529;QS=2.9873,0.0126984,0;SGB=-0.556633;RPBZ=0.28942;MQBZ=-2.23607;MQSBZ=-1.30384;BQBZ=-1.6486;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,171,24,174,171:9:1:0:8,0,1,0:8,1,0 0,6,88,6,88,88:2:0:0:1,1,0,0:2,0,0 0,21,171,21,171,171:7:0:0:6,1,0,0:7,0,0 17 121 . G <*> 0 . DP=19;DPR=18,0;I16=16,2,0,0,650,25148,0,0,987,56523,0,0,298,6534,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,181:9:0:0:9,0,0,0:9,0 0,6,84:2:0:0:1,1,0,0:2,0 0,21,168:7:0:0:6,1,0,0:7,0 17 122 . C <*> 0 . DP=20;DPR=19,0;I16=17,2,0,0,696,27784,0,0,1047,60123,0,0,296,6560,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,180:9:0:0:9,0,0,0:9,0 0,9,107:3:0:0:2,1,0,0:3,0 0,21,178:7:0:0:6,1,0,0:7,0 17 123 . T <*> 0 . DP=18;DPR=17,0;I16=15,2,0,0,647,26145,0,0,927,52923,0,0,296,6554,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,24,170:8:0:0:8,0,0,0:8,0 0,9,123:3:0:0:2,1,0,0:3,0 0,18,166:6:0:0:5,1,0,0:6,0 17 124 . T <*> 0 . DP=19;DPR=18,0;I16=16,2,0,0,606,22002,0,0,987,56523,0,0,296,6564,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,154:9:0:0:9,0,0,0:9,0 0,9,114:3:0:0:2,1,0,0:3,0 0,18,154:6:0:0:5,1,0,0:6,0 -17 125 . A T,<*> 0 . DP=18;DPR=16,1,0;I16=14,2,1,0,589,22565,4,16,898,52082,29,841,272,5916,25,625;QS=2.98444,0.0155642,0;SGB=-0.556633;RPBZ=1.02125;MQBZ=-2.16025;MQSBZ=-1.23956;BQBZ=-1.64106;NMBZ=2.91548;SCBZ=2.91548;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,15,149,21,152,149:8:1:0:7,0,1,0:7,1,0 0,9,114,9,114,114:3:0:0:2,1,0,0:3,0,0 0,18,162,18,162,162:6:0:0:5,1,0,0:6,0,0 +17 125 . A T,<*> 0 . DP=18;DPR=16,1,0;I16=14,2,1,0,589,22565,4,16,898,52082,29,841,272,5916,25,625;QS=2.98444,0.0155642,0;SGB=-0.556633;RPBZ=1.02125;MQBZ=-2.16025;MQSBZ=-1.23956;BQBZ=-1.64106;SCBZ=2.91548;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,15,149,21,152,149:8:1:0:7,0,1,0:7,1,0 0,9,114,9,114,114:3:0:0:2,1,0,0:3,0,0 0,18,162,18,162,162:6:0:0:5,1,0,0:6,0,0 17 126 . A <*> 0 . DP=18;DPR=17,0;I16=15,2,0,0,629,24725,0,0,927,52923,0,0,298,6536,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,24,162:8:0:0:8,0,0,0:8,0 0,9,117:3:0:0:2,1,0,0:3,0 0,18,174:6:0:0:5,1,0,0:6,0 17 127 . C <*> 0 . DP=18;DPR=17,0;I16=15,2,0,0,627,24331,0,0,927,52923,0,0,299,6549,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,24,163:8:0:0:8,0,0,0:8,0 0,9,119:3:0:0:2,1,0,0:3,0 0,18,160:6:0:0:5,1,0,0:6,0 17 128 . A <*> 0 . DP=18;DPR=17,0;I16=15,2,0,0,660,26364,0,0,927,52923,0,0,300,6580,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,24,169:8:0:0:8,0,0,0:8,0 0,9,121:3:0:0:2,1,0,0:3,0 0,18,168:6:0:0:5,1,0,0:6,0 @@ -85,7 +84,7 @@ 17 156 . C <*> 0 . DP=14;DPR=14,0;I16=12,2,0,0,536,20884,0,0,809,47641,0,0,266,5934,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,163:7:0:0:7,0,0,0:7,0 0,6,84:2:0:0:1,1,0,0:2,0 0,15,150:5:0:0:4,1,0,0:5,0 17 157 . C <*> 0 . DP=14;DPR=14,0;I16=12,2,0,0,555,22081,0,0,809,47641,0,0,264,5904,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,169:7:0:0:7,0,0,0:7,0 0,6,85:2:0:0:1,1,0,0:2,0 0,15,149:5:0:0:4,1,0,0:5,0 17 158 . T <*> 0 . DP=14;DPR=14,0;I16=12,2,0,0,568,23154,0,0,809,47641,0,0,262,5886,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,170:7:0:0:7,0,0,0:7,0 0,6,84:2:0:0:1,1,0,0:2,0 0,15,159:5:0:0:4,1,0,0:5,0 -17 159 . A G,<*> 0 . DP=15;DPR=14,1,0;I16=12,2,1,0,519,19467,5,25,809,47641,60,3600,260,5880,0,0;QS=2.97076,0.0292398,0;SGB=-0.556633;RPBZ=-1.62019;MQBZ=0.267261;MQSBZ=-2.54951;BQBZ=-1.63041;NMBZ=0;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,157,21,157,157:7:0:0:7,0,0,0:7,0,0 0,6,83,6,83,83:2:0:0:1,1,0,0:2,0,0 0,10,129,15,132,129:6:1:0:4,1,1,0:5,1,0 +17 159 . A G,<*> 0 . DP=15;DPR=14,1,0;I16=12,2,1,0,519,19467,5,25,809,47641,60,3600,260,5880,0,0;QS=2.97076,0.0292398,0;SGB=-0.556633;RPBZ=-1.62019;MQBZ=0.267261;MQSBZ=-2.54951;BQBZ=-1.63041;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,157,21,157,157:7:0:0:7,0,0,0:7,0,0 0,6,83,6,83,83:2:0:0:1,1,0,0:2,0,0 0,10,129,15,132,129:6:1:0:4,1,1,0:5,1,0 17 160 . G <*> 0 . DP=15;DPR=15,0;I16=13,2,0,0,547,20633,0,0,869,51241,0,0,259,5887,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,165:7:0:0:7,0,0,0:7,0 0,6,85:2:0:0:1,1,0,0:2,0 0,18,139:6:0:0:5,1,0,0:6,0 17 161 . A <*> 0 . DP=15;DPR=15,0;I16=13,2,0,0,568,21610,0,0,869,51241,0,0,258,5908,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,157:7:0:0:7,0,0,0:7,0 0,6,83:2:0:0:1,1,0,0:2,0 0,18,162:6:0:0:5,1,0,0:6,0 17 162 . A <*> 0 . DP=15;DPR=15,0;I16=13,2,0,0,558,21206,0,0,869,51241,0,0,255,5843,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,147:7:0:0:7,0,0,0:7,0 0,6,87:2:0:0:1,1,0,0:2,0 0,18,167:6:0:0:5,1,0,0:6,0 @@ -116,7 +115,7 @@ 17 187 . C <*> 0 . DP=14;DPR=14,0;I16=13,1,0,0,511,18979,0,0,809,47641,0,0,266,5952,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,147:6:0:0:6,0,0,0:6,0 0,3,38:1:0:0:1,0,0,0:1,0 0,21,172:7:0:0:6,1,0,0:7,0 17 188 . C <*> 0 . DP=14;DPR=14,0;I16=13,1,0,0,496,18042,0,0,809,47641,0,0,267,5989,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,147:6:0:0:6,0,0,0:6,0 0,3,37:1:0:0:1,0,0,0:1,0 0,21,162:7:0:0:6,1,0,0:7,0 17 189 . C <*> 0 . DP=15;DPR=15,0;I16=13,2,0,0,552,20504,0,0,838,48482,0,0,268,6040,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,152:6:0:0:6,0,0,0:6,0 0,6,67:2:0:0:1,1,0,0:2,0 0,21,167:7:0:0:6,1,0,0:7,0 -17 190 . A C,<*> 0 . DP=15;DPR=14,1,0;I16=12,2,1,0,500,18230,5,25,778,44882,60,3600,243,5381,25,625;QS=2.97664,0.0233645,0;SGB=-0.556633;RPBZ=0;MQBZ=0.392232;MQSBZ=-3.74166;BQBZ=-1.63041;NMBZ=-0.267261;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,138,18,138,138:6:0:0:6,0,0,0:6,0,0 0,6,68,6,68,68:2:0:0:1,1,0,0:2,0,0 0,12,153,18,156,153:7:1:0:5,1,1,0:6,1,0 +17 190 . A C,<*> 0 . DP=15;DPR=14,1,0;I16=12,2,1,0,500,18230,5,25,778,44882,60,3600,243,5381,25,625;QS=2.97664,0.0233645,0;SGB=-0.556633;RPBZ=0;MQBZ=0.392232;MQSBZ=-3.74166;BQBZ=-1.63041;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,138,18,138,138:6:0:0:6,0,0,0:6,0,0 0,6,68,6,68,68:2:0:0:1,1,0,0:2,0,0 0,12,153,18,156,153:7:1:0:5,1,1,0:6,1,0 17 191 . T <*> 0 . DP=15;DPR=15,0;I16=13,2,0,0,534,19276,0,0,838,48482,0,0,267,5939,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,143:6:0:0:6,0,0,0:6,0 0,6,67:2:0:0:1,1,0,0:2,0 0,21,169:7:0:0:6,1,0,0:7,0 17 192 . G <*> 0 . DP=15;DPR=15,0;I16=13,2,0,0,499,17439,0,0,838,48482,0,0,266,5890,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,143:6:0:0:6,0,0,0:6,0 0,6,67:2:0:0:1,1,0,0:2,0 0,21,151:7:0:0:6,1,0,0:7,0 17 193 . T <*> 0 . DP=15;DPR=15,0;I16=13,2,0,0,505,17811,0,0,838,48482,0,0,265,5859,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,140:6:0:0:6,0,0,0:6,0 0,6,63:2:0:0:1,1,0,0:2,0 0,21,157:7:0:0:6,1,0,0:7,0 @@ -149,10 +148,10 @@ 17 220 . G <*> 0 . DP=14;DPR=14,0;I16=11,3,0,0,495,18407,0,0,747,42123,0,0,267,6079,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,188:7:0:0:6,1,0,0:7,0 0,9,88:3:0:0:1,2,0,0:3,0 0,12,84:4:0:0:4,0,0,0:4,0 17 221 . A <*> 0 . DP=14;DPR=14,0;I16=11,3,0,0,488,17688,0,0,747,42123,0,0,267,6135,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,176:7:0:0:6,1,0,0:7,0 0,9,89:3:0:0:1,2,0,0:3,0 0,12,101:4:0:0:4,0,0,0:4,0 17 222 . A <*> 0 . DP=14;DPR=14,0;I16=11,3,0,0,479,17747,0,0,747,42123,0,0,267,6203,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,186:7:0:0:6,1,0,0:7,0 0,9,89:3:0:0:1,2,0,0:3,0 0,12,73:4:0:0:4,0,0,0:4,0 -17 223 . G T,<*> 0 . DP=13;DPR=12,1,0;I16=9,3,1,0,412,14782,8,64,627,34923,60,3600,243,5657,25,625;QS=2.96596,0.0340426,0;SGB=-0.556633;RPBZ=1.07052;MQBZ=0.547723;MQSBZ=-3.4641;BQBZ=-1.60577;NMBZ=-0.288675;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,11,166,18,169,167:7:1:0:5,1,1,0:6,1,0 0,6,53,6,53,53:2:0:0:0,2,0,0:2,0,0 0,12,81,12,81,81:4:0:0:4,0,0,0:4,0,0 +17 223 . G T,<*> 0 . DP=13;DPR=12,1,0;I16=9,3,1,0,412,14782,8,64,627,34923,60,3600,243,5657,25,625;QS=2.96596,0.0340426,0;SGB=-0.556633;RPBZ=1.07052;MQBZ=0.547723;MQSBZ=-3.4641;BQBZ=-1.60577;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,11,166,18,169,167:7:1:0:5,1,1,0:6,1,0 0,6,53,6,53,53:2:0:0:0,2,0,0:2,0,0 0,12,81,12,81,81:4:0:0:4,0,0,0:4,0,0 17 224 . G <*> 0 . DP=12;DPR=12,0;I16=9,3,0,0,379,12759,0,0,627,34923,0,0,270,6370,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,168:6:0:0:5,1,0,0:6,0 0,6,50:2:0:0:0,2,0,0:2,0 0,12,70:4:0:0:4,0,0,0:4,0 17 225 . C <*> 0 . DP=12;DPR=12,0;I16=9,3,0,0,390,13960,0,0,627,34923,0,0,272,6466,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,165:6:0:0:5,1,0,0:6,0 0,6,48:2:0:0:0,2,0,0:2,0 0,12,86:4:0:0:4,0,0,0:4,0 -17 226 . A G,C,<*> 0 . DP=13;DPR=11,1,1,0;I16=8,3,1,1,381,13669,6,18,567,31323,89,4441,248,5894,44,986;QS=2.94293,0.0392157,0.0178571,0;VDB=0.84;SGB=-2.62246;RPBZ=-0.592157;MQBZ=-0.615457;MQSBZ=-3.4641;BQBZ=-2.17723;NMBZ=2.34521;SCBZ=2.34521;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,159,12,162,159,18,159,162,159:7:1:0:5,1,0,1:6,0,1,0 0,6,53,6,53,53,6,53,53,53:2:0:0:0,2,0,0:2,0,0,0 0,5,79,9,82,80,9,82,80,80:4:1:0:3,0,1,0:3,1,0,0 +17 226 . A G,C,<*> 0 . DP=13;DPR=11,1,1,0;I16=8,3,1,1,381,13669,6,18,567,31323,89,4441,248,5894,44,986;QS=2.94293,0.0392157,0.0178571,0;VDB=0.84;SGB=-2.62246;RPBZ=-0.592157;MQBZ=-0.615457;MQSBZ=-3.4641;BQBZ=-2.17723;SCBZ=2.34521;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,159,12,162,159,18,159,162,159:7:1:0:5,1,0,1:6,0,1,0 0,6,53,6,53,53,6,53,53,53:2:0:0:0,2,0,0:2,0,0,0 0,5,79,9,82,80,9,82,80,80:4:1:0:3,0,1,0:3,1,0,0 17 227 . C <*> 0 . DP=13;DPR=13,0;I16=9,4,0,0,412,14342,0,0,656,35764,0,0,292,6878,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,190:7:0:0:5,2,0,0:7,0 0,6,53:2:0:0:0,2,0,0:2,0 0,12,75:4:0:0:4,0,0,0:4,0 17 228 . C <*> 0 . DP=13;DPR=13,0;I16=9,4,0,0,417,14381,0,0,656,35764,0,0,292,6884,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,187:7:0:0:5,2,0,0:7,0 0,6,45:2:0:0:0,2,0,0:2,0 0,12,96:4:0:0:4,0,0,0:4,0 17 229 . G <*> 0 . DP=13;DPR=13,0;I16=9,4,0,0,368,11524,0,0,656,35764,0,0,292,6898,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,145:7:0:0:5,2,0,0:7,0 0,6,53:2:0:0:0,2,0,0:2,0 0,12,70:4:0:0:4,0,0,0:4,0 @@ -163,7 +162,7 @@ 17 234 . A <*> 0 . DP=14;DPR=14,0;I16=10,4,0,0,502,18390,0,0,716,39364,0,0,292,6988,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,185:7:0:0:5,2,0,0:7,0 0,6,53:2:0:0:0,2,0,0:2,0 0,15,123:5:0:0:5,0,0,0:5,0 17 235 . A <*> 0 . DP=14;DPR=14,0;I16=10,4,0,0,488,17796,0,0,716,39364,0,0,291,6951,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,186:7:0:0:5,2,0,0:7,0 0,6,53:2:0:0:0,2,0,0:2,0 0,15,115:5:0:0:5,0,0,0:5,0 17 236 . G <*> 0 . DP=15;DPR=15,0;I16=11,4,0,0,501,17481,0,0,776,42964,0,0,290,6924,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,24,206:8:0:0:6,2,0,0:8,0 0,6,53:2:0:0:0,2,0,0:2,0 0,15,103:5:0:0:5,0,0,0:5,0 -17 237 . A C,<*> 0 . DP=14;DPR=13,1,0;I16=9,4,1,0,465,16877,8,64,656,35764,60,3600,266,6282,25,625;QS=2.93162,0.0683761,0;SGB=-0.556633;RPBZ=1.11754;MQBZ=0.632456;MQSBZ=-3.60555;BQBZ=-1.61959;NMBZ=-0.27735;SCBZ=-0.27735;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,24,206,24,206,206:8:0:0:6,2,0,0:8,0,0 0,6,53,6,53,53:2:0:0:0,2,0,0:2,0,0 0,3,84,9,87,87:4:1:0:3,0,1,0:3,1,0 +17 237 . A C,<*> 0 . DP=14;DPR=13,1,0;I16=9,4,1,0,465,16877,8,64,656,35764,60,3600,266,6282,25,625;QS=2.93162,0.0683761,0;SGB=-0.556633;RPBZ=1.11754;MQBZ=0.632456;MQSBZ=-3.60555;BQBZ=-1.61959;SCBZ=-0.27735;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,24,206,24,206,206:8:0:0:6,2,0,0:8,0,0 0,6,53,6,53,53:2:0:0:0,2,0,0:2,0,0 0,3,84,9,87,87:4:1:0:3,0,1,0:3,1,0 17 238 . C <*> 0 . DP=14;DPR=14,0;I16=10,4,0,0,482,17238,0,0,716,39364,0,0,292,6900,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,24,211:8:0:0:6,2,0,0:8,0 0,6,53:2:0:0:0,2,0,0:2,0 0,12,82:4:0:0:4,0,0,0:4,0 17 239 . A <*> 0 . DP=15;DPR=15,0;I16=10,5,0,0,525,19155,0,0,776,42964,0,0,292,6852,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,223:9:0:0:6,3,0,0:9,0 0,6,50:2:0:0:0,2,0,0:2,0 0,12,108:4:0:0:4,0,0,0:4,0 17 240 . C <*> 0 . DP=15;DPR=15,0;I16=10,5,0,0,512,17930,0,0,776,42964,0,0,292,6764,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,220:9:0:0:6,3,0,0:9,0 0,6,53:2:0:0:0,2,0,0:2,0 0,12,106:4:0:0:4,0,0,0:4,0 @@ -193,18 +192,18 @@ 17 264 . C <*> 0 . DP=22;DPR=22,0;I16=10,12,0,0,821,31325,0,0,1049,54897,0,0,386,8326,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:7,4,0,0:11,0 0,15,104:5:0:0:0,5,0,0:5,0 0,18,172:6:0:0:3,3,0,0:6,0 17 265 . A <*> 0 . DP=21;DPR=21,0;I16=9,12,0,0,800,31906,0,0,989,51297,0,0,390,8380,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:7,4,0,0:11,0 0,15,114:5:0:0:0,5,0,0:5,0 0,15,129:5:0:0:2,3,0,0:5,0 17 266 . G <*> 0 . DP=21;DPR=21,0;I16=9,12,0,0,754,28204,0,0,989,51297,0,0,394,8458,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:7,4,0,0:11,0 0,15,99:5:0:0:0,5,0,0:5,0 0,15,138:5:0:0:2,3,0,0:5,0 -17 267 . T G,<*> 0 . DP=21;DPR=20,1,0;I16=9,11,0,1,739,27465,8,64,960,50456,29,841,373,7935,25,625;QS=2.94203,0.057971,0;SGB=-0.556633;RPBZ=-0.330396;MQBZ=-1.23153;MQSBZ=-3.3021;BQBZ=-1.66282;NMBZ=2.4409;SCBZ=2.91633;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,254,33,254,254:11:0:0:7,4,0,0:11,0,0 0,6,93,12,96,96:5:1:0:0,4,0,1:4,1,0 0,15,149,15,149,149:5:0:0:2,3,0,0:5,0,0 +17 267 . T G,<*> 0 . DP=21;DPR=20,1,0;I16=9,11,0,1,739,27465,8,64,960,50456,29,841,373,7935,25,625;QS=2.94203,0.057971,0;SGB=-0.556633;RPBZ=-0.330396;MQBZ=-1.23153;MQSBZ=-3.3021;BQBZ=-1.66282;SCBZ=2.91633;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,254,33,254,254:11:0:0:7,4,0,0:11,0,0 0,6,93,12,96,96:5:1:0:0,4,0,1:4,1,0 0,15,149,15,149,149:5:0:0:2,3,0,0:5,0,0 17 268 . T <*> 0 . DP=21;DPR=21,0;I16=9,12,0,0,748,27708,0,0,989,51297,0,0,402,8686,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,238:11:0:0:7,4,0,0:11,0 0,15,110:5:0:0:0,5,0,0:5,0 0,15,156:5:0:0:2,3,0,0:5,0 17 269 . C <*> 0 . DP=22;DPR=22,0;I16=9,13,0,0,767,28641,0,0,1018,52138,0,0,406,8836,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:7,5,0,0:12,0 0,15,91:5:0:0:0,5,0,0:5,0 0,15,154:5:0:0:2,3,0,0:5,0 17 270 . C <*> 0 . DP=22;DPR=22,0;I16=9,13,0,0,766,28210,0,0,1018,52138,0,0,410,8962,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:7,5,0,0:12,0 0,15,98:5:0:0:0,5,0,0:5,0 0,15,143:5:0:0:2,3,0,0:5,0 17 271 . T <*> 0 . DP=22;DPR=22,0;I16=9,13,0,0,847,32935,0,0,1018,52138,0,0,413,9065,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:7,5,0,0:12,0 0,15,113:5:0:0:0,5,0,0:5,0 0,15,152:5:0:0:2,3,0,0:5,0 17 272 . C <*> 0 . DP=22;DPR=22,0;I16=9,13,0,0,815,31449,0,0,1018,52138,0,0,415,9143,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:7,5,0,0:12,0 0,15,97:5:0:0:0,5,0,0:5,0 0,15,149:5:0:0:2,3,0,0:5,0 -17 273 . T C,<*> 0 . DP=22;DPR=21,1,0;I16=9,12,0,1,798,30664,5,25,989,51297,29,841,392,8620,25,625;QS=2.96094,0.0390625,0;SGB=-0.556633;RPBZ=-0.236567;MQBZ=-1.16701;MQSBZ=-3.42286;BQBZ=-1.66779;NMBZ=2.50862;SCBZ=3.00076;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255,36,255,255:12:0:0:7,5,0,0:12,0,0 0,7,89,12,92,90:5:1:0:0,4,0,1:4,1,0 0,15,161,15,161,161:5:0:0:2,3,0,0:5,0,0 +17 273 . T C,<*> 0 . DP=22;DPR=21,1,0;I16=9,12,0,1,798,30664,5,25,989,51297,29,841,392,8620,25,625;QS=2.96094,0.0390625,0;SGB=-0.556633;RPBZ=-0.236567;MQBZ=-1.16701;MQSBZ=-3.42286;BQBZ=-1.66779;SCBZ=3.00076;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255,36,255,255:12:0:0:7,5,0,0:12,0,0 0,7,89,12,92,90:5:1:0:0,4,0,1:4,1,0 0,15,161,15,161,161:5:0:0:2,3,0,0:5,0,0 17 274 . C <*> 0 . DP=22;DPR=22,0;I16=9,13,0,0,767,28193,0,0,1018,52138,0,0,419,9371,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:7,5,0,0:12,0 0,15,101:5:0:0:0,5,0,0:5,0 0,15,144:5:0:0:2,3,0,0:5,0 17 275 . C <*> 0 . DP=20;DPR=20,0;I16=7,13,0,0,768,29994,0,0,898,44938,0,0,423,9519,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,15,114:5:0:0:0,5,0,0:5,0 0,12,122:4:0:0:1,3,0,0:4,0 17 276 . A <*> 0 . DP=20;DPR=20,0;I16=7,13,0,0,805,32931,0,0,898,44938,0,0,424,9538,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,253:11:0:0:6,5,0,0:11,0 0,15,122:5:0:0:0,5,0,0:5,0 0,12,124:4:0:0:1,3,0,0:4,0 17 277 . G <*> 0 . DP=20;DPR=20,0;I16=7,13,0,0,764,29732,0,0,898,44938,0,0,425,9579,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,15,114:5:0:0:0,5,0,0:5,0 0,12,121:4:0:0:1,3,0,0:4,0 -17 278 . A C,<*> 0 . DP=21;DPR=20,1,0;I16=6,14,1,0,722,26452,7,49,867,42179,60,3600,415,9521,11,121;QS=2.97935,0.020649,0;SGB=-0.556633;RPBZ=1.65198;MQBZ=1.0247;MQSBZ=-3.24037;BQBZ=-1.66667;NMBZ=-0.406816;SCBZ=-0.324037;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,22,231,30,234,231:11:1:0:5,5,1,0:10,1,0 0,18,123,18,123,123:6:0:0:0,6,0,0:6,0,0 0,12,121,12,121,121:4:0:0:1,3,0,0:4,0,0 +17 278 . A C,<*> 0 . DP=21;DPR=20,1,0;I16=6,14,1,0,722,26452,7,49,867,42179,60,3600,415,9521,11,121;QS=2.97935,0.020649,0;SGB=-0.556633;RPBZ=1.65198;MQBZ=1.0247;MQSBZ=-3.24037;BQBZ=-1.66667;SCBZ=-0.324037;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,22,231,30,234,231:11:1:0:5,5,1,0:10,1,0 0,18,123,18,123,123:6:0:0:0,6,0,0:6,0,0 0,12,121,12,121,121:4:0:0:1,3,0,0:4,0,0 17 279 . A <*> 0 . DP=22;DPR=22,0;I16=7,15,0,0,786,28694,0,0,956,46620,0,0,427,9677,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:6,6,0,0:12,0 0,18,123:6:0:0:0,6,0,0:6,0 0,12,122:4:0:0:1,3,0,0:4,0 17 280 . A <*> 0 . DP=22;DPR=22,0;I16=7,15,0,0,815,31561,0,0,956,46620,0,0,428,9684,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,253:12:0:0:6,6,0,0:12,0 0,18,130:6:0:0:0,6,0,0:6,0 0,12,129:4:0:0:1,3,0,0:4,0 17 281 . G <*> 0 . DP=22;DPR=22,0;I16=7,15,0,0,820,31416,0,0,956,46620,0,0,428,9662,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:6,6,0,0:12,0 0,18,122:6:0:0:0,6,0,0:6,0 0,12,123:4:0:0:1,3,0,0:4,0 @@ -223,13 +222,13 @@ 17 294 . A <*> 0 . DP=26;DPR=26,0;I16=10,16,0,0,931,33937,0,0,1227,63779,0,0,443,9785,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,252:12:0:0:6,6,0,0:12,0 0,24,201:8:0:0:3,5,0,0:8,0 0,18,161:6:0:0:1,5,0,0:6,0 17 295 . C <*> 0 . DP=25;DPR=25,0;I16=10,15,0,0,909,34117,0,0,1198,62938,0,0,447,9833,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,183:8:0:0:3,5,0,0:8,0 0,18,159:6:0:0:1,5,0,0:6,0 17 296 . A <*> 0 . DP=25;DPR=25,0;I16=10,15,0,0,874,31846,0,0,1198,62938,0,0,451,9905,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,169:8:0:0:3,5,0,0:8,0 0,18,169:6:0:0:1,5,0,0:6,0 -17 297 . C G,<*> 0 . DP=25;DPR=24,1,0;I16=9,15,1,0,901,34305,4,16,1138,59338,60,3600,445,9901,10,100;QS=2.98261,0.0173913,0;SGB=-0.556633;RPBZ=-1.24856;MQBZ=0.806872;MQSBZ=-3.22749;BQBZ=-1.67542;NMBZ=-0.434372;SCBZ=-0.368383;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255,33,255,255:11:0:0:6,5,0,0:11,0,0 0,15,168,21,171,168:8:1:0:2,5,1,0:7,1,0 0,18,161,18,161,161:6:0:0:1,5,0,0:6,0,0 +17 297 . C G,<*> 0 . DP=25;DPR=24,1,0;I16=9,15,1,0,901,34305,4,16,1138,59338,60,3600,445,9901,10,100;QS=2.98261,0.0173913,0;SGB=-0.556633;RPBZ=-1.24856;MQBZ=0.806872;MQSBZ=-3.22749;BQBZ=-1.67542;SCBZ=-0.368383;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255,33,255,255:11:0:0:6,5,0,0:11,0,0 0,15,168,21,171,168:8:1:0:2,5,1,0:7,1,0 0,18,161,18,161,161:6:0:0:1,5,0,0:6,0,0 17 298 . A <*> 0 . DP=26;DPR=26,0;I16=11,15,0,0,936,34652,0,0,1258,66538,0,0,459,10121,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,184:8:0:0:3,5,0,0:8,0 0,21,191:7:0:0:2,5,0,0:7,0 17 299 . C <*> 0 . DP=27;DPR=26,0;I16=11,15,0,0,971,36863,0,0,1258,66538,0,0,464,10266,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,193:8:0:0:3,5,0,0:8,0 0,21,189:7:0:0:2,5,0,0:7,0 17 300 . A <*> 0 . DP=27;DPR=26,0;I16=11,15,0,0,1001,39455,0,0,1258,66538,0,0,469,10437,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,204:8:0:0:3,5,0,0:8,0 0,21,210:7:0:0:2,5,0,0:7,0 17 301 . G <*> 0 . DP=25;DPR=24,0;I16=10,14,0,0,928,36116,0,0,1169,62097,0,0,476,10632,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,255:10:0:0:5,5,0,0:10,0 0,21,195:7:0:0:3,4,0,0:7,0 0,21,196:7:0:0:2,5,0,0:7,0 17 302 . T <*> 0 . DP=25;DPR=24,0;I16=10,14,0,0,879,32885,0,0,1169,62097,0,0,483,10849,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,231:10:0:0:5,5,0,0:10,0 0,21,172:7:0:0:3,4,0,0:7,0 0,21,202:7:0:0:2,5,0,0:7,0 -17 302 . T TA 0 . INDEL;IDV=7;IMF=1;DP=25;DPR=6,19;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.539485,2.46052;VDB=0.241622;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.22749;BQBZ=-1.67542;NMBZ=-0.199304;SCBZ=-0.268121;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 161,0,99:11:6:6:1,4,4,2:5,6 158,0,14:7:6:0:1,0,2,4:1,6 201,21,0:7:7:0:0,0,2,5:0,7 +17 302 . T TA 0 . INDEL;IDV=7;IMF=1;DP=25;DPR=6,19;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.539485,2.46052;VDB=0.241622;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.22749;BQBZ=-1.67542;SCBZ=-0.268121;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 161,0,99:11:6:6:1,4,4,2:5,6 158,0,14:7:6:0:1,0,2,4:1,6 201,21,0:7:7:0:0,0,2,5:0,7 17 303 . G <*> 0 . DP=25;DPR=25,0;I16=10,15,0,0,968,37972,0,0,1229,65697,0,0,497,11181,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:5,6,0,0:11,0 0,21,197:7:0:0:3,4,0,0:7,0 0,21,195:7:0:0:2,5,0,0:7,0 17 304 . C <*> 0 . DP=27;DPR=27,0;I16=11,16,0,0,991,37005,0,0,1318,70138,0,0,503,11359,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:5,6,0,0:11,0 0,24,206:8:0:0:4,4,0,0:8,0 0,24,200:8:0:0:2,6,0,0:8,0 17 305 . C <*> 0 . DP=27;DPR=27,0;I16=11,16,0,0,1057,41761,0,0,1318,70138,0,0,510,11508,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:5,6,0,0:11,0 0,24,213:8:0:0:4,4,0,0:8,0 0,24,211:8:0:0:2,6,0,0:8,0 @@ -262,9 +261,9 @@ 17 332 . A <*> 0 . DP=32;DPR=32,0;I16=14,18,0,0,1156,42666,0,0,1649,90897,0,0,560,12178,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:6,6,0,0:12,0 0,27,214:9:0:0:4,5,0,0:9,0 0,33,255:11:0:0:4,7,0,0:11,0 17 333 . A <*> 0 . DP=32;DPR=32,0;I16=14,18,0,0,1141,41987,0,0,1649,90897,0,0,558,12064,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:6,6,0,0:12,0 0,27,223:9:0:0:4,5,0,0:9,0 0,33,255:11:0:0:4,7,0,0:11,0 17 334 . A <*> 0 . DP=32;DPR=32,0;I16=14,18,0,0,1162,43328,0,0,1649,90897,0,0,556,11986,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:6,6,0,0:12,0 0,27,221:9:0:0:4,5,0,0:9,0 0,33,255:11:0:0:4,7,0,0:11,0 -17 335 . A G,<*> 0 . DP=32;DPR=31,1,0;I16=13,18,1,0,1084,40336,4,16,1589,87297,60,3600,555,11943,0,0;QS=2.98919,0.0108108,0;SGB=-0.556633;RPBZ=-1.67936;MQBZ=0.622171;MQSBZ=-2.25492;BQBZ=-1.68602;NMBZ=-0.428353;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,252,33,252,252:11:0:0:5,6,0,0:11,0,0 0,27,219,27,219,219:9:0:0:4,5,0,0:9,0,0 0,25,245,33,248,245:12:1:0:4,7,1,0:11,1,0 +17 335 . A G,<*> 0 . DP=32;DPR=31,1,0;I16=13,18,1,0,1084,40336,4,16,1589,87297,60,3600,555,11943,0,0;QS=2.98919,0.0108108,0;SGB=-0.556633;RPBZ=-1.67936;MQBZ=0.622171;MQSBZ=-2.25492;BQBZ=-1.68602;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,252,33,252,252:11:0:0:5,6,0,0:11,0,0 0,27,219,27,219,219:9:0:0:4,5,0,0:9,0,0 0,25,245,33,248,245:12:1:0:4,7,1,0:11,1,0 17 336 . A <*> 0 . DP=32;DPR=32,0;I16=14,18,0,0,1094,39794,0,0,1649,90897,0,0,555,11935,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:5,6,0,0:11,0 0,27,212:9:0:0:4,5,0,0:9,0 0,36,255:12:0:0:5,7,0,0:12,0 -17 337 . C A,<*> 0 . DP=32;DPR=31,1,0;I16=14,17,0,1,1125,42481,5,25,1612,89528,37,1369,536,11590,18,324;QS=2.98113,0.0188679,0;SGB=-0.556633;RPBZ=0.812593;MQBZ=-1.03695;MQSBZ=-2.25492;BQBZ=-1.68353;NMBZ=-0.376914;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255,33,255,255:11:0:0:5,6,0,0:11,0,0 0,17,195,24,198,195:9:1:0:4,4,0,1:8,1,0 0,36,255,36,255,255:12:0:0:5,7,0,0:12,0,0 +17 337 . C A,<*> 0 . DP=32;DPR=31,1,0;I16=14,17,0,1,1125,42481,5,25,1612,89528,37,1369,536,11590,18,324;QS=2.98113,0.0188679,0;SGB=-0.556633;RPBZ=0.812593;MQBZ=-1.03695;MQSBZ=-2.25492;BQBZ=-1.68353;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255,33,255,255:11:0:0:5,6,0,0:11,0,0 0,17,195,24,198,195:9:1:0:4,4,0,1:8,1,0 0,36,255,36,255,255:12:0:0:5,7,0,0:12,0,0 17 338 . T <*> 0 . DP=30;DPR=30,0;I16=14,16,0,0,1190,47898,0,0,1560,86456,0,0,554,11878,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,255:10:0:0:5,5,0,0:10,0 0,24,226:8:0:0:4,4,0,0:8,0 0,36,255:12:0:0:5,7,0,0:12,0 17 339 . C <*> 0 . DP=31;DPR=31,0;I16=14,17,0,0,1130,43210,0,0,1589,87297,0,0,554,11874,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:5,6,0,0:11,0 0,24,185:8:0:0:4,4,0,0:8,0 0,36,255:12:0:0:5,7,0,0:12,0 17 340 . C <*> 0 . DP=31;DPR=31,0;I16=14,17,0,0,1196,47044,0,0,1589,87297,0,0,554,11852,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:5,6,0,0:11,0 0,24,221:8:0:0:4,4,0,0:8,0 0,36,255:12:0:0:5,7,0,0:12,0 @@ -282,11 +281,11 @@ 17 352 . A <*> 0 . DP=31;DPR=31,0;I16=16,15,0,0,1162,45664,0,0,1651,92815,0,0,569,13029,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,27,230:9:0:0:5,4,0,0:9,0 0,33,255:11:0:0:5,6,0,0:11,0 17 353 . G <*> 0 . DP=29;DPR=29,0;I16=15,14,0,0,1109,43095,0,0,1562,88374,0,0,570,13064,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,255:10:0:0:5,5,0,0:10,0 0,27,231:9:0:0:5,4,0,0:9,0 0,30,255:10:0:0:5,5,0,0:10,0 17 354 . A <*> 0 . DP=28;DPR=28,0;I16=14,14,0,0,1078,42938,0,0,1502,84774,0,0,571,13075,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,225:9:0:0:4,5,0,0:9,0 0,27,244:9:0:0:5,4,0,0:9,0 0,30,255:10:0:0:5,5,0,0:10,0 -17 355 . G T,<*> 0 . DP=28;DPR=27,1,0;I16=14,13,0,1,1001,37907,41,1681,1442,81174,60,3600,547,12487,25,625;QS=2.875,0.125,0;SGB=-0.556633;RPBZ=0.185772;MQBZ=0.520126;MQSBZ=-1.7696;BQBZ=0.683978;NMBZ=2.33874;SCBZ=-0.27735;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 14,0,200,38,203,231:9:1:0:4,4,0,1:8,1,0 0,27,222,27,222,222:9:0:0:5,4,0,0:9,0,0 0,30,255,30,255,255:10:0:0:5,5,0,0:10,0,0 +17 355 . G T,<*> 0 . DP=28;DPR=27,1,0;I16=14,13,0,1,1001,37907,41,1681,1442,81174,60,3600,547,12487,25,625;QS=2.875,0.125,0;SGB=-0.556633;RPBZ=0.185772;MQBZ=0.520126;MQSBZ=-1.7696;BQBZ=0.683978;SCBZ=-0.27735;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 14,0,200,38,203,231:9:1:0:4,4,0,1:8,1,0 0,27,222,27,222,222:9:0:0:5,4,0,0:9,0,0 0,30,255,30,255,255:10:0:0:5,5,0,0:10,0,0 17 356 . G <*> 0 . DP=27;DPR=27,0;I16=14,13,0,0,993,37481,0,0,1465,83405,0,0,574,13174,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,228:9:0:0:4,5,0,0:9,0 0,24,201:8:0:0:5,3,0,0:8,0 0,30,255:10:0:0:5,5,0,0:10,0 17 357 . C <*> 0 . DP=28;DPR=28,0;I16=15,13,0,0,1026,39496,0,0,1525,87005,0,0,575,13209,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,255:10:0:0:5,5,0,0:10,0 0,24,205:8:0:0:5,3,0,0:8,0 0,30,252:10:0:0:5,5,0,0:10,0 17 358 . A <*> 0 . DP=28;DPR=28,0;I16=15,13,0,0,1050,40518,0,0,1525,87005,0,0,576,13216,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,254:10:0:0:5,5,0,0:10,0 0,24,197:8:0:0:5,3,0,0:8,0 0,30,255:10:0:0:5,5,0,0:10,0 -17 359 . G T,<*> 0 . DP=29;DPR=28,1,0;I16=15,13,0,1,1085,42761,10,100,1525,87005,60,3600,552,12620,25,625;QS=2.96032,0.0396825,0;SGB=-0.556633;RPBZ=-0.119611;MQBZ=0.456435;MQSBZ=-1.53333;BQBZ=-1.68246;NMBZ=3.0531;SCBZ=5.2915;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,255,30,255,255:10:0:0:5,5,0,0:10,0,0 0,13,178,21,181,180:8:1:0:5,2,0,1:7,1,0 0,33,255,33,255,255:11:0:0:5,6,0,0:11,0,0 +17 359 . G T,<*> 0 . DP=29;DPR=28,1,0;I16=15,13,0,1,1085,42761,10,100,1525,87005,60,3600,552,12620,25,625;QS=2.96032,0.0396825,0;SGB=-0.556633;RPBZ=-0.119611;MQBZ=0.456435;MQSBZ=-1.53333;BQBZ=-1.68246;SCBZ=5.2915;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,255,30,255,255:10:0:0:5,5,0,0:10,0,0 0,13,178,21,181,180:8:1:0:5,2,0,1:7,1,0 0,33,255,33,255,255:11:0:0:5,6,0,0:11,0,0 17 360 . A <*> 0 . DP=29;DPR=29,0;I16=15,14,0,0,1111,43259,0,0,1585,90605,0,0,579,13297,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,252:10:0:0:5,5,0,0:10,0 0,24,220:8:0:0:5,3,0,0:8,0 0,33,255:11:0:0:5,6,0,0:11,0 17 361 . A <*> 0 . DP=29;DPR=29,0;I16=15,14,0,0,1116,43442,0,0,1585,90605,0,0,579,13273,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,252:10:0:0:5,5,0,0:10,0 0,24,219:8:0:0:5,3,0,0:8,0 0,33,255:11:0:0:5,6,0,0:11,0 17 362 . A <*> 0 . DP=29;DPR=29,0;I16=16,13,0,0,1104,42700,0,0,1585,90605,0,0,580,13272,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,218:8:0:0:5,3,0,0:8,0 0,30,255:10:0:0:5,5,0,0:10,0 @@ -296,13 +295,13 @@ 17 366 . A <*> 0 . DP=29;DPR=29,0;I16=16,13,0,0,1090,41562,0,0,1585,90605,0,0,581,13167,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,211:8:0:0:5,3,0,0:8,0 0,30,255:10:0:0:5,5,0,0:10,0 17 367 . T <*> 0 . DP=29;DPR=29,0;I16=16,13,0,0,1055,39149,0,0,1585,90605,0,0,579,13093,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,204:8:0:0:5,3,0,0:8,0 0,30,255:10:0:0:5,5,0,0:10,0 17 368 . A <*> 0 . DP=29;DPR=29,0;I16=16,13,0,0,1054,39632,0,0,1585,90605,0,0,576,12998,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,208:8:0:0:5,3,0,0:8,0 0,30,255:10:0:0:5,5,0,0:10,0 -17 369 . T G,<*> 0 . DP=28;DPR=27,1,0;I16=16,11,0,1,1037,40275,6,36,1496,86164,60,3600,548,12256,25,625;QS=2.97683,0.023166,0;SGB=-0.556633;RPBZ=0.12395;MQBZ=0.408248;MQSBZ=-1.37784;BQBZ=-1.68703;NMBZ=2.99794;SCBZ=5.19615;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,250,30,250,250:10:0:0:6,4,0,0:10,0,0 0,15,189,21,192,190:8:1:0:5,2,0,1:7,1,0 0,30,255,30,255,255:10:0:0:5,5,0,0:10,0,0 +17 369 . T G,<*> 0 . DP=28;DPR=27,1,0;I16=16,11,0,1,1037,40275,6,36,1496,86164,60,3600,548,12256,25,625;QS=2.97683,0.023166,0;SGB=-0.556633;RPBZ=0.12395;MQBZ=0.408248;MQSBZ=-1.37784;BQBZ=-1.68703;SCBZ=5.19615;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,250,30,250,250:10:0:0:6,4,0,0:10,0,0 0,15,189,21,192,190:8:1:0:5,2,0,1:7,1,0 0,30,255,30,255,255:10:0:0:5,5,0,0:10,0,0 17 370 . C <*> 0 . DP=28;DPR=28,0;I16=16,12,0,0,1045,40219,0,0,1556,89764,0,0,570,12790,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,255:10:0:0:6,4,0,0:10,0 0,24,201:8:0:0:5,3,0,0:8,0 0,30,255:10:0:0:5,5,0,0:10,0 17 371 . T <*> 0 . DP=29;DPR=29,0;I16=16,13,0,0,1155,46591,0,0,1616,93364,0,0,567,12725,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,255:10:0:0:6,4,0,0:10,0 0,24,227:8:0:0:5,3,0,0:8,0 0,33,255:11:0:0:5,6,0,0:11,0 17 372 . C <*> 0 . DP=30;DPR=30,0;I16=16,14,0,0,1139,44019,0,0,1676,96964,0,0,564,12636,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,215:8:0:0:5,3,0,0:8,0 0,33,255:11:0:0:5,6,0,0:11,0 17 373 . A <*> 0 . DP=30;DPR=30,0;I16=16,14,0,0,1142,44118,0,0,1676,96964,0,0,561,12525,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,220:8:0:0:5,3,0,0:8,0 0,33,255:11:0:0:5,6,0,0:11,0 17 374 . T <*> 0 . DP=30;DPR=30,0;I16=16,14,0,0,1098,41180,0,0,1676,96964,0,0,556,12344,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,221:8:0:0:5,3,0,0:8,0 0,33,255:11:0:0:5,6,0,0:11,0 -17 375 . A T,<*> 0 . DP=31;DPR=30,1,0;I16=17,13,0,1,1138,43798,14,196,1676,96964,60,3600,547,12177,4,16;QS=2.9661,0.0338983,0;SGB=-0.556633;RPBZ=-1.45432;MQBZ=0.3849;MQSBZ=-1.26404;BQBZ=-1.68488;NMBZ=2.30253;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255,36,255,255:12:0:0:7,5,0,0:12,0,0 0,24,218,24,218,218:8:0:0:5,3,0,0:8,0,0 0,18,255,30,255,255:11:1:0:5,5,0,1:10,1,0 +17 375 . A T,<*> 0 . DP=31;DPR=30,1,0;I16=17,13,0,1,1138,43798,14,196,1676,96964,60,3600,547,12177,4,16;QS=2.9661,0.0338983,0;SGB=-0.556633;RPBZ=-1.45432;MQBZ=0.3849;MQSBZ=-1.26404;BQBZ=-1.68488;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255,36,255,255:12:0:0:7,5,0,0:12,0,0 0,24,218,24,218,218:8:0:0:5,3,0,0:8,0,0 0,18,255,30,255,255:11:1:0:5,5,0,1:10,1,0 17 376 . G <*> 0 . DP=31;DPR=31,0;I16=17,14,0,0,1131,42581,0,0,1736,100564,0,0,547,12073,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:7,5,0,0:12,0 0,24,220:8:0:0:5,3,0,0:8,0 0,33,255:11:0:0:5,6,0,0:11,0 17 377 . T <*> 0 . DP=31;DPR=31,0;I16=17,14,0,0,1116,41750,0,0,1736,100564,0,0,543,11985,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:7,5,0,0:12,0 0,24,211:8:0:0:5,3,0,0:8,0 0,33,255:11:0:0:5,6,0,0:11,0 17 378 . T <*> 0 . DP=30;DPR=30,0;I16=18,12,0,0,1098,41066,0,0,1707,99723,0,0,541,11927,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255:13:0:0:8,5,0,0:13,0 0,21,186:7:0:0:5,2,0,0:7,0 0,30,255:10:0:0:5,5,0,0:10,0 @@ -311,7 +310,7 @@ 17 381 . T <*> 0 . DP=29;DPR=29,0;I16=18,11,0,0,1167,47337,0,0,1678,98882,0,0,537,11729,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:8,4,0,0:12,0 0,21,211:7:0:0:5,2,0,0:7,0 0,30,255:10:0:0:5,5,0,0:10,0 17 382 . T <*> 0 . DP=29;DPR=29,0;I16=18,11,0,0,1062,40514,0,0,1678,98882,0,0,535,11693,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:8,4,0,0:12,0 0,21,182:7:0:0:5,2,0,0:7,0 0,30,255:10:0:0:5,5,0,0:10,0 17 383 . T <*> 0 . DP=29;DPR=29,0;I16=18,11,0,0,1059,39847,0,0,1678,98882,0,0,532,11638,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:8,4,0,0:12,0 0,21,172:7:0:0:5,2,0,0:7,0 0,30,255:10:0:0:5,5,0,0:10,0 -17 384 . A C,<*> 0 . DP=31;DPR=30,1,0;I16=19,11,0,1,1077,39885,4,16,1738,102482,60,3600,504,10988,25,625;QS=2.98419,0.0158103,0;SGB=-0.556633;RPBZ=0.615229;MQBZ=0.262613;MQSBZ=-0.333409;BQBZ=-1.68746;NMBZ=3.26825;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255,39,255,255:13:0:0:8,5,0,0:13,0,0 0,15,171,21,174,171:8:1:0:6,1,0,1:7,1,0 0,30,255,30,255,255:10:0:0:5,5,0,0:10,0,0 +17 384 . A C,<*> 0 . DP=31;DPR=30,1,0;I16=19,11,0,1,1077,39885,4,16,1738,102482,60,3600,504,10988,25,625;QS=2.98419,0.0158103,0;SGB=-0.556633;RPBZ=0.615229;MQBZ=0.262613;MQSBZ=-0.333409;BQBZ=-1.68746;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255,39,255,255:13:0:0:8,5,0,0:13,0,0 0,15,171,21,174,171:8:1:0:6,1,0,1:7,1,0 0,30,255,30,255,255:10:0:0:5,5,0,0:10,0,0 17 385 . C <*> 0 . DP=31;DPR=31,0;I16=19,12,0,0,1118,41180,0,0,1798,106082,0,0,527,11569,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255:13:0:0:8,5,0,0:13,0 0,24,186:8:0:0:6,2,0,0:8,0 0,30,255:10:0:0:5,5,0,0:10,0 17 386 . T <*> 0 . DP=30;DPR=30,0;I16=18,12,0,0,1158,45592,0,0,1738,102482,0,0,526,11556,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255:13:0:0:8,5,0,0:13,0 0,21,191:7:0:0:5,2,0,0:7,0 0,30,255:10:0:0:5,5,0,0:10,0 17 387 . T <*> 0 . DP=30;DPR=30,0;I16=18,12,0,0,1105,41821,0,0,1738,102482,0,0,525,11573,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255:13:0:0:8,5,0,0:13,0 0,21,187:7:0:0:5,2,0,0:7,0 0,30,255:10:0:0:5,5,0,0:10,0 @@ -328,7 +327,7 @@ 17 398 . A <*> 0 . DP=28;DPR=28,0;I16=17,11,0,0,1025,38361,0,0,1587,92523,0,0,524,11850,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255:13:0:0:8,5,0,0:13,0 0,15,144:5:0:0:3,2,0,0:5,0 0,30,255:10:0:0:6,4,0,0:10,0 17 399 . A <*> 0 . DP=28;DPR=28,0;I16=17,11,0,0,1023,38949,0,0,1587,92523,0,0,526,11900,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255:13:0:0:8,5,0,0:13,0 0,15,140:5:0:0:3,2,0,0:5,0 0,30,255:10:0:0:6,4,0,0:10,0 17 400 . A <*> 0 . DP=29;DPR=29,0;I16=17,12,0,0,1070,40554,0,0,1647,96123,0,0,526,11828,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255:13:0:0:8,5,0,0:13,0 0,15,159:5:0:0:3,2,0,0:5,0 0,33,255:11:0:0:6,5,0,0:11,0 -17 401 . A C,<*> 0 . DP=29;DPR=28,1,0;I16=17,11,0,1,1063,41001,8,64,1587,92523,60,3600,501,11113,25,625;QS=2.97985,0.0201511,0;SGB=-0.556633;RPBZ=-0.478622;MQBZ=0.339683;MQSBZ=0.29364;BQBZ=-1.68267;NMBZ=3.53589;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255,39,255,255:13:0:0:8,5,0,0:13,0,0 0,15,160,15,160,160:5:0:0:3,2,0,0:5,0,0 0,22,255,30,255,255:11:1:0:6,4,0,1:10,1,0 +17 401 . A C,<*> 0 . DP=29;DPR=28,1,0;I16=17,11,0,1,1063,41001,8,64,1587,92523,60,3600,501,11113,25,625;QS=2.97985,0.0201511,0;SGB=-0.556633;RPBZ=-0.478622;MQBZ=0.339683;MQSBZ=0.29364;BQBZ=-1.68267;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255,39,255,255:13:0:0:8,5,0,0:13,0,0 0,15,160,15,160,160:5:0:0:3,2,0,0:5,0,0 0,22,255,30,255,255:11:1:0:6,4,0,1:10,1,0 17 402 . T <*> 0 . DP=29;DPR=29,0;I16=17,12,0,0,1076,40740,0,0,1647,96123,0,0,526,11680,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255:13:0:0:8,5,0,0:13,0 0,15,149:5:0:0:3,2,0,0:5,0 0,33,255:11:0:0:6,5,0,0:11,0 17 403 . T <*> 0 . DP=29;DPR=29,0;I16=17,12,0,0,1085,40985,0,0,1647,96123,0,0,526,11654,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255:13:0:0:8,5,0,0:13,0 0,15,148:5:0:0:3,2,0,0:5,0 0,33,255:11:0:0:6,5,0,0:11,0 17 404 . G <*> 0 . DP=29;DPR=29,0;I16=17,12,0,0,1074,40524,0,0,1647,96123,0,0,525,11609,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255:13:0:0:8,5,0,0:13,0 0,15,131:5:0:0:3,2,0,0:5,0 0,33,255:11:0:0:6,5,0,0:11,0 @@ -339,7 +338,7 @@ 17 409 . T <*> 0 . DP=29;DPR=29,0;I16=17,12,0,0,1100,42734,0,0,1678,98882,0,0,525,11503,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,42,255:14:0:0:8,6,0,0:14,0 0,12,131:4:0:0:2,2,0,0:4,0 0,33,255:11:0:0:7,4,0,0:11,0 17 410 . T <*> 0 . DP=29;DPR=29,0;I16=17,12,0,0,1035,38325,0,0,1678,98882,0,0,524,11432,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,42,255:14:0:0:8,6,0,0:14,0 0,12,125:4:0:0:2,2,0,0:4,0 0,33,255:11:0:0:7,4,0,0:11,0 17 411 . T <*> 0 . DP=29;DPR=29,0;I16=17,12,0,0,1022,37928,0,0,1678,98882,0,0,522,11342,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,42,255:14:0:0:8,6,0,0:14,0 0,12,111:4:0:0:2,2,0,0:4,0 0,33,255:11:0:0:7,4,0,0:11,0 -17 412 . C T,<*> 0 . DP=30;DPR=29,1,0;I16=17,12,1,0,1094,42458,14,196,1678,98882,60,3600,495,10659,25,625;QS=2.97455,0.0254545,0;SGB=-0.556633;RPBZ=-0.40473;MQBZ=0.267261;MQSBZ=-0.293785;BQBZ=-1.6942;NMBZ=-0.267102;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,255,42,255,255:15:1:0:8,6,1,0:14,1,0 0,12,124,12,124,124:4:0:0:2,2,0,0:4,0,0 0,33,255,33,255,255:11:0:0:7,4,0,0:11,0,0 +17 412 . C T,<*> 0 . DP=30;DPR=29,1,0;I16=17,12,1,0,1094,42458,14,196,1678,98882,60,3600,495,10659,25,625;QS=2.97455,0.0254545,0;SGB=-0.556633;RPBZ=-0.40473;MQBZ=0.267261;MQSBZ=-0.293785;BQBZ=-1.6942;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,255,42,255,255:15:1:0:8,6,1,0:14,1,0 0,12,124,12,124,124:4:0:0:2,2,0,0:4,0,0 0,33,255,33,255,255:11:0:0:7,4,0,0:11,0,0 17 413 . A <*> 0 . DP=31;DPR=31,0;I16=18,13,0,0,1189,45985,0,0,1798,106082,0,0,520,11258,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:9,8,0,0:17,0 0,9,102:3:0:0:2,1,0,0:3,0 0,33,255:11:0:0:7,4,0,0:11,0 17 414 . T <*> 0 . DP=30;DPR=30,0;I16=18,12,0,0,1151,44355,0,0,1738,102482,0,0,523,11265,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:9,7,0,0:16,0 0,9,109:3:0:0:2,1,0,0:3,0 0,33,255:11:0:0:7,4,0,0:11,0 17 415 . G <*> 0 . DP=30;DPR=30,0;I16=18,12,0,0,1131,43175,0,0,1738,102482,0,0,526,11306,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:9,7,0,0:16,0 0,9,110:3:0:0:2,1,0,0:3,0 0,33,255:11:0:0:7,4,0,0:11,0 @@ -364,7 +363,7 @@ 17 434 . T <*> 0 . DP=29;DPR=29,0;I16=15,14,0,0,1036,37654,0,0,1647,96123,0,0,561,12567,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:8,8,0,0:16,0 0,9,98:3:0:0:2,1,0,0:3,0 0,30,243:10:0:0:5,5,0,0:10,0 17 435 . A <*> 0 . DP=29;DPR=29,0;I16=15,14,0,0,1035,38091,0,0,1647,96123,0,0,562,12596,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:8,8,0,0:16,0 0,9,103:3:0:0:2,1,0,0:3,0 0,30,237:10:0:0:5,5,0,0:10,0 17 436 . T <*> 0 . DP=28;DPR=28,0;I16=14,14,0,0,998,36220,0,0,1587,92523,0,0,564,12654,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:8,8,0,0:16,0 0,9,110:3:0:0:2,1,0,0:3,0 0,27,223:9:0:0:4,5,0,0:9,0 -17 437 . T G,<*> 0 . DP=28;DPR=27,1,0;I16=13,14,1,0,990,36832,6,36,1558,91682,29,841,549,12435,16,256;QS=2.9781,0.0218978,0;SGB=-0.556633;RPBZ=-1.36214;MQBZ=-2.88675;MQSBZ=0.6;BQBZ=-1.67909;NMBZ=-0.19245;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255,48,255,255:16:0:0:8,8,0,0:16,0,0 0,9,109,9,109,109:3:0:0:2,1,0,0:3,0,0 0,17,200,24,203,201:9:1:0:3,5,1,0:8,1,0 +17 437 . T G,<*> 0 . DP=28;DPR=27,1,0;I16=13,14,1,0,990,36832,6,36,1558,91682,29,841,549,12435,16,256;QS=2.9781,0.0218978,0;SGB=-0.556633;RPBZ=-1.36214;MQBZ=-2.88675;MQSBZ=0.6;BQBZ=-1.67909;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255,48,255,255:16:0:0:8,8,0,0:16,0,0 0,9,109,9,109,109:3:0:0:2,1,0,0:3,0,0 0,17,200,24,203,201:9:1:0:3,5,1,0:8,1,0 17 438 . A <*> 0 . DP=28;DPR=28,0;I16=14,14,0,0,984,35784,0,0,1587,92523,0,0,565,12707,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:8,8,0,0:16,0 0,9,107:3:0:0:2,1,0,0:3,0 0,27,220:9:0:0:4,5,0,0:9,0 17 439 . C <*> 0 . DP=28;DPR=28,0;I16=14,14,0,0,1055,40273,0,0,1587,92523,0,0,563,12649,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:8,8,0,0:16,0 0,9,107:3:0:0:2,1,0,0:3,0 0,27,224:9:0:0:4,5,0,0:9,0 17 440 . A <*> 0 . DP=28;DPR=28,0;I16=14,14,0,0,1095,43251,0,0,1587,92523,0,0,561,12615,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:8,8,0,0:16,0 0,9,115:3:0:0:2,1,0,0:3,0 0,27,247:9:0:0:4,5,0,0:9,0 @@ -392,13 +391,13 @@ 17 462 . G <*> 0 . DP=32;DPR=31,0;I16=18,13,0,0,1169,46001,0,0,1775,103851,0,0,577,12669,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:10,7,0,0:17,0 0,12,131:4:0:0:3,1,0,0:4,0 0,30,241:10:0:0:5,5,0,0:10,0 17 463 . G <*> 0 . DP=32;DPR=31,0;I16=18,13,0,0,1095,41573,0,0,1775,103851,0,0,583,12729,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:10,7,0,0:17,0 0,12,126:4:0:0:3,1,0,0:4,0 0,30,221:10:0:0:5,5,0,0:10,0 17 464 . A <*> 0 . DP=32;DPR=31,0;I16=18,13,0,0,1100,41724,0,0,1775,103851,0,0,589,12821,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:10,7,0,0:17,0 0,12,148:4:0:0:3,1,0,0:4,0 0,30,217:10:0:0:5,5,0,0:10,0 -17 465 . C T,<*> 0 . DP=33;DPR=31,1,0;I16=19,12,0,1,1173,45601,4,16,1775,103851,60,3600,589,12909,6,36;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.67982;MQBZ=0.321288;MQSBZ=0.341466;BQBZ=-1.68493;NMBZ=3.21288;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255,51,255,255:17:0:0:10,7,0,0:17,0,0 0,15,158,15,158,158:5:0:0:4,1,0,0:5,0,0 0,20,224,27,227,224:10:1:0:5,4,0,1:9,1,0 +17 465 . C T,<*> 0 . DP=33;DPR=31,1,0;I16=19,12,0,1,1173,45601,4,16,1775,103851,60,3600,589,12909,6,36;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.67982;MQBZ=0.321288;MQSBZ=0.341466;BQBZ=-1.68493;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255,51,255,255:17:0:0:10,7,0,0:17,0,0 0,15,158,15,158,158:5:0:0:4,1,0,0:5,0,0 0,20,224,27,227,224:10:1:0:5,4,0,1:9,1,0 17 466 . A <*> 0 . DP=34;DPR=33,0;I16=20,13,0,0,1268,49686,0,0,1895,111051,0,0,602,13102,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:11,7,0,0:18,0 0,15,173:5:0:0:4,1,0,0:5,0 0,30,255:10:0:0:5,5,0,0:10,0 17 467 . A <*> 0 . DP=34;DPR=33,0;I16=20,13,0,0,1246,48610,0,0,1895,111051,0,0,608,13194,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:11,7,0,0:18,0 0,15,177:5:0:0:4,1,0,0:5,0 0,30,251:10:0:0:5,5,0,0:10,0 17 468 . A <*> 0 . DP=35;DPR=34,0;I16=21,13,0,0,1253,48095,0,0,1955,114651,0,0,613,13273,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:12,7,0,0:19,0 0,15,174:5:0:0:4,1,0,0:5,0 0,30,251:10:0:0:5,5,0,0:10,0 17 469 . A <*> 0 . DP=35;DPR=34,0;I16=21,13,0,0,1260,49028,0,0,1955,114651,0,0,618,13340,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:12,7,0,0:19,0 0,15,165:5:0:0:4,1,0,0:5,0 0,30,255:10:0:0:5,5,0,0:10,0 17 470 . G <*> 0 . DP=35;DPR=34,0;I16=21,13,0,0,1265,48879,0,0,1955,114651,0,0,623,13445,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:12,7,0,0:19,0 0,15,167:5:0:0:4,1,0,0:5,0 0,30,238:10:0:0:5,5,0,0:10,0 -17 471 . T G,C,<*> 0 . DP=36;DPR=33,1,1,0;I16=21,12,0,2,1220,46380,18,162,1918,113282,97,4969,611,13281,16,256;QS=2.94529,0.0273556,0.0273556,0;VDB=0.96;SGB=0.346553;RPBZ=0.497712;MQBZ=-1.9761;MQSBZ=0.312094;BQBZ=-2.35032;NMBZ=2.19566;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255,57,255,255,57,255,255,255:19:0:0:12,7,0,0:19,0,0,0 0,15,169,15,169,169,15,169,169,169:5:0:0:4,1,0,0:5,0,0,0 0,19,219,19,221,219,27,222,222,221:11:2:3:5,4,0,2:9,1,1,0 +17 471 . T G,C,<*> 0 . DP=36;DPR=33,1,1,0;I16=21,12,0,2,1220,46380,18,162,1918,113282,97,4969,611,13281,16,256;QS=2.94529,0.0273556,0.0273556,0;VDB=0.96;SGB=0.346553;RPBZ=0.497712;MQBZ=-1.9761;MQSBZ=0.312094;BQBZ=-2.35032;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255,57,255,255,57,255,255,255:19:0:0:12,7,0,0:19,0,0,0 0,15,169,15,169,169,15,169,169,169:5:0:0:4,1,0,0:5,0,0,0 0,19,219,19,221,219,27,222,222,221:11:2:3:5,4,0,2:9,1,1,0 17 472 . T <*> 0 . DP=35;DPR=34,0;I16=21,13,0,0,1234,46640,0,0,1955,114651,0,0,633,13665,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:12,7,0,0:19,0 0,15,172:5:0:0:4,1,0,0:5,0 0,30,241:10:0:0:5,5,0,0:10,0 17 473 . G <*> 0 . DP=35;DPR=34,0;I16=21,13,0,0,1303,51953,0,0,1955,114651,0,0,638,13780,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:12,7,0,0:19,0 0,15,159:5:0:0:4,1,0,0:5,0 0,30,250:10:0:0:5,5,0,0:10,0 17 474 . G <*> 0 . DP=36;DPR=35,0;I16=22,13,0,0,1279,49235,0,0,2015,118251,0,0,642,13884,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:12,7,0,0:19,0 0,15,146:5:0:0:4,1,0,0:5,0 0,33,255:11:0:0:6,5,0,0:11,0 @@ -415,7 +414,7 @@ 17 485 . G <*> 0 . DP=35;DPR=35,0;I16=23,12,0,0,1329,51411,0,0,2015,118251,0,0,669,14931,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:12,6,0,0:18,0 0,18,160:6:0:0:5,1,0,0:6,0 0,33,255:11:0:0:6,5,0,0:11,0 17 486 . A <*> 0 . DP=34;DPR=34,0;I16=22,12,0,0,1313,51667,0,0,1955,114651,0,0,671,14989,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:11,6,0,0:17,0 0,18,173:6:0:0:5,1,0,0:6,0 0,33,255:11:0:0:6,5,0,0:11,0 17 487 . G <*> 0 . DP=34;DPR=34,0;I16=22,12,0,0,1300,50304,0,0,1955,114651,0,0,672,15030,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:11,6,0,0:17,0 0,18,169:6:0:0:5,1,0,0:6,0 0,33,255:11:0:0:6,5,0,0:11,0 -17 488 . A G,<*> 0 . DP=35;DPR=34,1,0;I16=22,12,1,0,1278,48412,4,16,1986,117410,29,841,646,14380,25,625;QS=2.98947,0.0105263,0;SGB=-0.556633;RPBZ=0.594463;MQBZ=-3.36505;MQSBZ=0.10737;BQBZ=-1.69552;NMBZ=-0.171499;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255,54,255,255:18:0:0:12,6,0,0:18,0,0 0,18,177,18,177,177:6:0:0:5,1,0,0:6,0,0 0,23,255,30,255,255:11:1:0:5,5,1,0:10,1,0 +17 488 . A G,<*> 0 . DP=35;DPR=34,1,0;I16=22,12,1,0,1278,48412,4,16,1986,117410,29,841,646,14380,25,625;QS=2.98947,0.0105263,0;SGB=-0.556633;RPBZ=0.594463;MQBZ=-3.36505;MQSBZ=0.10737;BQBZ=-1.69552;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255,54,255,255:18:0:0:12,6,0,0:18,0,0 0,18,177,18,177,177:6:0:0:5,1,0,0:6,0,0 0,23,255,30,255,255:11:1:0:5,5,1,0:10,1,0 17 489 . A <*> 0 . DP=35;DPR=35,0;I16=23,12,0,0,1264,46916,0,0,2015,118251,0,0,671,15015,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:12,6,0,0:18,0 0,18,175:6:0:0:5,1,0,0:6,0 0,33,255:11:0:0:6,5,0,0:11,0 17 490 . A <*> 0 . DP=36;DPR=36,0;I16=24,12,0,0,1332,50280,0,0,2075,121851,0,0,671,15061,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:12,6,0,0:18,0 0,21,188:7:0:0:6,1,0,0:7,0 0,33,255:11:0:0:6,5,0,0:11,0 17 491 . T <*> 0 . DP=36;DPR=36,0;I16=24,12,0,0,1284,46802,0,0,2075,121851,0,0,671,15093,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:12,6,0,0:18,0 0,21,178:7:0:0:6,1,0,0:7,0 0,33,255:11:0:0:6,5,0,0:11,0 @@ -439,9 +438,9 @@ 17 509 . C <*> 0 . DP=34;DPR=34,0;I16=24,10,0,0,1272,48272,0,0,1986,117410,0,0,640,14430,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:13,5,0,0:18,0 0,21,186:7:0:0:6,1,0,0:7,0 0,27,241:9:0:0:5,4,0,0:9,0 17 510 . A <*> 0 . DP=34;DPR=34,0;I16=23,11,0,0,1211,44827,0,0,1986,117410,0,0,638,14398,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:13,6,0,0:19,0 0,21,187:7:0:0:6,1,0,0:7,0 0,24,221:8:0:0:4,4,0,0:8,0 17 511 . A <*> 0 . DP=34;DPR=34,0;I16=23,11,0,0,1238,46516,0,0,1986,117410,0,0,637,14395,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:13,6,0,0:19,0 0,21,195:7:0:0:6,1,0,0:7,0 0,24,233:8:0:0:4,4,0,0:8,0 -17 512 . A C,<*> 0 . DP=33;DPR=32,1,0;I16=22,10,0,1,1133,41513,13,169,1866,110210,60,3600,628,14340,9,81;QS=2.97766,0.0223368,0;SGB=-0.556633;RPBZ=-1.47079;MQBZ=0.253876;MQSBZ=-0.461593;BQBZ=-1.68442;NMBZ=2.68627;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255,51,255,255:18:1:0:12,5,0,1:17,1,0 0,21,183,21,183,183:7:0:0:6,1,0,0:7,0,0 0,24,231,24,231,231:8:0:0:4,4,0,0:8,0,0 -17 513 . A T,<*> 0 . DP=32;DPR=31,1,0;I16=21,10,1,0,1125,42283,12,144,1806,106610,60,3600,623,14249,15,225;QS=2.97966,0.020339,0;SGB=-0.556633;RPBZ=-1.24609;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.57376;NMBZ=2.63913;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,37,255,48,255,255:17:1:0:11,5,1,0:16,1,0 0,21,177,21,177,177:7:0:0:6,1,0,0:7,0,0 0,24,233,24,233,233:8:0:0:4,4,0,0:8,0,0 -17 514 . A T,<*> 0 . DP=32;DPR=31,1,0;I16=22,9,0,1,1086,40204,16,256,1806,106610,60,3600,627,14381,11,121;QS=2.97127,0.0287253,0;SGB=-0.556633;RPBZ=-1.4628;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.46657;NMBZ=2.63913;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,34,255,48,255,255:17:1:0:12,4,0,1:16,1,0 0,21,172,21,172,172:7:0:0:6,1,0,0:7,0,0 0,24,235,24,235,235:8:0:0:4,4,0,0:8,0,0 +17 512 . A C,<*> 0 . DP=33;DPR=32,1,0;I16=22,10,0,1,1133,41513,13,169,1866,110210,60,3600,628,14340,9,81;QS=2.97766,0.0223368,0;SGB=-0.556633;RPBZ=-1.47079;MQBZ=0.253876;MQSBZ=-0.461593;BQBZ=-1.68442;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255,51,255,255:18:1:0:12,5,0,1:17,1,0 0,21,183,21,183,183:7:0:0:6,1,0,0:7,0,0 0,24,231,24,231,231:8:0:0:4,4,0,0:8,0,0 +17 513 . A T,<*> 0 . DP=32;DPR=31,1,0;I16=21,10,1,0,1125,42283,12,144,1806,106610,60,3600,623,14249,15,225;QS=2.97966,0.020339,0;SGB=-0.556633;RPBZ=-1.24609;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.57376;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,37,255,48,255,255:17:1:0:11,5,1,0:16,1,0 0,21,177,21,177,177:7:0:0:6,1,0,0:7,0,0 0,24,233,24,233,233:8:0:0:4,4,0,0:8,0,0 +17 514 . A T,<*> 0 . DP=32;DPR=31,1,0;I16=22,9,0,1,1086,40204,16,256,1806,106610,60,3600,627,14381,11,121;QS=2.97127,0.0287253,0;SGB=-0.556633;RPBZ=-1.4628;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.46657;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,34,255,48,255,255:17:1:0:12,4,0,1:16,1,0 0,21,172,21,172,172:7:0:0:6,1,0,0:7,0,0 0,24,235,24,235,235:8:0:0:4,4,0,0:8,0,0 17 515 . C <*> 0 . DP=32;DPR=32,0;I16=22,10,0,0,1050,37704,0,0,1866,110210,0,0,638,14554,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:12,5,0,0:17,0 0,21,169:7:0:0:6,1,0,0:7,0 0,24,211:8:0:0:4,4,0,0:8,0 17 516 . C <*> 0 . DP=32;DPR=32,0;I16=22,10,0,0,1109,40651,0,0,1866,110210,0,0,637,14579,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:12,5,0,0:17,0 0,21,187:7:0:0:6,1,0,0:7,0 0,24,215:8:0:0:4,4,0,0:8,0 17 517 . T <*> 0 . DP=33;DPR=33,0;I16=23,10,0,0,1269,49995,0,0,1926,113810,0,0,636,14626,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:13,5,0,0:18,0 0,21,201:7:0:0:6,1,0,0:7,0 0,24,242:8:0:0:4,4,0,0:8,0 @@ -450,7 +449,7 @@ 17 520 . T <*> 0 . DP=36;DPR=36,0;I16=25,11,0,0,1243,45051,0,0,2106,124610,0,0,638,14818,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,63,255:21:0:0:15,6,0,0:21,0 0,21,180:7:0:0:6,1,0,0:7,0 0,24,223:8:0:0:4,4,0,0:8,0 17 521 . C <*> 0 . DP=34;DPR=34,0;I16=25,9,0,0,1281,49527,0,0,1986,117410,0,0,641,14875,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,60,255:20:0:0:15,5,0,0:20,0 0,21,191:7:0:0:6,1,0,0:7,0 0,21,204:7:0:0:4,3,0,0:7,0 17 522 . A <*> 0 . DP=32;DPR=32,0;I16=24,8,0,0,1158,43228,0,0,1897,112969,0,0,646,14960,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,60,255:20:0:0:15,5,0,0:20,0 0,21,185:7:0:0:6,1,0,0:7,0 0,15,170:5:0:0:3,2,0,0:5,0 -17 523 . T G,<*> 0 . DP=32;DPR=31,1,0;I16=23,8,1,0,1184,45708,15,225,1837,109369,60,3600,626,14446,25,625;QS=2.9794,0.0206044,0;SGB=-0.556633;RPBZ=1.13742;MQBZ=0.179605;MQSBZ=-1.73205;BQBZ=-1.68805;NMBZ=2.89159;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,44,255,57,255,255:20:1:0:14,5,1,0:19,1,0 0,21,191,21,191,191:7:0:0:6,1,0,0:7,0,0 0,15,166,15,166,166:5:0:0:3,2,0,0:5,0,0 +17 523 . T G,<*> 0 . DP=32;DPR=31,1,0;I16=23,8,1,0,1184,45708,15,225,1837,109369,60,3600,626,14446,25,625;QS=2.9794,0.0206044,0;SGB=-0.556633;RPBZ=1.13742;MQBZ=0.179605;MQSBZ=-1.73205;BQBZ=-1.68805;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,44,255,57,255,255:20:1:0:14,5,1,0:19,1,0 0,21,191,21,191,191:7:0:0:6,1,0,0:7,0,0 0,15,166,15,166,166:5:0:0:3,2,0,0:5,0,0 17 524 . T <*> 0 . DP=32;DPR=32,0;I16=24,8,0,0,1096,39618,0,0,1897,112969,0,0,654,15108,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,60,255:20:0:0:15,5,0,0:20,0 0,21,194:7:0:0:6,1,0,0:7,0 0,15,150:5:0:0:3,2,0,0:5,0 17 525 . G <*> 0 . DP=32;DPR=32,0;I16=24,8,0,0,1188,45718,0,0,1897,112969,0,0,656,15120,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,60,255:20:0:0:15,5,0,0:20,0 0,21,188:7:0:0:6,1,0,0:7,0 0,15,133:5:0:0:3,2,0,0:5,0 17 526 . C <*> 0 . DP=32;DPR=32,0;I16=24,8,0,0,1154,44014,0,0,1897,112969,0,0,658,15156,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,60,255:20:0:0:15,5,0,0:20,0 0,21,185:7:0:0:6,1,0,0:7,0 0,15,137:5:0:0:3,2,0,0:5,0 @@ -462,7 +461,7 @@ 17 532 . T <*> 0 . DP=32;DPR=32,0;I16=25,7,0,0,1161,43607,0,0,1897,112969,0,0,649,14477,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:15,4,0,0:19,0 0,21,181:7:0:0:6,1,0,0:7,0 0,18,192:6:0:0:4,2,0,0:6,0 17 533 . C <*> 0 . DP=32;DPR=32,0;I16=25,7,0,0,1154,44084,0,0,1897,112969,0,0,644,14274,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:15,4,0,0:19,0 0,21,178:7:0:0:6,1,0,0:7,0 0,18,180:6:0:0:4,2,0,0:6,0 17 534 . T <*> 0 . DP=31;DPR=31,0;I16=24,7,0,0,1222,49526,0,0,1837,109369,0,0,640,14104,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:14,4,0,0:18,0 0,21,205:7:0:0:6,1,0,0:7,0 0,18,205:6:0:0:4,2,0,0:6,0 -17 535 . A G,<*> 0 . DP=31;DPR=30,1,0;I16=24,6,0,1,1080,39870,8,64,1777,105769,60,3600,611,13341,25,625;QS=2.98623,0.0137694,0;SGB=-0.556633;RPBZ=-0.894788;MQBZ=0.182574;MQSBZ=-1.85164;BQBZ=-1.6854;NMBZ=2.94255;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,41,255,51,255,255:18:1:0:14,3,0,1:17,1,0 0,21,194,21,194,194:7:0:0:6,1,0,0:7,0,0 0,18,189,18,189,189:6:0:0:4,2,0,0:6,0,0 +17 535 . A G,<*> 0 . DP=31;DPR=30,1,0;I16=24,6,0,1,1080,39870,8,64,1777,105769,60,3600,611,13341,25,625;QS=2.98623,0.0137694,0;SGB=-0.556633;RPBZ=-0.894788;MQBZ=0.182574;MQSBZ=-1.85164;BQBZ=-1.6854;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,41,255,51,255,255:18:1:0:14,3,0,1:17,1,0 0,21,194,21,194,194:7:0:0:6,1,0,0:7,0,0 0,18,189,18,189,189:6:0:0:4,2,0,0:6,0,0 17 536 . C <*> 0 . DP=31;DPR=31,0;I16=24,7,0,0,1095,40551,0,0,1837,109369,0,0,631,13809,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:14,4,0,0:18,0 0,21,184:7:0:0:6,1,0,0:7,0 0,18,157:6:0:0:4,2,0,0:6,0 17 537 . C <*> 0 . DP=31;DPR=31,0;I16=24,7,0,0,1049,38677,0,0,1837,109369,0,0,626,13682,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:14,4,0,0:18,0 0,21,172:7:0:0:6,1,0,0:7,0 0,18,183:6:0:0:4,2,0,0:6,0 17 538 . A <*> 0 . DP=31;DPR=31,0;I16=24,7,0,0,1138,42478,0,0,1837,109369,0,0,620,13536,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:14,4,0,0:18,0 0,21,189:7:0:0:6,1,0,0:7,0 0,18,181:6:0:0:4,2,0,0:6,0 @@ -475,8 +474,8 @@ 17 545 . A <*> 0 . DP=33;DPR=33,0;I16=25,8,0,0,1197,44795,0,0,1926,113810,0,0,587,12951,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:14,5,0,0:19,0 0,24,196:8:0:0:7,1,0,0:8,0 0,18,184:6:0:0:4,2,0,0:6,0 17 546 . A <*> 0 . DP=32;DPR=32,0;I16=24,8,0,0,1136,41758,0,0,1866,110210,0,0,580,12802,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:14,5,0,0:19,0 0,21,166:7:0:0:6,1,0,0:7,0 0,18,193:6:0:0:4,2,0,0:6,0 17 547 . A <*> 0 . DP=32;DPR=32,0;I16=24,8,0,0,1159,43539,0,0,1866,110210,0,0,572,12634,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:14,5,0,0:19,0 0,21,180:7:0:0:6,1,0,0:7,0 0,18,195:6:0:0:4,2,0,0:6,0 -17 548 . A C,<*> 0 . DP=33;DPR=32,1,0;I16=23,9,1,0,1153,42673,9,81,1866,110210,60,3600,561,12489,3,9;QS=2.98607,0.0139319,0;SGB=-0.556633;RPBZ=1.57584;MQBZ=0.253876;MQSBZ=-2.34521;BQBZ=-1.68939;NMBZ=2.40838;SCBZ=3.80814;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,44,255,54,255,255:19:1:0:13,5,1,0:18,1,0 0,21,181,21,181,181:7:0:0:6,1,0,0:7,0,0 0,21,211,21,211,211:7:0:0:4,3,0,0:7,0,0 -17 549 . T G,<*> 0 . DP=32;DPR=31,1,0;I16=23,8,0,1,1135,42143,20,400,1806,106610,60,3600,532,11720,25,625;QS=2.96918,0.0308166,0;SGB=-0.556633;RPBZ=-0.487556;MQBZ=0.258065;MQSBZ=-2.29695;BQBZ=-1.68602;NMBZ=2.45062;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,34,255,51,255,255:18:1:0:13,4,0,1:17,1,0 0,21,168,21,168,168:7:0:0:6,1,0,0:7,0,0 0,21,208,21,208,208:7:0:0:4,3,0,0:7,0,0 +17 548 . A C,<*> 0 . DP=33;DPR=32,1,0;I16=23,9,1,0,1153,42673,9,81,1866,110210,60,3600,561,12489,3,9;QS=2.98607,0.0139319,0;SGB=-0.556633;RPBZ=1.57584;MQBZ=0.253876;MQSBZ=-2.34521;BQBZ=-1.68939;SCBZ=3.80814;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,44,255,54,255,255:19:1:0:13,5,1,0:18,1,0 0,21,181,21,181,181:7:0:0:6,1,0,0:7,0,0 0,21,211,21,211,211:7:0:0:4,3,0,0:7,0,0 +17 549 . T G,<*> 0 . DP=32;DPR=31,1,0;I16=23,8,0,1,1135,42143,20,400,1806,106610,60,3600,532,11720,25,625;QS=2.96918,0.0308166,0;SGB=-0.556633;RPBZ=-0.487556;MQBZ=0.258065;MQSBZ=-2.29695;BQBZ=-1.68602;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,34,255,51,255,255:18:1:0:13,4,0,1:17,1,0 0,21,168,21,168,168:7:0:0:6,1,0,0:7,0,0 0,21,208,21,208,208:7:0:0:4,3,0,0:7,0,0 17 550 . T <*> 0 . DP=32;DPR=32,0;I16=23,9,0,0,1056,37314,0,0,1866,110210,0,0,549,12177,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:13,5,0,0:18,0 0,21,150:7:0:0:6,1,0,0:7,0 0,21,220:7:0:0:4,3,0,0:7,0 17 551 . G <*> 0 . DP=31;DPR=31,0;I16=22,9,0,0,1121,41639,0,0,1806,106610,0,0,541,12045,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:12,5,0,0:17,0 0,21,172:7:0:0:6,1,0,0:7,0 0,21,208:7:0:0:4,3,0,0:7,0 17 552 . C <*> 0 . DP=30;DPR=30,0;I16=21,9,0,0,1093,41365,0,0,1746,103010,0,0,535,11947,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:11,5,0,0:16,0 0,21,167:7:0:0:6,1,0,0:7,0 0,21,208:7:0:0:4,3,0,0:7,0 @@ -486,14 +485,14 @@ 17 556 . C <*> 0 . DP=29;DPR=29,0;I16=20,9,0,0,1055,39195,0,0,1709,101641,0,0,509,11219,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:11,6,0,0:17,0 0,18,158:6:0:0:5,1,0,0:6,0 0,18,186:6:0:0:4,2,0,0:6,0 17 557 . A <*> 0 . DP=27;DPR=27,0;I16=18,9,0,0,987,36749,0,0,1589,94441,0,0,506,11074,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,45,255:15:0:0:9,6,0,0:15,0 0,18,157:6:0:0:5,1,0,0:6,0 0,18,186:6:0:0:4,2,0,0:6,0 17 558 . A <*> 0 . DP=27;DPR=27,0;I16=18,9,0,0,956,35872,0,0,1589,94441,0,0,502,10906,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,45,255:15:0:0:9,6,0,0:15,0 0,18,153:6:0:0:5,1,0,0:6,0 0,18,177:6:0:0:4,2,0,0:6,0 -17 559 . C A,<*> 0 . DP=27;DPR=26,1,0;I16=18,8,0,1,915,33775,14,196,1560,93600,29,841,473,10141,25,625;QS=2.92708,0.0729167,0;SGB=-0.556633;RPBZ=-1.02726;MQBZ=-5.09902;MQSBZ=-1.41421;BQBZ=-1.54776;NMBZ=3.05941;SCBZ=5.09902;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,45,255,45,255,255:15:0:0:9,6,0,0:15,0,0 0,4,116,15,119,123:6:1:0:5,0,0,1:5,1,0 0,18,169,18,169,169:6:0:0:4,2,0,0:6,0,0 +17 559 . C A,<*> 0 . DP=27;DPR=26,1,0;I16=18,8,0,1,915,33775,14,196,1560,93600,29,841,473,10141,25,625;QS=2.92708,0.0729167,0;SGB=-0.556633;RPBZ=-1.02726;MQBZ=-5.09902;MQSBZ=-1.41421;BQBZ=-1.54776;SCBZ=5.09902;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,45,255,45,255,255:15:0:0:9,6,0,0:15,0,0 0,4,116,15,119,123:6:1:0:5,0,0,1:5,1,0 0,18,169,18,169,169:6:0:0:4,2,0,0:6,0,0 17 560 . C <*> 0 . DP=28;DPR=28,0;I16=19,9,0,0,992,36552,0,0,1649,98041,0,0,494,10654,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,45,255:15:0:0:9,6,0,0:15,0 0,18,160:6:0:0:5,1,0,0:6,0 0,21,181:7:0:0:5,2,0,0:7,0 17 561 . A <*> 0 . DP=28;DPR=28,0;I16=19,9,0,0,973,35555,0,0,1649,98041,0,0,491,10571,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,45,255:15:0:0:9,6,0,0:15,0 0,18,158:6:0:0:5,1,0,0:6,0 0,21,194:7:0:0:5,2,0,0:7,0 17 562 . C <*> 0 . DP=28;DPR=28,0;I16=19,9,0,0,1014,38392,0,0,1649,98041,0,0,488,10518,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,45,255:15:0:0:9,6,0,0:15,0 0,18,153:6:0:0:5,1,0,0:6,0 0,21,187:7:0:0:5,2,0,0:7,0 17 563 . A <*> 0 . DP=27;DPR=27,0;I16=18,9,0,0,903,32513,0,0,1589,94441,0,0,485,10445,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,45,255:15:0:0:9,6,0,0:15,0 0,15,149:5:0:0:4,1,0,0:5,0 0,21,179:7:0:0:5,2,0,0:7,0 17 564 . C <*> 0 . DP=27;DPR=27,0;I16=18,9,0,0,859,28747,0,0,1589,94441,0,0,482,10402,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,45,255:15:0:0:9,6,0,0:15,0 0,15,121:5:0:0:4,1,0,0:5,0 0,21,182:7:0:0:5,2,0,0:7,0 17 565 . G <*> 0 . DP=30;DPR=30,0;I16=18,12,0,0,842,27104,0,0,1769,105241,0,0,479,10389,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:9,8,0,0:17,0 0,18,100:6:0:0:4,2,0,0:6,0 0,21,154:7:0:0:5,2,0,0:7,0 -17 566 . C A,<*> 0 . DP=29;DPR=28,1,0;I16=16,12,1,0,920,33998,9,81,1649,98041,60,3600,454,9734,25,625;QS=2.98321,0.016791,0;SGB=-0.556633;RPBZ=0.239193;MQBZ=0.188982;MQSBZ=-1.19024;BQBZ=-1.43942;NMBZ=-0.339233;SCBZ=-0.188982;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,38,255,48,255,255:17:1:0:8,8,1,0:16,1,0 0,15,155,15,155,155:5:0:0:3,2,0,0:5,0,0 0,21,170,21,170,170:7:0:0:5,2,0,0:7,0,0 +17 566 . C A,<*> 0 . DP=29;DPR=28,1,0;I16=16,12,1,0,920,33998,9,81,1649,98041,60,3600,454,9734,25,625;QS=2.98321,0.016791,0;SGB=-0.556633;RPBZ=0.239193;MQBZ=0.188982;MQSBZ=-1.19024;BQBZ=-1.43942;SCBZ=-0.188982;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,38,255,48,255,255:17:1:0:8,8,1,0:16,1,0 0,15,155,15,155,155:5:0:0:3,2,0,0:5,0,0 0,21,170,21,170,170:7:0:0:5,2,0,0:7,0,0 17 567 . C <*> 0 . DP=30;DPR=30,0;I16=17,13,0,0,956,34312,0,0,1769,105241,0,0,496,10638,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:9,8,0,0:17,0 0,18,156:6:0:0:3,3,0,0:6,0 0,21,194:7:0:0:5,2,0,0:7,0 17 568 . C <*> 0 . DP=29;DPR=29,0;I16=16,13,0,0,1060,40304,0,0,1709,101641,0,0,497,10663,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:8,8,0,0:16,0 0,18,179:6:0:0:3,3,0,0:6,0 0,21,193:7:0:0:5,2,0,0:7,0 17 569 . T <*> 0 . DP=30;DPR=29,0;I16=16,13,0,0,1061,41321,0,0,1709,101641,0,0,497,10671,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:8,8,0,0:16,0 0,18,190:6:0:0:3,3,0,0:6,0 0,21,213:7:0:0:5,2,0,0:7,0 @@ -501,15 +500,15 @@ 17 571 . C <*> 0 . DP=31;DPR=30,0;I16=17,13,0,0,1069,40739,0,0,1769,105241,0,0,497,10783,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:9,8,0,0:17,0 0,18,159:6:0:0:3,3,0,0:6,0 0,21,193:7:0:0:5,2,0,0:7,0 17 572 . A <*> 0 . DP=31;DPR=30,0;I16=18,12,0,0,1092,41268,0,0,1769,105241,0,0,499,10887,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:9,8,0,0:17,0 0,21,204:7:0:0:4,3,0,0:7,0 0,18,175:6:0:0:5,1,0,0:6,0 17 573 . A <*> 0 . DP=31;DPR=30,0;I16=18,12,0,0,1060,38698,0,0,1769,105241,0,0,501,10975,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:9,8,0,0:17,0 0,21,201:7:0:0:4,3,0,0:7,0 0,18,178:6:0:0:5,1,0,0:6,0 -17 574 . C A,<*> 0 . DP=31;DPR=29,1,0;I16=18,11,0,1,1088,41328,15,225,1740,104400,29,841,478,10422,25,625;QS=2.94071,0.0592885,0;SGB=-0.556633;RPBZ=-0.173514;MQBZ=-5.38516;MQSBZ=-1.22474;BQBZ=-1.68578;NMBZ=2.63996;SCBZ=3.60588;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255,48,255,255:16:0:0:8,8,0,0:16,0,0 0,9,170,21,173,177:8:1:0:5,2,0,1:7,1,0 0,18,173,18,173,173:6:0:0:5,1,0,0:6,0,0 -17 575 . T C,<*> 0 . DP=30;DPR=28,1,0;I16=17,11,0,1,1048,41548,9,81,1680,100800,29,841,480,10426,25,625;QS=2.96786,0.0321429,0;SGB=-0.556633;RPBZ=-0.119685;MQBZ=-5.2915;MQSBZ=-1.19024;BQBZ=-1.68121;NMBZ=2.59197;SCBZ=3.53589;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255,48,255,255:16:0:0:8,8,0,0:16,0,0 0,13,200,21,203,202:8:1:0:5,2,0,1:7,1,0 0,15,163,15,163,163:5:0:0:4,1,0,0:5,0,0 +17 574 . C A,<*> 0 . DP=31;DPR=29,1,0;I16=18,11,0,1,1088,41328,15,225,1740,104400,29,841,478,10422,25,625;QS=2.94071,0.0592885,0;SGB=-0.556633;RPBZ=-0.173514;MQBZ=-5.38516;MQSBZ=-1.22474;BQBZ=-1.68578;SCBZ=3.60588;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255,48,255,255:16:0:0:8,8,0,0:16,0,0 0,9,170,21,173,177:8:1:0:5,2,0,1:7,1,0 0,18,173,18,173,173:6:0:0:5,1,0,0:6,0,0 +17 575 . T C,<*> 0 . DP=30;DPR=28,1,0;I16=17,11,0,1,1048,41548,9,81,1680,100800,29,841,480,10426,25,625;QS=2.96786,0.0321429,0;SGB=-0.556633;RPBZ=-0.119685;MQBZ=-5.2915;MQSBZ=-1.19024;BQBZ=-1.68121;SCBZ=3.53589;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255,48,255,255:16:0:0:8,8,0,0:16,0,0 0,13,200,21,203,202:8:1:0:5,2,0,1:7,1,0 0,15,163,15,163,163:5:0:0:4,1,0,0:5,0,0 17 576 . G <*> 0 . DP=30;DPR=29,0;I16=17,12,0,0,1043,39581,0,0,1709,101641,0,0,507,11087,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:8,8,0,0:16,0 0,24,208:8:0:0:5,3,0,0:8,0 0,15,151:5:0:0:4,1,0,0:5,0 17 577 . G <*> 0 . DP=30;DPR=29,0;I16=17,12,0,0,997,37255,0,0,1709,101641,0,0,509,11155,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:8,8,0,0:16,0 0,24,204:8:0:0:5,3,0,0:8,0 0,15,146:5:0:0:4,1,0,0:5,0 17 578 . G <*> 0 . DP=29;DPR=29,0;I16=16,13,0,0,975,34803,0,0,1709,101641,0,0,520,11286,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:7,9,0,0:16,0 0,24,198:8:0:0:5,3,0,0:8,0 0,15,151:5:0:0:4,1,0,0:5,0 17 579 . G <*> 0 . DP=30;DPR=30,0;I16=16,14,0,0,1038,38820,0,0,1769,105241,0,0,523,11335,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:8,9,0,0:17,0 0,24,224:8:0:0:4,4,0,0:8,0 0,15,144:5:0:0:4,1,0,0:5,0 -17 580 . A C,<*> 0 . DP=30;DPR=29,1,0;I16=15,14,1,0,1060,39178,16,256,1709,101641,60,3600,510,11078,17,289;QS=2.97338,0.0266223,0;SGB=-0.556633;RPBZ=1.32953;MQBZ=0.185695;MQSBZ=-1.06904;BQBZ=-1.69093;NMBZ=1.86885;SCBZ=-0.267102;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,34,255,48,255,255:17:1:0:7,9,1,0:16,1,0 0,24,221,24,221,221:8:0:0:4,4,0,0:8,0,0 0,15,155,15,155,155:5:0:0:4,1,0,0:5,0,0 +17 580 . A C,<*> 0 . DP=30;DPR=29,1,0;I16=15,14,1,0,1060,39178,16,256,1709,101641,60,3600,510,11078,17,289;QS=2.97338,0.0266223,0;SGB=-0.556633;RPBZ=1.32953;MQBZ=0.185695;MQSBZ=-1.06904;BQBZ=-1.69093;SCBZ=-0.267102;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,34,255,48,255,255:17:1:0:7,9,1,0:16,1,0 0,24,221,24,221,221:8:0:0:4,4,0,0:8,0,0 0,15,155,15,155,155:5:0:0:4,1,0,0:5,0,0 17 581 . A <*> 0 . DP=31;DPR=31,0;I16=16,15,0,0,1083,39215,0,0,1829,108841,0,0,530,11384,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:8,10,0,0:18,0 0,24,223:8:0:0:4,4,0,0:8,0 0,15,153:5:0:0:4,1,0,0:5,0 -17 582 . C G,<*> 0 . DP=31;DPR=30,1,0;I16=15,15,1,0,1080,39870,8,64,1769,105241,60,3600,519,11211,15,225;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.34259;MQBZ=0.182574;MQSBZ=-1.0328;BQBZ=-1.68266;NMBZ=1.92049;SCBZ=-0.262467;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,41,255,51,255,255:18:1:0:7,10,1,0:17,1,0 0,24,207,24,207,207:8:0:0:4,4,0,0:8,0,0 0,15,151,15,151,151:5:0:0:4,1,0,0:5,0,0 +17 582 . C G,<*> 0 . DP=31;DPR=30,1,0;I16=15,15,1,0,1080,39870,8,64,1769,105241,60,3600,519,11211,15,225;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.34259;MQBZ=0.182574;MQSBZ=-1.0328;BQBZ=-1.68266;SCBZ=-0.262467;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,41,255,51,255,255:18:1:0:7,10,1,0:17,1,0 0,24,207,24,207,207:8:0:0:4,4,0,0:8,0,0 0,15,151,15,151,151:5:0:0:4,1,0,0:5,0,0 17 583 . T <*> 0 . DP=30;DPR=30,0;I16=16,14,0,0,1135,43913,0,0,1769,105241,0,0,539,11523,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:8,9,0,0:17,0 0,24,238:8:0:0:4,4,0,0:8,0 0,15,163:5:0:0:4,1,0,0:5,0 17 584 . C <*> 0 . DP=31;DPR=31,0;I16=17,14,0,0,1069,39521,0,0,1798,106082,0,0,544,11644,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:9,9,0,0:18,0 0,24,209:8:0:0:4,4,0,0:8,0 0,15,157:5:0:0:4,1,0,0:5,0 17 585 . A <*> 0 . DP=31;DPR=31,0;I16=17,14,0,0,1096,39866,0,0,1798,106082,0,0,549,11751,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:9,9,0,0:18,0 0,24,211:8:0:0:4,4,0,0:8,0 0,15,157:5:0:0:4,1,0,0:5,0 @@ -520,10 +519,10 @@ 17 590 . C <*> 0 . DP=32;DPR=32,0;I16=17,15,0,0,1103,41355,0,0,1858,109682,0,0,574,12576,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:9,9,0,0:18,0 0,24,194:8:0:0:4,4,0,0:8,0 0,18,175:6:0:0:4,2,0,0:6,0 17 591 . A <*> 0 . DP=31;DPR=31,0;I16=16,15,0,0,1164,44088,0,0,1798,106082,0,0,579,12695,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:9,9,0,0:18,0 0,21,209:7:0:0:3,4,0,0:7,0 0,18,188:6:0:0:4,2,0,0:6,0 17 592 . A <*> 0 . DP=31;DPR=31,0;I16=16,15,0,0,1121,42193,0,0,1798,106082,0,0,583,12795,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:9,9,0,0:18,0 0,21,215:7:0:0:3,4,0,0:7,0 0,18,182:6:0:0:4,2,0,0:6,0 -17 593 . C A,<*> 0 . DP=31;DPR=30,1,0;I16=16,14,0,1,1071,39925,7,49,1769,105241,29,841,561,12253,25,625;QS=2.97021,0.0297872,0;SGB=-0.556633;RPBZ=0.559355;MQBZ=-3.80789;MQSBZ=-0.0464238;BQBZ=-1.57464;NMBZ=2.13779;SCBZ=3.67454;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255,54,255,255:18:0:0:9,9,0,0:18,0,0 0,12,184,18,187,185:7:1:0:3,3,0,1:6,1,0 0,18,174,18,174,174:6:0:0:4,2,0,0:6,0,0 -17 594 . A G,<*> 0 . DP=33;DPR=32,1,0;I16=16,16,1,0,1161,42757,4,16,1858,109682,60,3600,572,12672,15,225;QS=2.99359,0.00641026,0;SGB=-0.556633;RPBZ=-0.998367;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68954;NMBZ=1.76408;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,42,255,51,255,255:18:1:0:8,9,1,0:17,1,0 0,21,205,21,205,205:7:0:0:3,4,0,0:7,0,0 0,24,213,24,213,213:8:0:0:5,3,0,0:8,0,0 +17 593 . C A,<*> 0 . DP=31;DPR=30,1,0;I16=16,14,0,1,1071,39925,7,49,1769,105241,29,841,561,12253,25,625;QS=2.97021,0.0297872,0;SGB=-0.556633;RPBZ=0.559355;MQBZ=-3.80789;MQSBZ=-0.0464238;BQBZ=-1.57464;SCBZ=3.67454;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255,54,255,255:18:0:0:9,9,0,0:18,0,0 0,12,184,18,187,185:7:1:0:3,3,0,1:6,1,0 0,18,174,18,174,174:6:0:0:4,2,0,0:6,0,0 +17 594 . A G,<*> 0 . DP=33;DPR=32,1,0;I16=16,16,1,0,1161,42757,4,16,1858,109682,60,3600,572,12672,15,225;QS=2.99359,0.00641026,0;SGB=-0.556633;RPBZ=-0.998367;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68954;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,42,255,51,255,255:18:1:0:8,9,1,0:17,1,0 0,21,205,21,205,205:7:0:0:3,4,0,0:7,0,0 0,24,213,24,213,213:8:0:0:5,3,0,0:8,0,0 17 595 . A <*> 0 . DP=33;DPR=33,0;I16=17,16,0,0,1136,40412,0,0,1918,113282,0,0,589,12905,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:9,9,0,0:18,0 0,21,198:7:0:0:3,4,0,0:7,0 0,24,218:8:0:0:5,3,0,0:8,0 -17 596 . A G,<*> 0 . DP=33;DPR=32,1,0;I16=16,16,1,0,1061,37187,8,64,1858,109682,60,3600,590,12952,1,1;QS=2.98564,0.0143627,0;SGB=-0.556633;RPBZ=1.68146;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68357;NMBZ=1.61602;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,41,255,51,255,255:18:1:0:8,9,1,0:17,1,0 0,21,169,21,169,169:7:0:0:3,4,0,0:7,0,0 0,24,231,24,231,231:8:0:0:5,3,0,0:8,0,0 +17 596 . A G,<*> 0 . DP=33;DPR=32,1,0;I16=16,16,1,0,1061,37187,8,64,1858,109682,60,3600,590,12952,1,1;QS=2.98564,0.0143627,0;SGB=-0.556633;RPBZ=1.68146;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68357;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,41,255,51,255,255:18:1:0:8,9,1,0:17,1,0 0,21,169,21,169,169:7:0:0:3,4,0,0:7,0,0 0,24,231,24,231,231:8:0:0:5,3,0,0:8,0,0 17 597 . C <*> 0 . DP=33;DPR=33,0;I16=17,16,0,0,1196,44890,0,0,1918,113282,0,0,592,12990,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:9,9,0,0:18,0 0,21,204:7:0:0:3,4,0,0:7,0 0,24,220:8:0:0:5,3,0,0:8,0 17 598 . T <*> 0 . DP=33;DPR=33,0;I16=16,17,0,0,1219,47333,0,0,1918,113282,0,0,597,13029,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:8,9,0,0:17,0 0,21,217:7:0:0:3,4,0,0:7,0 0,27,242:9:0:0:5,4,0,0:9,0 17 599 . T <*> 0 . DP=33;DPR=33,0;I16=16,17,0,0,1182,43598,0,0,1918,113282,0,0,599,13095,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:8,9,0,0:17,0 0,21,197:7:0:0:3,4,0,0:7,0 0,27,247:9:0:0:5,4,0,0:9,0 diff --git a/test/mpileup/mpileup.5.out b/test/mpileup/mpileup.5.out index da1c3b892..5dcfa01ca 100644 --- a/test/mpileup/mpileup.5.out +++ b/test/mpileup/mpileup.5.out @@ -11,7 +11,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -31,29 +30,29 @@ 17 100 . C <*> 0 . DP=18;ADF=16,0;ADR=1,0;AD=17,0;I16=16,1,0,0,672,27586,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,189:9:0:9,0:0,0:9,0 0,9,118:3:0:2,0:1,0:3,0 0,15,134:5:0:5,0:0,0:5,0 17 101 . C <*> 0 . DP=18;ADF=16,0;ADR=1,0;AD=17,0;I16=16,1,0,0,630,24730,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,182:9:0:9,0:0,0:9,0 0,9,108:3:0:2,0:1,0:3,0 0,15,132:5:0:5,0:0,0:5,0 17 102 . C <*> 0 . DP=18;ADF=16,0;ADR=1,0;AD=17,0;I16=16,1,0,0,676,27812,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,188:9:0:9,0:0,0:9,0 0,9,121:3:0:2,0:1,0:3,0 0,15,139:5:0:5,0:0,0:5,0 -17 103 . T C,<*> 0 . DP=18;ADF=15,1,0;ADR=1,0,0;AD=16,1,0;I16=15,1,1,0,668,28542,6,36,929,54841,29,841,323,7035,6,36;QS=2.98256,0.0174419,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64924;NMBZ=2.45514;SCBZ=4;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,17,184,24,187,185:9:0:8,1,0:0,0,0:8,1,0 0,9,118,9,118,118:3:0:2,0,0:1,0,0:3,0,0 0,15,147,15,147,147:5:0:5,0,0:0,0,0:5,0,0 -17 104 . G C,<*> 0 . DP=18;ADF=15,1,0;ADR=1,0,0;AD=16,1,0;I16=15,1,1,0,601,24163,3,9,929,54841,29,841,320,6884,7,49;QS=2.98726,0.0127389,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64309;NMBZ=2.45514;SCBZ=4;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,173,24,176,173:9:0:8,1,0:0,0,0:8,1,0 0,9,101,9,101,101:3:0:2,0,0:1,0,0:3,0,0 0,15,133,15,133,133:5:0:5,0,0:0,0,0:5,0,0 +17 103 . T C,<*> 0 . DP=18;ADF=15,1,0;ADR=1,0,0;AD=16,1,0;I16=15,1,1,0,668,28542,6,36,929,54841,29,841,323,7035,6,36;QS=2.98256,0.0174419,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64924;SCBZ=4;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,17,184,24,187,185:9:0:8,1,0:0,0,0:8,1,0 0,9,118,9,118,118:3:0:2,0,0:1,0,0:3,0,0 0,15,147,15,147,147:5:0:5,0,0:0,0,0:5,0,0 +17 104 . G C,<*> 0 . DP=18;ADF=15,1,0;ADR=1,0,0;AD=16,1,0;I16=15,1,1,0,601,24163,3,9,929,54841,29,841,320,6884,7,49;QS=2.98726,0.0127389,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64309;SCBZ=4;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,173,24,176,173:9:0:8,1,0:0,0,0:8,1,0 0,9,101,9,101,101:3:0:2,0,0:1,0,0:3,0,0 0,15,133,15,133,133:5:0:5,0,0:0,0,0:5,0,0 17 105 . G <*> 0 . DP=19;ADF=17,0;ADR=1,0;AD=18,0;I16=17,1,0,0,603,22351,0,0,1018,59282,0,0,325,6815,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,171:10:0:10,0:0,0:10,0 0,9,106:3:0:2,0:1,0:3,0 0,15,125:5:0:5,0:0,0:5,0 17 106 . G <*> 0 . DP=19;ADF=17,0;ADR=1,0;AD=18,0;I16=17,1,0,0,636,25058,0,0,1018,59282,0,0,324,6718,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,190:10:0:10,0:0,0:10,0 0,9,92:3:0:2,0:1,0:3,0 0,15,124:5:0:5,0:0,0:5,0 17 107 . C <*> 0 . DP=19;ADF=17,0;ADR=1,0;AD=18,0;I16=17,1,0,0,686,27952,0,0,1018,59282,0,0,323,6643,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,192:10:0:10,0:0,0:10,0 0,9,119:3:0:2,0:1,0:3,0 0,15,136:5:0:5,0:0,0:5,0 17 108 . C <*> 0 . DP=19;ADF=17,0;ADR=1,0;AD=18,0;I16=17,1,0,0,681,27429,0,0,1018,59282,0,0,322,6590,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,190:10:0:10,0:0,0:10,0 0,9,119:3:0:2,0:1,0:3,0 0,15,135:5:0:5,0:0,0:5,0 -17 109 . T C,<*> 0 . DP=19;ADF=16,1,0;ADR=1,0,0;AD=17,1,0;I16=16,1,1,0,716,30648,2,4,989,58441,29,841,309,6415,12,144;QS=2.98922,0.0107817,0;SGB=-0.556633;RPBZ=-0.674966;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.6661;NMBZ=2.52179;SCBZ=3;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,20,191,27,194,191:10:0:9,1,0:0,0,0:9,1,0 0,9,120,9,120,120:3:0:2,0,0:1,0,0:3,0,0 0,15,150,15,150,150:5:0:5,0,0:0,0,0:5,0,0 +17 109 . T C,<*> 0 . DP=19;ADF=16,1,0;ADR=1,0,0;AD=17,1,0;I16=16,1,1,0,716,30648,2,4,989,58441,29,841,309,6415,12,144;QS=2.98922,0.0107817,0;SGB=-0.556633;RPBZ=-0.674966;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.6661;SCBZ=3;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,20,191,27,194,191:10:0:9,1,0:0,0,0:9,1,0 0,9,120,9,120,120:3:0:2,0,0:1,0,0:3,0,0 0,15,150,15,150,150:5:0:5,0,0:0,0,0:5,0,0 17 110 . G <*> 0 . DP=19;ADF=17,0;ADR=1,0;AD=18,0;I16=17,1,0,0,688,28036,0,0,1018,59282,0,0,320,6550,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,194:10:0:10,0:0,0:10,0 0,9,113:3:0:2,0:1,0:3,0 0,15,136:5:0:5,0:0,0:5,0 17 111 . G <*> 0 . DP=19;ADF=17,0;ADR=1,0;AD=18,0;I16=17,1,0,0,573,21453,0,0,1018,59282,0,0,318,6514,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,167:10:0:10,0:0,0:10,0 0,9,95:3:0:2,0:1,0:3,0 0,15,119:5:0:5,0:0,0:5,0 -17 112 . C G,<*> 0 . DP=19;ADF=16,1,0;ADR=1,0,0;AD=17,1,0;I16=16,1,1,0,657,26565,2,4,989,58441,29,841,301,6277,15,225;QS=2.98907,0.010929,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65292;NMBZ=2.52179;SCBZ=3;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,20,187,27,190,187:10:0:9,1,0:0,0,0:9,1,0 0,9,103,9,103,103:3:0:2,0,0:1,0,0:3,0,0 0,15,135,15,135,135:5:0:5,0,0:0,0,0:5,0,0 -17 113 . A G,<*> 0 . DP=19;ADF=16,1,0;ADR=1,0,0;AD=17,1,0;I16=16,1,1,0,635,25055,4,16,989,58441,29,841,297,6207,16,256;QS=2.98817,0.0118343,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65205;NMBZ=2.52179;SCBZ=3;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,20,172,27,175,172:10:0:9,1,0:0,0,0:9,1,0 0,9,102,9,102,102:3:0:2,0,0:1,0,0:3,0,0 0,15,139,15,139,139:5:0:5,0,0:0,0,0:5,0,0 +17 112 . C G,<*> 0 . DP=19;ADF=16,1,0;ADR=1,0,0;AD=17,1,0;I16=16,1,1,0,657,26565,2,4,989,58441,29,841,301,6277,15,225;QS=2.98907,0.010929,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65292;SCBZ=3;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,20,187,27,190,187:10:0:9,1,0:0,0,0:9,1,0 0,9,103,9,103,103:3:0:2,0,0:1,0,0:3,0,0 0,15,135,15,135,135:5:0:5,0,0:0,0,0:5,0,0 +17 113 . A G,<*> 0 . DP=19;ADF=16,1,0;ADR=1,0,0;AD=17,1,0;I16=16,1,1,0,635,25055,4,16,989,58441,29,841,297,6207,16,256;QS=2.98817,0.0118343,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65205;SCBZ=3;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,20,172,27,175,172:10:0:9,1,0:0,0,0:9,1,0 0,9,102,9,102,102:3:0:2,0,0:1,0,0:3,0,0 0,15,139,15,139,139:5:0:5,0,0:0,0,0:5,0,0 17 114 . C <*> 0 . DP=19;ADF=17,0;ADR=1,0;AD=18,0;I16=17,1,0,0,660,25876,0,0,1018,59282,0,0,310,6446,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,181:10:0:10,0:0,0:10,0 0,9,113:3:0:2,0:1,0:3,0 0,15,133:5:0:5,0:0,0:5,0 -17 115 . C A,<*> 0 . DP=21;ADF=17,1,0;ADR=2,0,0;AD=19,1,0;I16=17,2,1,0,688,27426,12,144,1078,62882,29,841,283,5827,25,625;QS=2.88785,0.11215,0;SGB=-0.556633;RPBZ=0.260329;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.47798;NMBZ=2.3712;SCBZ=-0.418446;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,189,30,189,189:10:0:10,0,0:0,0,0:10,0,0 3,0,86,9,89,93:3:0:1,1,0:1,0,0:2,1,0 0,21,153,21,153,153:7:0:6,0,0:1,0,0:7,0,0 -17 116 . A C,<*> 0 . DP=21;ADF=17,1,0;ADR=2,0,0;AD=19,1,0;I16=17,2,1,0,705,27791,2,4,1078,62882,29,841,287,6073,19,361;QS=2.98873,0.0112676,0;SGB=-0.556633;RPBZ=0.0867763;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.65814;NMBZ=2.65016;SCBZ=2.65016;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,20,179,27,182,179:10:0:9,1,0:0,0,0:9,1,0 0,9,102,9,102,102:3:0:2,0,0:1,0,0:3,0,0 0,21,175,21,175,175:7:0:6,0,0:1,0,0:7,0,0 +17 115 . C A,<*> 0 . DP=21;ADF=17,1,0;ADR=2,0,0;AD=19,1,0;I16=17,2,1,0,688,27426,12,144,1078,62882,29,841,283,5827,25,625;QS=2.88785,0.11215,0;SGB=-0.556633;RPBZ=0.260329;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.47798;SCBZ=-0.418446;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,189,30,189,189:10:0:10,0,0:0,0,0:10,0,0 3,0,86,9,89,93:3:0:1,1,0:1,0,0:2,1,0 0,21,153,21,153,153:7:0:6,0,0:1,0,0:7,0,0 +17 116 . A C,<*> 0 . DP=21;ADF=17,1,0;ADR=2,0,0;AD=19,1,0;I16=17,2,1,0,705,27791,2,4,1078,62882,29,841,287,6073,19,361;QS=2.98873,0.0112676,0;SGB=-0.556633;RPBZ=0.0867763;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.65814;SCBZ=2.65016;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,20,179,27,182,179:10:0:9,1,0:0,0,0:9,1,0 0,9,102,9,102,102:3:0:2,0,0:1,0,0:3,0,0 0,21,175,21,175,175:7:0:6,0,0:1,0,0:7,0,0 17 117 . G <*> 0 . DP=21;ADF=18,0;ADR=2,0;AD=20,0;I16=18,2,0,0,715,28045,0,0,1107,63723,0,0,304,6444,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,185:10:0:10,0:0,0:10,0 0,9,97:3:0:2,0:1,0:3,0 0,21,177:7:0:6,0:1,0:7,0 17 118 . G <*> 0 . DP=20;ADF=17,0;ADR=2,0;AD=19,0;I16=17,2,0,0,620,23470,0,0,1047,60123,0,0,303,6481,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,175:9:0:9,0:0,0:9,0 0,9,65:3:0:2,0:1,0:3,0 0,21,162:7:0:6,0:1,0:7,0 17 119 . G <*> 0 . DP=19;ADF=16,0;ADR=2,0;AD=18,0;I16=16,2,0,0,619,23459,0,0,987,56523,0,0,301,6493,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,176:9:0:9,0:0,0:9,0 0,6,76:2:0:1,0:1,0:2,0 0,21,160:7:0:6,0:1,0:7,0 -17 120 . A G,<*> 0 . DP=19;ADF=15,1,0;ADR=2,0,0;AD=17,1,0;I16=15,2,1,0,646,25392,4,16,958,55682,29,841,277,5999,23,529;QS=2.9873,0.0126984,0;SGB=-0.556633;RPBZ=0.28942;MQBZ=-2.23607;MQSBZ=-1.30384;BQBZ=-1.6486;NMBZ=3;SCBZ=3;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,171,24,174,171:9:0:8,1,0:0,0,0:8,1,0 0,6,88,6,88,88:2:0:1,0,0:1,0,0:2,0,0 0,21,171,21,171,171:7:0:6,0,0:1,0,0:7,0,0 +17 120 . A G,<*> 0 . DP=19;ADF=15,1,0;ADR=2,0,0;AD=17,1,0;I16=15,2,1,0,646,25392,4,16,958,55682,29,841,277,5999,23,529;QS=2.9873,0.0126984,0;SGB=-0.556633;RPBZ=0.28942;MQBZ=-2.23607;MQSBZ=-1.30384;BQBZ=-1.6486;SCBZ=3;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,171,24,174,171:9:0:8,1,0:0,0,0:8,1,0 0,6,88,6,88,88:2:0:1,0,0:1,0,0:2,0,0 0,21,171,21,171,171:7:0:6,0,0:1,0,0:7,0,0 17 121 . G <*> 0 . DP=19;ADF=16,0;ADR=2,0;AD=18,0;I16=16,2,0,0,650,25148,0,0,987,56523,0,0,298,6534,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,181:9:0:9,0:0,0:9,0 0,6,84:2:0:1,0:1,0:2,0 0,21,168:7:0:6,0:1,0:7,0 17 122 . C <*> 0 . DP=20;ADF=17,0;ADR=2,0;AD=19,0;I16=17,2,0,0,696,27784,0,0,1047,60123,0,0,296,6560,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,180:9:0:9,0:0,0:9,0 0,9,107:3:0:2,0:1,0:3,0 0,21,178:7:0:6,0:1,0:7,0 17 123 . T <*> 0 . DP=18;ADF=15,0;ADR=2,0;AD=17,0;I16=15,2,0,0,647,26145,0,0,927,52923,0,0,296,6554,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,24,170:8:0:8,0:0,0:8,0 0,9,123:3:0:2,0:1,0:3,0 0,18,166:6:0:5,0:1,0:6,0 17 124 . T <*> 0 . DP=19;ADF=16,0;ADR=2,0;AD=18,0;I16=16,2,0,0,606,22002,0,0,987,56523,0,0,296,6564,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,154:9:0:9,0:0,0:9,0 0,9,114:3:0:2,0:1,0:3,0 0,18,154:6:0:5,0:1,0:6,0 -17 125 . A T,<*> 0 . DP=18;ADF=14,1,0;ADR=2,0,0;AD=16,1,0;I16=14,2,1,0,589,22565,4,16,898,52082,29,841,272,5916,25,625;QS=2.98444,0.0155642,0;SGB=-0.556633;RPBZ=1.02125;MQBZ=-2.16025;MQSBZ=-1.23956;BQBZ=-1.64106;NMBZ=2.91548;SCBZ=2.91548;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,15,149,21,152,149:8:0:7,1,0:0,0,0:7,1,0 0,9,114,9,114,114:3:0:2,0,0:1,0,0:3,0,0 0,18,162,18,162,162:6:0:5,0,0:1,0,0:6,0,0 +17 125 . A T,<*> 0 . DP=18;ADF=14,1,0;ADR=2,0,0;AD=16,1,0;I16=14,2,1,0,589,22565,4,16,898,52082,29,841,272,5916,25,625;QS=2.98444,0.0155642,0;SGB=-0.556633;RPBZ=1.02125;MQBZ=-2.16025;MQSBZ=-1.23956;BQBZ=-1.64106;SCBZ=2.91548;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,15,149,21,152,149:8:0:7,1,0:0,0,0:7,1,0 0,9,114,9,114,114:3:0:2,0,0:1,0,0:3,0,0 0,18,162,18,162,162:6:0:5,0,0:1,0,0:6,0,0 17 126 . A <*> 0 . DP=18;ADF=15,0;ADR=2,0;AD=17,0;I16=15,2,0,0,629,24725,0,0,927,52923,0,0,298,6536,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,24,162:8:0:8,0:0,0:8,0 0,9,117:3:0:2,0:1,0:3,0 0,18,174:6:0:5,0:1,0:6,0 17 127 . C <*> 0 . DP=18;ADF=15,0;ADR=2,0;AD=17,0;I16=15,2,0,0,627,24331,0,0,927,52923,0,0,299,6549,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,24,163:8:0:8,0:0,0:8,0 0,9,119:3:0:2,0:1,0:3,0 0,18,160:6:0:5,0:1,0:6,0 17 128 . A <*> 0 . DP=18;ADF=15,0;ADR=2,0;AD=17,0;I16=15,2,0,0,660,26364,0,0,927,52923,0,0,300,6580,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,24,169:8:0:8,0:0,0:8,0 0,9,121:3:0:2,0:1,0:3,0 0,18,168:6:0:5,0:1,0:6,0 @@ -87,7 +86,7 @@ 17 156 . C <*> 0 . DP=14;ADF=12,0;ADR=2,0;AD=14,0;I16=12,2,0,0,536,20884,0,0,809,47641,0,0,266,5934,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,163:7:0:7,0:0,0:7,0 0,6,84:2:0:1,0:1,0:2,0 0,15,150:5:0:4,0:1,0:5,0 17 157 . C <*> 0 . DP=14;ADF=12,0;ADR=2,0;AD=14,0;I16=12,2,0,0,555,22081,0,0,809,47641,0,0,264,5904,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,169:7:0:7,0:0,0:7,0 0,6,85:2:0:1,0:1,0:2,0 0,15,149:5:0:4,0:1,0:5,0 17 158 . T <*> 0 . DP=14;ADF=12,0;ADR=2,0;AD=14,0;I16=12,2,0,0,568,23154,0,0,809,47641,0,0,262,5886,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,170:7:0:7,0:0,0:7,0 0,6,84:2:0:1,0:1,0:2,0 0,15,159:5:0:4,0:1,0:5,0 -17 159 . A G,<*> 0 . DP=15;ADF=12,1,0;ADR=2,0,0;AD=14,1,0;I16=12,2,1,0,519,19467,5,25,809,47641,60,3600,260,5880,0,0;QS=2.97076,0.0292398,0;SGB=-0.556633;RPBZ=-1.62019;MQBZ=0.267261;MQSBZ=-2.54951;BQBZ=-1.63041;NMBZ=0;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,157,21,157,157:7:0:7,0,0:0,0,0:7,0,0 0,6,83,6,83,83:2:0:1,0,0:1,0,0:2,0,0 0,10,129,15,132,129:6:0:4,1,0:1,0,0:5,1,0 +17 159 . A G,<*> 0 . DP=15;ADF=12,1,0;ADR=2,0,0;AD=14,1,0;I16=12,2,1,0,519,19467,5,25,809,47641,60,3600,260,5880,0,0;QS=2.97076,0.0292398,0;SGB=-0.556633;RPBZ=-1.62019;MQBZ=0.267261;MQSBZ=-2.54951;BQBZ=-1.63041;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,157,21,157,157:7:0:7,0,0:0,0,0:7,0,0 0,6,83,6,83,83:2:0:1,0,0:1,0,0:2,0,0 0,10,129,15,132,129:6:0:4,1,0:1,0,0:5,1,0 17 160 . G <*> 0 . DP=15;ADF=13,0;ADR=2,0;AD=15,0;I16=13,2,0,0,547,20633,0,0,869,51241,0,0,259,5887,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,165:7:0:7,0:0,0:7,0 0,6,85:2:0:1,0:1,0:2,0 0,18,139:6:0:5,0:1,0:6,0 17 161 . A <*> 0 . DP=15;ADF=13,0;ADR=2,0;AD=15,0;I16=13,2,0,0,568,21610,0,0,869,51241,0,0,258,5908,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,157:7:0:7,0:0,0:7,0 0,6,83:2:0:1,0:1,0:2,0 0,18,162:6:0:5,0:1,0:6,0 17 162 . A <*> 0 . DP=15;ADF=13,0;ADR=2,0;AD=15,0;I16=13,2,0,0,558,21206,0,0,869,51241,0,0,255,5843,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,147:7:0:7,0:0,0:7,0 0,6,87:2:0:1,0:1,0:2,0 0,18,167:6:0:5,0:1,0:6,0 @@ -118,7 +117,7 @@ 17 187 . C <*> 0 . DP=14;ADF=13,0;ADR=1,0;AD=14,0;I16=13,1,0,0,511,18979,0,0,809,47641,0,0,266,5952,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,147:6:0:6,0:0,0:6,0 0,3,38:1:0:1,0:0,0:1,0 0,21,172:7:0:6,0:1,0:7,0 17 188 . C <*> 0 . DP=14;ADF=13,0;ADR=1,0;AD=14,0;I16=13,1,0,0,496,18042,0,0,809,47641,0,0,267,5989,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,147:6:0:6,0:0,0:6,0 0,3,37:1:0:1,0:0,0:1,0 0,21,162:7:0:6,0:1,0:7,0 17 189 . C <*> 0 . DP=15;ADF=13,0;ADR=2,0;AD=15,0;I16=13,2,0,0,552,20504,0,0,838,48482,0,0,268,6040,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,152:6:0:6,0:0,0:6,0 0,6,67:2:0:1,0:1,0:2,0 0,21,167:7:0:6,0:1,0:7,0 -17 190 . A C,<*> 0 . DP=15;ADF=12,1,0;ADR=2,0,0;AD=14,1,0;I16=12,2,1,0,500,18230,5,25,778,44882,60,3600,243,5381,25,625;QS=2.97664,0.0233645,0;SGB=-0.556633;RPBZ=0;MQBZ=0.392232;MQSBZ=-3.74166;BQBZ=-1.63041;NMBZ=-0.267261;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,138,18,138,138:6:0:6,0,0:0,0,0:6,0,0 0,6,68,6,68,68:2:0:1,0,0:1,0,0:2,0,0 0,12,153,18,156,153:7:0:5,1,0:1,0,0:6,1,0 +17 190 . A C,<*> 0 . DP=15;ADF=12,1,0;ADR=2,0,0;AD=14,1,0;I16=12,2,1,0,500,18230,5,25,778,44882,60,3600,243,5381,25,625;QS=2.97664,0.0233645,0;SGB=-0.556633;RPBZ=0;MQBZ=0.392232;MQSBZ=-3.74166;BQBZ=-1.63041;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,138,18,138,138:6:0:6,0,0:0,0,0:6,0,0 0,6,68,6,68,68:2:0:1,0,0:1,0,0:2,0,0 0,12,153,18,156,153:7:0:5,1,0:1,0,0:6,1,0 17 191 . T <*> 0 . DP=15;ADF=13,0;ADR=2,0;AD=15,0;I16=13,2,0,0,534,19276,0,0,838,48482,0,0,267,5939,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,143:6:0:6,0:0,0:6,0 0,6,67:2:0:1,0:1,0:2,0 0,21,169:7:0:6,0:1,0:7,0 17 192 . G <*> 0 . DP=15;ADF=13,0;ADR=2,0;AD=15,0;I16=13,2,0,0,499,17439,0,0,838,48482,0,0,266,5890,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,143:6:0:6,0:0,0:6,0 0,6,67:2:0:1,0:1,0:2,0 0,21,151:7:0:6,0:1,0:7,0 17 193 . T <*> 0 . DP=15;ADF=13,0;ADR=2,0;AD=15,0;I16=13,2,0,0,505,17811,0,0,838,48482,0,0,265,5859,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,140:6:0:6,0:0,0:6,0 0,6,63:2:0:1,0:1,0:2,0 0,21,157:7:0:6,0:1,0:7,0 @@ -151,10 +150,10 @@ 17 220 . G <*> 0 . DP=14;ADF=11,0;ADR=3,0;AD=14,0;I16=11,3,0,0,495,18407,0,0,747,42123,0,0,267,6079,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,188:7:0:6,0:1,0:7,0 0,9,88:3:0:1,0:2,0:3,0 0,12,84:4:0:4,0:0,0:4,0 17 221 . A <*> 0 . DP=14;ADF=11,0;ADR=3,0;AD=14,0;I16=11,3,0,0,488,17688,0,0,747,42123,0,0,267,6135,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,176:7:0:6,0:1,0:7,0 0,9,89:3:0:1,0:2,0:3,0 0,12,101:4:0:4,0:0,0:4,0 17 222 . A <*> 0 . DP=14;ADF=11,0;ADR=3,0;AD=14,0;I16=11,3,0,0,479,17747,0,0,747,42123,0,0,267,6203,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,186:7:0:6,0:1,0:7,0 0,9,89:3:0:1,0:2,0:3,0 0,12,73:4:0:4,0:0,0:4,0 -17 223 . G T,<*> 0 . DP=13;ADF=9,1,0;ADR=3,0,0;AD=12,1,0;I16=9,3,1,0,412,14782,8,64,627,34923,60,3600,243,5657,25,625;QS=2.96596,0.0340426,0;SGB=-0.556633;RPBZ=1.07052;MQBZ=0.547723;MQSBZ=-3.4641;BQBZ=-1.60577;NMBZ=-0.288675;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,11,166,18,169,167:7:0:5,1,0:1,0,0:6,1,0 0,6,53,6,53,53:2:0:0,0,0:2,0,0:2,0,0 0,12,81,12,81,81:4:0:4,0,0:0,0,0:4,0,0 +17 223 . G T,<*> 0 . DP=13;ADF=9,1,0;ADR=3,0,0;AD=12,1,0;I16=9,3,1,0,412,14782,8,64,627,34923,60,3600,243,5657,25,625;QS=2.96596,0.0340426,0;SGB=-0.556633;RPBZ=1.07052;MQBZ=0.547723;MQSBZ=-3.4641;BQBZ=-1.60577;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,11,166,18,169,167:7:0:5,1,0:1,0,0:6,1,0 0,6,53,6,53,53:2:0:0,0,0:2,0,0:2,0,0 0,12,81,12,81,81:4:0:4,0,0:0,0,0:4,0,0 17 224 . G <*> 0 . DP=12;ADF=9,0;ADR=3,0;AD=12,0;I16=9,3,0,0,379,12759,0,0,627,34923,0,0,270,6370,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,168:6:0:5,0:1,0:6,0 0,6,50:2:0:0,0:2,0:2,0 0,12,70:4:0:4,0:0,0:4,0 17 225 . C <*> 0 . DP=12;ADF=9,0;ADR=3,0;AD=12,0;I16=9,3,0,0,390,13960,0,0,627,34923,0,0,272,6466,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,165:6:0:5,0:1,0:6,0 0,6,48:2:0:0,0:2,0:2,0 0,12,86:4:0:4,0:0,0:4,0 -17 226 . A G,C,<*> 0 . DP=13;ADF=8,1,0,0;ADR=3,0,1,0;AD=11,1,1,0;I16=8,3,1,1,381,13669,6,18,567,31323,89,4441,248,5894,44,986;QS=2.94293,0.0392157,0.0178571,0;VDB=0.84;SGB=-2.62246;RPBZ=-0.592157;MQBZ=-0.615457;MQSBZ=-3.4641;BQBZ=-2.17723;NMBZ=2.34521;SCBZ=2.34521;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,159,12,162,159,18,159,162,159:7:0:5,0,0,0:1,0,1,0:6,0,1,0 0,6,53,6,53,53,6,53,53,53:2:0:0,0,0,0:2,0,0,0:2,0,0,0 0,5,79,9,82,80,9,82,80,80:4:0:3,1,0,0:0,0,0,0:3,1,0,0 +17 226 . A G,C,<*> 0 . DP=13;ADF=8,1,0,0;ADR=3,0,1,0;AD=11,1,1,0;I16=8,3,1,1,381,13669,6,18,567,31323,89,4441,248,5894,44,986;QS=2.94293,0.0392157,0.0178571,0;VDB=0.84;SGB=-2.62246;RPBZ=-0.592157;MQBZ=-0.615457;MQSBZ=-3.4641;BQBZ=-2.17723;SCBZ=2.34521;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,159,12,162,159,18,159,162,159:7:0:5,0,0,0:1,0,1,0:6,0,1,0 0,6,53,6,53,53,6,53,53,53:2:0:0,0,0,0:2,0,0,0:2,0,0,0 0,5,79,9,82,80,9,82,80,80:4:0:3,1,0,0:0,0,0,0:3,1,0,0 17 227 . C <*> 0 . DP=13;ADF=9,0;ADR=4,0;AD=13,0;I16=9,4,0,0,412,14342,0,0,656,35764,0,0,292,6878,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,190:7:0:5,0:2,0:7,0 0,6,53:2:0:0,0:2,0:2,0 0,12,75:4:0:4,0:0,0:4,0 17 228 . C <*> 0 . DP=13;ADF=9,0;ADR=4,0;AD=13,0;I16=9,4,0,0,417,14381,0,0,656,35764,0,0,292,6884,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,187:7:0:5,0:2,0:7,0 0,6,45:2:0:0,0:2,0:2,0 0,12,96:4:0:4,0:0,0:4,0 17 229 . G <*> 0 . DP=13;ADF=9,0;ADR=4,0;AD=13,0;I16=9,4,0,0,368,11524,0,0,656,35764,0,0,292,6898,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,145:7:0:5,0:2,0:7,0 0,6,53:2:0:0,0:2,0:2,0 0,12,70:4:0:4,0:0,0:4,0 @@ -165,7 +164,7 @@ 17 234 . A <*> 0 . DP=14;ADF=10,0;ADR=4,0;AD=14,0;I16=10,4,0,0,502,18390,0,0,716,39364,0,0,292,6988,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,185:7:0:5,0:2,0:7,0 0,6,53:2:0:0,0:2,0:2,0 0,15,123:5:0:5,0:0,0:5,0 17 235 . A <*> 0 . DP=14;ADF=10,0;ADR=4,0;AD=14,0;I16=10,4,0,0,488,17796,0,0,716,39364,0,0,291,6951,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,186:7:0:5,0:2,0:7,0 0,6,53:2:0:0,0:2,0:2,0 0,15,115:5:0:5,0:0,0:5,0 17 236 . G <*> 0 . DP=15;ADF=11,0;ADR=4,0;AD=15,0;I16=11,4,0,0,501,17481,0,0,776,42964,0,0,290,6924,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,24,206:8:0:6,0:2,0:8,0 0,6,53:2:0:0,0:2,0:2,0 0,15,103:5:0:5,0:0,0:5,0 -17 237 . A C,<*> 0 . DP=14;ADF=9,1,0;ADR=4,0,0;AD=13,1,0;I16=9,4,1,0,465,16877,8,64,656,35764,60,3600,266,6282,25,625;QS=2.93162,0.0683761,0;SGB=-0.556633;RPBZ=1.11754;MQBZ=0.632456;MQSBZ=-3.60555;BQBZ=-1.61959;NMBZ=-0.27735;SCBZ=-0.27735;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,24,206,24,206,206:8:0:6,0,0:2,0,0:8,0,0 0,6,53,6,53,53:2:0:0,0,0:2,0,0:2,0,0 0,3,84,9,87,87:4:0:3,1,0:0,0,0:3,1,0 +17 237 . A C,<*> 0 . DP=14;ADF=9,1,0;ADR=4,0,0;AD=13,1,0;I16=9,4,1,0,465,16877,8,64,656,35764,60,3600,266,6282,25,625;QS=2.93162,0.0683761,0;SGB=-0.556633;RPBZ=1.11754;MQBZ=0.632456;MQSBZ=-3.60555;BQBZ=-1.61959;SCBZ=-0.27735;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,24,206,24,206,206:8:0:6,0,0:2,0,0:8,0,0 0,6,53,6,53,53:2:0:0,0,0:2,0,0:2,0,0 0,3,84,9,87,87:4:0:3,1,0:0,0,0:3,1,0 17 238 . C <*> 0 . DP=14;ADF=10,0;ADR=4,0;AD=14,0;I16=10,4,0,0,482,17238,0,0,716,39364,0,0,292,6900,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,24,211:8:0:6,0:2,0:8,0 0,6,53:2:0:0,0:2,0:2,0 0,12,82:4:0:4,0:0,0:4,0 17 239 . A <*> 0 . DP=15;ADF=10,0;ADR=5,0;AD=15,0;I16=10,5,0,0,525,19155,0,0,776,42964,0,0,292,6852,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,223:9:0:6,0:3,0:9,0 0,6,50:2:0:0,0:2,0:2,0 0,12,108:4:0:4,0:0,0:4,0 17 240 . C <*> 0 . DP=15;ADF=10,0;ADR=5,0;AD=15,0;I16=10,5,0,0,512,17930,0,0,776,42964,0,0,292,6764,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,220:9:0:6,0:3,0:9,0 0,6,53:2:0:0,0:2,0:2,0 0,12,106:4:0:4,0:0,0:4,0 @@ -195,18 +194,18 @@ 17 264 . C <*> 0 . DP=22;ADF=10,0;ADR=12,0;AD=22,0;I16=10,12,0,0,821,31325,0,0,1049,54897,0,0,386,8326,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:7,0:4,0:11,0 0,15,104:5:0:0,0:5,0:5,0 0,18,172:6:0:3,0:3,0:6,0 17 265 . A <*> 0 . DP=21;ADF=9,0;ADR=12,0;AD=21,0;I16=9,12,0,0,800,31906,0,0,989,51297,0,0,390,8380,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:7,0:4,0:11,0 0,15,114:5:0:0,0:5,0:5,0 0,15,129:5:0:2,0:3,0:5,0 17 266 . G <*> 0 . DP=21;ADF=9,0;ADR=12,0;AD=21,0;I16=9,12,0,0,754,28204,0,0,989,51297,0,0,394,8458,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:7,0:4,0:11,0 0,15,99:5:0:0,0:5,0:5,0 0,15,138:5:0:2,0:3,0:5,0 -17 267 . T G,<*> 0 . DP=21;ADF=9,0,0;ADR=11,1,0;AD=20,1,0;I16=9,11,0,1,739,27465,8,64,960,50456,29,841,373,7935,25,625;QS=2.94203,0.057971,0;SGB=-0.556633;RPBZ=-0.330396;MQBZ=-1.23153;MQSBZ=-3.3021;BQBZ=-1.66282;NMBZ=2.4409;SCBZ=2.91633;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,254,33,254,254:11:0:7,0,0:4,0,0:11,0,0 0,6,93,12,96,96:5:0:0,0,0:4,1,0:4,1,0 0,15,149,15,149,149:5:0:2,0,0:3,0,0:5,0,0 +17 267 . T G,<*> 0 . DP=21;ADF=9,0,0;ADR=11,1,0;AD=20,1,0;I16=9,11,0,1,739,27465,8,64,960,50456,29,841,373,7935,25,625;QS=2.94203,0.057971,0;SGB=-0.556633;RPBZ=-0.330396;MQBZ=-1.23153;MQSBZ=-3.3021;BQBZ=-1.66282;SCBZ=2.91633;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,254,33,254,254:11:0:7,0,0:4,0,0:11,0,0 0,6,93,12,96,96:5:0:0,0,0:4,1,0:4,1,0 0,15,149,15,149,149:5:0:2,0,0:3,0,0:5,0,0 17 268 . T <*> 0 . DP=21;ADF=9,0;ADR=12,0;AD=21,0;I16=9,12,0,0,748,27708,0,0,989,51297,0,0,402,8686,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,238:11:0:7,0:4,0:11,0 0,15,110:5:0:0,0:5,0:5,0 0,15,156:5:0:2,0:3,0:5,0 17 269 . C <*> 0 . DP=22;ADF=9,0;ADR=13,0;AD=22,0;I16=9,13,0,0,767,28641,0,0,1018,52138,0,0,406,8836,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:7,0:5,0:12,0 0,15,91:5:0:0,0:5,0:5,0 0,15,154:5:0:2,0:3,0:5,0 17 270 . C <*> 0 . DP=22;ADF=9,0;ADR=13,0;AD=22,0;I16=9,13,0,0,766,28210,0,0,1018,52138,0,0,410,8962,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:7,0:5,0:12,0 0,15,98:5:0:0,0:5,0:5,0 0,15,143:5:0:2,0:3,0:5,0 17 271 . T <*> 0 . DP=22;ADF=9,0;ADR=13,0;AD=22,0;I16=9,13,0,0,847,32935,0,0,1018,52138,0,0,413,9065,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:7,0:5,0:12,0 0,15,113:5:0:0,0:5,0:5,0 0,15,152:5:0:2,0:3,0:5,0 17 272 . C <*> 0 . DP=22;ADF=9,0;ADR=13,0;AD=22,0;I16=9,13,0,0,815,31449,0,0,1018,52138,0,0,415,9143,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:7,0:5,0:12,0 0,15,97:5:0:0,0:5,0:5,0 0,15,149:5:0:2,0:3,0:5,0 -17 273 . T C,<*> 0 . DP=22;ADF=9,0,0;ADR=12,1,0;AD=21,1,0;I16=9,12,0,1,798,30664,5,25,989,51297,29,841,392,8620,25,625;QS=2.96094,0.0390625,0;SGB=-0.556633;RPBZ=-0.236567;MQBZ=-1.16701;MQSBZ=-3.42286;BQBZ=-1.66779;NMBZ=2.50862;SCBZ=3.00076;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255,36,255,255:12:0:7,0,0:5,0,0:12,0,0 0,7,89,12,92,90:5:0:0,0,0:4,1,0:4,1,0 0,15,161,15,161,161:5:0:2,0,0:3,0,0:5,0,0 +17 273 . T C,<*> 0 . DP=22;ADF=9,0,0;ADR=12,1,0;AD=21,1,0;I16=9,12,0,1,798,30664,5,25,989,51297,29,841,392,8620,25,625;QS=2.96094,0.0390625,0;SGB=-0.556633;RPBZ=-0.236567;MQBZ=-1.16701;MQSBZ=-3.42286;BQBZ=-1.66779;SCBZ=3.00076;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255,36,255,255:12:0:7,0,0:5,0,0:12,0,0 0,7,89,12,92,90:5:0:0,0,0:4,1,0:4,1,0 0,15,161,15,161,161:5:0:2,0,0:3,0,0:5,0,0 17 274 . C <*> 0 . DP=22;ADF=9,0;ADR=13,0;AD=22,0;I16=9,13,0,0,767,28193,0,0,1018,52138,0,0,419,9371,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:7,0:5,0:12,0 0,15,101:5:0:0,0:5,0:5,0 0,15,144:5:0:2,0:3,0:5,0 17 275 . C <*> 0 . DP=20;ADF=7,0;ADR=13,0;AD=20,0;I16=7,13,0,0,768,29994,0,0,898,44938,0,0,423,9519,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,15,114:5:0:0,0:5,0:5,0 0,12,122:4:0:1,0:3,0:4,0 17 276 . A <*> 0 . DP=20;ADF=7,0;ADR=13,0;AD=20,0;I16=7,13,0,0,805,32931,0,0,898,44938,0,0,424,9538,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,253:11:0:6,0:5,0:11,0 0,15,122:5:0:0,0:5,0:5,0 0,12,124:4:0:1,0:3,0:4,0 17 277 . G <*> 0 . DP=20;ADF=7,0;ADR=13,0;AD=20,0;I16=7,13,0,0,764,29732,0,0,898,44938,0,0,425,9579,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,15,114:5:0:0,0:5,0:5,0 0,12,121:4:0:1,0:3,0:4,0 -17 278 . A C,<*> 0 . DP=21;ADF=6,1,0;ADR=14,0,0;AD=20,1,0;I16=6,14,1,0,722,26452,7,49,867,42179,60,3600,415,9521,11,121;QS=2.97935,0.020649,0;SGB=-0.556633;RPBZ=1.65198;MQBZ=1.0247;MQSBZ=-3.24037;BQBZ=-1.66667;NMBZ=-0.406816;SCBZ=-0.324037;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,22,231,30,234,231:11:0:5,1,0:5,0,0:10,1,0 0,18,123,18,123,123:6:0:0,0,0:6,0,0:6,0,0 0,12,121,12,121,121:4:0:1,0,0:3,0,0:4,0,0 +17 278 . A C,<*> 0 . DP=21;ADF=6,1,0;ADR=14,0,0;AD=20,1,0;I16=6,14,1,0,722,26452,7,49,867,42179,60,3600,415,9521,11,121;QS=2.97935,0.020649,0;SGB=-0.556633;RPBZ=1.65198;MQBZ=1.0247;MQSBZ=-3.24037;BQBZ=-1.66667;SCBZ=-0.324037;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,22,231,30,234,231:11:0:5,1,0:5,0,0:10,1,0 0,18,123,18,123,123:6:0:0,0,0:6,0,0:6,0,0 0,12,121,12,121,121:4:0:1,0,0:3,0,0:4,0,0 17 279 . A <*> 0 . DP=22;ADF=7,0;ADR=15,0;AD=22,0;I16=7,15,0,0,786,28694,0,0,956,46620,0,0,427,9677,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:6,0:6,0:12,0 0,18,123:6:0:0,0:6,0:6,0 0,12,122:4:0:1,0:3,0:4,0 17 280 . A <*> 0 . DP=22;ADF=7,0;ADR=15,0;AD=22,0;I16=7,15,0,0,815,31561,0,0,956,46620,0,0,428,9684,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,253:12:0:6,0:6,0:12,0 0,18,130:6:0:0,0:6,0:6,0 0,12,129:4:0:1,0:3,0:4,0 17 281 . G <*> 0 . DP=22;ADF=7,0;ADR=15,0;AD=22,0;I16=7,15,0,0,820,31416,0,0,956,46620,0,0,428,9662,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:6,0:6,0:12,0 0,18,122:6:0:0,0:6,0:6,0 0,12,123:4:0:1,0:3,0:4,0 @@ -225,13 +224,13 @@ 17 294 . A <*> 0 . DP=26;ADF=10,0;ADR=16,0;AD=26,0;I16=10,16,0,0,931,33937,0,0,1227,63779,0,0,443,9785,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,252:12:0:6,0:6,0:12,0 0,24,201:8:0:3,0:5,0:8,0 0,18,161:6:0:1,0:5,0:6,0 17 295 . C <*> 0 . DP=25;ADF=10,0;ADR=15,0;AD=25,0;I16=10,15,0,0,909,34117,0,0,1198,62938,0,0,447,9833,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,183:8:0:3,0:5,0:8,0 0,18,159:6:0:1,0:5,0:6,0 17 296 . A <*> 0 . DP=25;ADF=10,0;ADR=15,0;AD=25,0;I16=10,15,0,0,874,31846,0,0,1198,62938,0,0,451,9905,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,169:8:0:3,0:5,0:8,0 0,18,169:6:0:1,0:5,0:6,0 -17 297 . C G,<*> 0 . DP=25;ADF=9,1,0;ADR=15,0,0;AD=24,1,0;I16=9,15,1,0,901,34305,4,16,1138,59338,60,3600,445,9901,10,100;QS=2.98261,0.0173913,0;SGB=-0.556633;RPBZ=-1.24856;MQBZ=0.806872;MQSBZ=-3.22749;BQBZ=-1.67542;NMBZ=-0.434372;SCBZ=-0.368383;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255,33,255,255:11:0:6,0,0:5,0,0:11,0,0 0,15,168,21,171,168:8:0:2,1,0:5,0,0:7,1,0 0,18,161,18,161,161:6:0:1,0,0:5,0,0:6,0,0 +17 297 . C G,<*> 0 . DP=25;ADF=9,1,0;ADR=15,0,0;AD=24,1,0;I16=9,15,1,0,901,34305,4,16,1138,59338,60,3600,445,9901,10,100;QS=2.98261,0.0173913,0;SGB=-0.556633;RPBZ=-1.24856;MQBZ=0.806872;MQSBZ=-3.22749;BQBZ=-1.67542;SCBZ=-0.368383;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255,33,255,255:11:0:6,0,0:5,0,0:11,0,0 0,15,168,21,171,168:8:0:2,1,0:5,0,0:7,1,0 0,18,161,18,161,161:6:0:1,0,0:5,0,0:6,0,0 17 298 . A <*> 0 . DP=26;ADF=11,0;ADR=15,0;AD=26,0;I16=11,15,0,0,936,34652,0,0,1258,66538,0,0,459,10121,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,184:8:0:3,0:5,0:8,0 0,21,191:7:0:2,0:5,0:7,0 17 299 . C <*> 0 . DP=27;ADF=11,0;ADR=15,0;AD=26,0;I16=11,15,0,0,971,36863,0,0,1258,66538,0,0,464,10266,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,193:8:0:3,0:5,0:8,0 0,21,189:7:0:2,0:5,0:7,0 17 300 . A <*> 0 . DP=27;ADF=11,0;ADR=15,0;AD=26,0;I16=11,15,0,0,1001,39455,0,0,1258,66538,0,0,469,10437,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,204:8:0:3,0:5,0:8,0 0,21,210:7:0:2,0:5,0:7,0 17 301 . G <*> 0 . DP=25;ADF=10,0;ADR=14,0;AD=24,0;I16=10,14,0,0,928,36116,0,0,1169,62097,0,0,476,10632,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,255:10:0:5,0:5,0:10,0 0,21,195:7:0:3,0:4,0:7,0 0,21,196:7:0:2,0:5,0:7,0 17 302 . T <*> 0 . DP=25;ADF=10,0;ADR=14,0;AD=24,0;I16=10,14,0,0,879,32885,0,0,1169,62097,0,0,483,10849,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,231:10:0:5,0:5,0:10,0 0,21,172:7:0:3,0:4,0:7,0 0,21,202:7:0:2,0:5,0:7,0 -17 302 . T TA 0 . INDEL;IDV=7;IMF=1;DP=25;ADF=2,8;ADR=4,11;AD=6,19;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.539485,2.46052;VDB=0.241622;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.22749;BQBZ=-1.67542;NMBZ=-0.199304;SCBZ=-0.268121;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 161,0,99:11:6:1,4:4,2:5,6 158,0,14:7:0:1,2:0,4:1,6 201,21,0:7:0:0,2:0,5:0,7 +17 302 . T TA 0 . INDEL;IDV=7;IMF=1;DP=25;ADF=2,8;ADR=4,11;AD=6,19;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.539485,2.46052;VDB=0.241622;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.22749;BQBZ=-1.67542;SCBZ=-0.268121;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 161,0,99:11:6:1,4:4,2:5,6 158,0,14:7:0:1,2:0,4:1,6 201,21,0:7:0:0,2:0,5:0,7 17 303 . G <*> 0 . DP=25;ADF=10,0;ADR=15,0;AD=25,0;I16=10,15,0,0,968,37972,0,0,1229,65697,0,0,497,11181,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:5,0:6,0:11,0 0,21,197:7:0:3,0:4,0:7,0 0,21,195:7:0:2,0:5,0:7,0 17 304 . C <*> 0 . DP=27;ADF=11,0;ADR=16,0;AD=27,0;I16=11,16,0,0,991,37005,0,0,1318,70138,0,0,503,11359,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:5,0:6,0:11,0 0,24,206:8:0:4,0:4,0:8,0 0,24,200:8:0:2,0:6,0:8,0 17 305 . C <*> 0 . DP=27;ADF=11,0;ADR=16,0;AD=27,0;I16=11,16,0,0,1057,41761,0,0,1318,70138,0,0,510,11508,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:5,0:6,0:11,0 0,24,213:8:0:4,0:4,0:8,0 0,24,211:8:0:2,0:6,0:8,0 @@ -264,9 +263,9 @@ 17 332 . A <*> 0 . DP=32;ADF=14,0;ADR=18,0;AD=32,0;I16=14,18,0,0,1156,42666,0,0,1649,90897,0,0,560,12178,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:6,0:6,0:12,0 0,27,214:9:0:4,0:5,0:9,0 0,33,255:11:0:4,0:7,0:11,0 17 333 . A <*> 0 . DP=32;ADF=14,0;ADR=18,0;AD=32,0;I16=14,18,0,0,1141,41987,0,0,1649,90897,0,0,558,12064,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:6,0:6,0:12,0 0,27,223:9:0:4,0:5,0:9,0 0,33,255:11:0:4,0:7,0:11,0 17 334 . A <*> 0 . DP=32;ADF=14,0;ADR=18,0;AD=32,0;I16=14,18,0,0,1162,43328,0,0,1649,90897,0,0,556,11986,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:6,0:6,0:12,0 0,27,221:9:0:4,0:5,0:9,0 0,33,255:11:0:4,0:7,0:11,0 -17 335 . A G,<*> 0 . DP=32;ADF=13,1,0;ADR=18,0,0;AD=31,1,0;I16=13,18,1,0,1084,40336,4,16,1589,87297,60,3600,555,11943,0,0;QS=2.98919,0.0108108,0;SGB=-0.556633;RPBZ=-1.67936;MQBZ=0.622171;MQSBZ=-2.25492;BQBZ=-1.68602;NMBZ=-0.428353;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,252,33,252,252:11:0:5,0,0:6,0,0:11,0,0 0,27,219,27,219,219:9:0:4,0,0:5,0,0:9,0,0 0,25,245,33,248,245:12:0:4,1,0:7,0,0:11,1,0 +17 335 . A G,<*> 0 . DP=32;ADF=13,1,0;ADR=18,0,0;AD=31,1,0;I16=13,18,1,0,1084,40336,4,16,1589,87297,60,3600,555,11943,0,0;QS=2.98919,0.0108108,0;SGB=-0.556633;RPBZ=-1.67936;MQBZ=0.622171;MQSBZ=-2.25492;BQBZ=-1.68602;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,252,33,252,252:11:0:5,0,0:6,0,0:11,0,0 0,27,219,27,219,219:9:0:4,0,0:5,0,0:9,0,0 0,25,245,33,248,245:12:0:4,1,0:7,0,0:11,1,0 17 336 . A <*> 0 . DP=32;ADF=14,0;ADR=18,0;AD=32,0;I16=14,18,0,0,1094,39794,0,0,1649,90897,0,0,555,11935,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:5,0:6,0:11,0 0,27,212:9:0:4,0:5,0:9,0 0,36,255:12:0:5,0:7,0:12,0 -17 337 . C A,<*> 0 . DP=32;ADF=14,0,0;ADR=17,1,0;AD=31,1,0;I16=14,17,0,1,1125,42481,5,25,1612,89528,37,1369,536,11590,18,324;QS=2.98113,0.0188679,0;SGB=-0.556633;RPBZ=0.812593;MQBZ=-1.03695;MQSBZ=-2.25492;BQBZ=-1.68353;NMBZ=-0.376914;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255,33,255,255:11:0:5,0,0:6,0,0:11,0,0 0,17,195,24,198,195:9:0:4,0,0:4,1,0:8,1,0 0,36,255,36,255,255:12:0:5,0,0:7,0,0:12,0,0 +17 337 . C A,<*> 0 . DP=32;ADF=14,0,0;ADR=17,1,0;AD=31,1,0;I16=14,17,0,1,1125,42481,5,25,1612,89528,37,1369,536,11590,18,324;QS=2.98113,0.0188679,0;SGB=-0.556633;RPBZ=0.812593;MQBZ=-1.03695;MQSBZ=-2.25492;BQBZ=-1.68353;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255,33,255,255:11:0:5,0,0:6,0,0:11,0,0 0,17,195,24,198,195:9:0:4,0,0:4,1,0:8,1,0 0,36,255,36,255,255:12:0:5,0,0:7,0,0:12,0,0 17 338 . T <*> 0 . DP=30;ADF=14,0;ADR=16,0;AD=30,0;I16=14,16,0,0,1190,47898,0,0,1560,86456,0,0,554,11878,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,255:10:0:5,0:5,0:10,0 0,24,226:8:0:4,0:4,0:8,0 0,36,255:12:0:5,0:7,0:12,0 17 339 . C <*> 0 . DP=31;ADF=14,0;ADR=17,0;AD=31,0;I16=14,17,0,0,1130,43210,0,0,1589,87297,0,0,554,11874,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:5,0:6,0:11,0 0,24,185:8:0:4,0:4,0:8,0 0,36,255:12:0:5,0:7,0:12,0 17 340 . C <*> 0 . DP=31;ADF=14,0;ADR=17,0;AD=31,0;I16=14,17,0,0,1196,47044,0,0,1589,87297,0,0,554,11852,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:5,0:6,0:11,0 0,24,221:8:0:4,0:4,0:8,0 0,36,255:12:0:5,0:7,0:12,0 @@ -284,11 +283,11 @@ 17 352 . A <*> 0 . DP=31;ADF=16,0;ADR=15,0;AD=31,0;I16=16,15,0,0,1162,45664,0,0,1651,92815,0,0,569,13029,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,27,230:9:0:5,0:4,0:9,0 0,33,255:11:0:5,0:6,0:11,0 17 353 . G <*> 0 . DP=29;ADF=15,0;ADR=14,0;AD=29,0;I16=15,14,0,0,1109,43095,0,0,1562,88374,0,0,570,13064,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,255:10:0:5,0:5,0:10,0 0,27,231:9:0:5,0:4,0:9,0 0,30,255:10:0:5,0:5,0:10,0 17 354 . A <*> 0 . DP=28;ADF=14,0;ADR=14,0;AD=28,0;I16=14,14,0,0,1078,42938,0,0,1502,84774,0,0,571,13075,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,225:9:0:4,0:5,0:9,0 0,27,244:9:0:5,0:4,0:9,0 0,30,255:10:0:5,0:5,0:10,0 -17 355 . G T,<*> 0 . DP=28;ADF=14,0,0;ADR=13,1,0;AD=27,1,0;I16=14,13,0,1,1001,37907,41,1681,1442,81174,60,3600,547,12487,25,625;QS=2.875,0.125,0;SGB=-0.556633;RPBZ=0.185772;MQBZ=0.520126;MQSBZ=-1.7696;BQBZ=0.683978;NMBZ=2.33874;SCBZ=-0.27735;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 14,0,200,38,203,231:9:0:4,0,0:4,1,0:8,1,0 0,27,222,27,222,222:9:0:5,0,0:4,0,0:9,0,0 0,30,255,30,255,255:10:0:5,0,0:5,0,0:10,0,0 +17 355 . G T,<*> 0 . DP=28;ADF=14,0,0;ADR=13,1,0;AD=27,1,0;I16=14,13,0,1,1001,37907,41,1681,1442,81174,60,3600,547,12487,25,625;QS=2.875,0.125,0;SGB=-0.556633;RPBZ=0.185772;MQBZ=0.520126;MQSBZ=-1.7696;BQBZ=0.683978;SCBZ=-0.27735;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 14,0,200,38,203,231:9:0:4,0,0:4,1,0:8,1,0 0,27,222,27,222,222:9:0:5,0,0:4,0,0:9,0,0 0,30,255,30,255,255:10:0:5,0,0:5,0,0:10,0,0 17 356 . G <*> 0 . DP=27;ADF=14,0;ADR=13,0;AD=27,0;I16=14,13,0,0,993,37481,0,0,1465,83405,0,0,574,13174,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,228:9:0:4,0:5,0:9,0 0,24,201:8:0:5,0:3,0:8,0 0,30,255:10:0:5,0:5,0:10,0 17 357 . C <*> 0 . DP=28;ADF=15,0;ADR=13,0;AD=28,0;I16=15,13,0,0,1026,39496,0,0,1525,87005,0,0,575,13209,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,255:10:0:5,0:5,0:10,0 0,24,205:8:0:5,0:3,0:8,0 0,30,252:10:0:5,0:5,0:10,0 17 358 . A <*> 0 . DP=28;ADF=15,0;ADR=13,0;AD=28,0;I16=15,13,0,0,1050,40518,0,0,1525,87005,0,0,576,13216,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,254:10:0:5,0:5,0:10,0 0,24,197:8:0:5,0:3,0:8,0 0,30,255:10:0:5,0:5,0:10,0 -17 359 . G T,<*> 0 . DP=29;ADF=15,0,0;ADR=13,1,0;AD=28,1,0;I16=15,13,0,1,1085,42761,10,100,1525,87005,60,3600,552,12620,25,625;QS=2.96032,0.0396825,0;SGB=-0.556633;RPBZ=-0.119611;MQBZ=0.456435;MQSBZ=-1.53333;BQBZ=-1.68246;NMBZ=3.0531;SCBZ=5.2915;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,255,30,255,255:10:0:5,0,0:5,0,0:10,0,0 0,13,178,21,181,180:8:0:5,0,0:2,1,0:7,1,0 0,33,255,33,255,255:11:0:5,0,0:6,0,0:11,0,0 +17 359 . G T,<*> 0 . DP=29;ADF=15,0,0;ADR=13,1,0;AD=28,1,0;I16=15,13,0,1,1085,42761,10,100,1525,87005,60,3600,552,12620,25,625;QS=2.96032,0.0396825,0;SGB=-0.556633;RPBZ=-0.119611;MQBZ=0.456435;MQSBZ=-1.53333;BQBZ=-1.68246;SCBZ=5.2915;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,255,30,255,255:10:0:5,0,0:5,0,0:10,0,0 0,13,178,21,181,180:8:0:5,0,0:2,1,0:7,1,0 0,33,255,33,255,255:11:0:5,0,0:6,0,0:11,0,0 17 360 . A <*> 0 . DP=29;ADF=15,0;ADR=14,0;AD=29,0;I16=15,14,0,0,1111,43259,0,0,1585,90605,0,0,579,13297,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,252:10:0:5,0:5,0:10,0 0,24,220:8:0:5,0:3,0:8,0 0,33,255:11:0:5,0:6,0:11,0 17 361 . A <*> 0 . DP=29;ADF=15,0;ADR=14,0;AD=29,0;I16=15,14,0,0,1116,43442,0,0,1585,90605,0,0,579,13273,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,252:10:0:5,0:5,0:10,0 0,24,219:8:0:5,0:3,0:8,0 0,33,255:11:0:5,0:6,0:11,0 17 362 . A <*> 0 . DP=29;ADF=16,0;ADR=13,0;AD=29,0;I16=16,13,0,0,1104,42700,0,0,1585,90605,0,0,580,13272,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,218:8:0:5,0:3,0:8,0 0,30,255:10:0:5,0:5,0:10,0 @@ -298,13 +297,13 @@ 17 366 . A <*> 0 . DP=29;ADF=16,0;ADR=13,0;AD=29,0;I16=16,13,0,0,1090,41562,0,0,1585,90605,0,0,581,13167,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,211:8:0:5,0:3,0:8,0 0,30,255:10:0:5,0:5,0:10,0 17 367 . T <*> 0 . DP=29;ADF=16,0;ADR=13,0;AD=29,0;I16=16,13,0,0,1055,39149,0,0,1585,90605,0,0,579,13093,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,204:8:0:5,0:3,0:8,0 0,30,255:10:0:5,0:5,0:10,0 17 368 . A <*> 0 . DP=29;ADF=16,0;ADR=13,0;AD=29,0;I16=16,13,0,0,1054,39632,0,0,1585,90605,0,0,576,12998,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,208:8:0:5,0:3,0:8,0 0,30,255:10:0:5,0:5,0:10,0 -17 369 . T G,<*> 0 . DP=28;ADF=16,0,0;ADR=11,1,0;AD=27,1,0;I16=16,11,0,1,1037,40275,6,36,1496,86164,60,3600,548,12256,25,625;QS=2.97683,0.023166,0;SGB=-0.556633;RPBZ=0.12395;MQBZ=0.408248;MQSBZ=-1.37784;BQBZ=-1.68703;NMBZ=2.99794;SCBZ=5.19615;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,250,30,250,250:10:0:6,0,0:4,0,0:10,0,0 0,15,189,21,192,190:8:0:5,0,0:2,1,0:7,1,0 0,30,255,30,255,255:10:0:5,0,0:5,0,0:10,0,0 +17 369 . T G,<*> 0 . DP=28;ADF=16,0,0;ADR=11,1,0;AD=27,1,0;I16=16,11,0,1,1037,40275,6,36,1496,86164,60,3600,548,12256,25,625;QS=2.97683,0.023166,0;SGB=-0.556633;RPBZ=0.12395;MQBZ=0.408248;MQSBZ=-1.37784;BQBZ=-1.68703;SCBZ=5.19615;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,250,30,250,250:10:0:6,0,0:4,0,0:10,0,0 0,15,189,21,192,190:8:0:5,0,0:2,1,0:7,1,0 0,30,255,30,255,255:10:0:5,0,0:5,0,0:10,0,0 17 370 . C <*> 0 . DP=28;ADF=16,0;ADR=12,0;AD=28,0;I16=16,12,0,0,1045,40219,0,0,1556,89764,0,0,570,12790,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,255:10:0:6,0:4,0:10,0 0,24,201:8:0:5,0:3,0:8,0 0,30,255:10:0:5,0:5,0:10,0 17 371 . T <*> 0 . DP=29;ADF=16,0;ADR=13,0;AD=29,0;I16=16,13,0,0,1155,46591,0,0,1616,93364,0,0,567,12725,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,255:10:0:6,0:4,0:10,0 0,24,227:8:0:5,0:3,0:8,0 0,33,255:11:0:5,0:6,0:11,0 17 372 . C <*> 0 . DP=30;ADF=16,0;ADR=14,0;AD=30,0;I16=16,14,0,0,1139,44019,0,0,1676,96964,0,0,564,12636,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,215:8:0:5,0:3,0:8,0 0,33,255:11:0:5,0:6,0:11,0 17 373 . A <*> 0 . DP=30;ADF=16,0;ADR=14,0;AD=30,0;I16=16,14,0,0,1142,44118,0,0,1676,96964,0,0,561,12525,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,220:8:0:5,0:3,0:8,0 0,33,255:11:0:5,0:6,0:11,0 17 374 . T <*> 0 . DP=30;ADF=16,0;ADR=14,0;AD=30,0;I16=16,14,0,0,1098,41180,0,0,1676,96964,0,0,556,12344,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,221:8:0:5,0:3,0:8,0 0,33,255:11:0:5,0:6,0:11,0 -17 375 . A T,<*> 0 . DP=31;ADF=17,0,0;ADR=13,1,0;AD=30,1,0;I16=17,13,0,1,1138,43798,14,196,1676,96964,60,3600,547,12177,4,16;QS=2.9661,0.0338983,0;SGB=-0.556633;RPBZ=-1.45432;MQBZ=0.3849;MQSBZ=-1.26404;BQBZ=-1.68488;NMBZ=2.30253;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255,36,255,255:12:0:7,0,0:5,0,0:12,0,0 0,24,218,24,218,218:8:0:5,0,0:3,0,0:8,0,0 0,18,255,30,255,255:11:0:5,0,0:5,1,0:10,1,0 +17 375 . A T,<*> 0 . DP=31;ADF=17,0,0;ADR=13,1,0;AD=30,1,0;I16=17,13,0,1,1138,43798,14,196,1676,96964,60,3600,547,12177,4,16;QS=2.9661,0.0338983,0;SGB=-0.556633;RPBZ=-1.45432;MQBZ=0.3849;MQSBZ=-1.26404;BQBZ=-1.68488;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255,36,255,255:12:0:7,0,0:5,0,0:12,0,0 0,24,218,24,218,218:8:0:5,0,0:3,0,0:8,0,0 0,18,255,30,255,255:11:0:5,0,0:5,1,0:10,1,0 17 376 . G <*> 0 . DP=31;ADF=17,0;ADR=14,0;AD=31,0;I16=17,14,0,0,1131,42581,0,0,1736,100564,0,0,547,12073,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:7,0:5,0:12,0 0,24,220:8:0:5,0:3,0:8,0 0,33,255:11:0:5,0:6,0:11,0 17 377 . T <*> 0 . DP=31;ADF=17,0;ADR=14,0;AD=31,0;I16=17,14,0,0,1116,41750,0,0,1736,100564,0,0,543,11985,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:7,0:5,0:12,0 0,24,211:8:0:5,0:3,0:8,0 0,33,255:11:0:5,0:6,0:11,0 17 378 . T <*> 0 . DP=30;ADF=18,0;ADR=12,0;AD=30,0;I16=18,12,0,0,1098,41066,0,0,1707,99723,0,0,541,11927,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255:13:0:8,0:5,0:13,0 0,21,186:7:0:5,0:2,0:7,0 0,30,255:10:0:5,0:5,0:10,0 @@ -313,7 +312,7 @@ 17 381 . T <*> 0 . DP=29;ADF=18,0;ADR=11,0;AD=29,0;I16=18,11,0,0,1167,47337,0,0,1678,98882,0,0,537,11729,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:8,0:4,0:12,0 0,21,211:7:0:5,0:2,0:7,0 0,30,255:10:0:5,0:5,0:10,0 17 382 . T <*> 0 . DP=29;ADF=18,0;ADR=11,0;AD=29,0;I16=18,11,0,0,1062,40514,0,0,1678,98882,0,0,535,11693,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:8,0:4,0:12,0 0,21,182:7:0:5,0:2,0:7,0 0,30,255:10:0:5,0:5,0:10,0 17 383 . T <*> 0 . DP=29;ADF=18,0;ADR=11,0;AD=29,0;I16=18,11,0,0,1059,39847,0,0,1678,98882,0,0,532,11638,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:8,0:4,0:12,0 0,21,172:7:0:5,0:2,0:7,0 0,30,255:10:0:5,0:5,0:10,0 -17 384 . A C,<*> 0 . DP=31;ADF=19,0,0;ADR=11,1,0;AD=30,1,0;I16=19,11,0,1,1077,39885,4,16,1738,102482,60,3600,504,10988,25,625;QS=2.98419,0.0158103,0;SGB=-0.556633;RPBZ=0.615229;MQBZ=0.262613;MQSBZ=-0.333409;BQBZ=-1.68746;NMBZ=3.26825;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255,39,255,255:13:0:8,0,0:5,0,0:13,0,0 0,15,171,21,174,171:8:0:6,0,0:1,1,0:7,1,0 0,30,255,30,255,255:10:0:5,0,0:5,0,0:10,0,0 +17 384 . A C,<*> 0 . DP=31;ADF=19,0,0;ADR=11,1,0;AD=30,1,0;I16=19,11,0,1,1077,39885,4,16,1738,102482,60,3600,504,10988,25,625;QS=2.98419,0.0158103,0;SGB=-0.556633;RPBZ=0.615229;MQBZ=0.262613;MQSBZ=-0.333409;BQBZ=-1.68746;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255,39,255,255:13:0:8,0,0:5,0,0:13,0,0 0,15,171,21,174,171:8:0:6,0,0:1,1,0:7,1,0 0,30,255,30,255,255:10:0:5,0,0:5,0,0:10,0,0 17 385 . C <*> 0 . DP=31;ADF=19,0;ADR=12,0;AD=31,0;I16=19,12,0,0,1118,41180,0,0,1798,106082,0,0,527,11569,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255:13:0:8,0:5,0:13,0 0,24,186:8:0:6,0:2,0:8,0 0,30,255:10:0:5,0:5,0:10,0 17 386 . T <*> 0 . DP=30;ADF=18,0;ADR=12,0;AD=30,0;I16=18,12,0,0,1158,45592,0,0,1738,102482,0,0,526,11556,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255:13:0:8,0:5,0:13,0 0,21,191:7:0:5,0:2,0:7,0 0,30,255:10:0:5,0:5,0:10,0 17 387 . T <*> 0 . DP=30;ADF=18,0;ADR=12,0;AD=30,0;I16=18,12,0,0,1105,41821,0,0,1738,102482,0,0,525,11573,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255:13:0:8,0:5,0:13,0 0,21,187:7:0:5,0:2,0:7,0 0,30,255:10:0:5,0:5,0:10,0 @@ -330,7 +329,7 @@ 17 398 . A <*> 0 . DP=28;ADF=17,0;ADR=11,0;AD=28,0;I16=17,11,0,0,1025,38361,0,0,1587,92523,0,0,524,11850,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255:13:0:8,0:5,0:13,0 0,15,144:5:0:3,0:2,0:5,0 0,30,255:10:0:6,0:4,0:10,0 17 399 . A <*> 0 . DP=28;ADF=17,0;ADR=11,0;AD=28,0;I16=17,11,0,0,1023,38949,0,0,1587,92523,0,0,526,11900,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255:13:0:8,0:5,0:13,0 0,15,140:5:0:3,0:2,0:5,0 0,30,255:10:0:6,0:4,0:10,0 17 400 . A <*> 0 . DP=29;ADF=17,0;ADR=12,0;AD=29,0;I16=17,12,0,0,1070,40554,0,0,1647,96123,0,0,526,11828,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255:13:0:8,0:5,0:13,0 0,15,159:5:0:3,0:2,0:5,0 0,33,255:11:0:6,0:5,0:11,0 -17 401 . A C,<*> 0 . DP=29;ADF=17,0,0;ADR=11,1,0;AD=28,1,0;I16=17,11,0,1,1063,41001,8,64,1587,92523,60,3600,501,11113,25,625;QS=2.97985,0.0201511,0;SGB=-0.556633;RPBZ=-0.478622;MQBZ=0.339683;MQSBZ=0.29364;BQBZ=-1.68267;NMBZ=3.53589;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255,39,255,255:13:0:8,0,0:5,0,0:13,0,0 0,15,160,15,160,160:5:0:3,0,0:2,0,0:5,0,0 0,22,255,30,255,255:11:0:6,0,0:4,1,0:10,1,0 +17 401 . A C,<*> 0 . DP=29;ADF=17,0,0;ADR=11,1,0;AD=28,1,0;I16=17,11,0,1,1063,41001,8,64,1587,92523,60,3600,501,11113,25,625;QS=2.97985,0.0201511,0;SGB=-0.556633;RPBZ=-0.478622;MQBZ=0.339683;MQSBZ=0.29364;BQBZ=-1.68267;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255,39,255,255:13:0:8,0,0:5,0,0:13,0,0 0,15,160,15,160,160:5:0:3,0,0:2,0,0:5,0,0 0,22,255,30,255,255:11:0:6,0,0:4,1,0:10,1,0 17 402 . T <*> 0 . DP=29;ADF=17,0;ADR=12,0;AD=29,0;I16=17,12,0,0,1076,40740,0,0,1647,96123,0,0,526,11680,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255:13:0:8,0:5,0:13,0 0,15,149:5:0:3,0:2,0:5,0 0,33,255:11:0:6,0:5,0:11,0 17 403 . T <*> 0 . DP=29;ADF=17,0;ADR=12,0;AD=29,0;I16=17,12,0,0,1085,40985,0,0,1647,96123,0,0,526,11654,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255:13:0:8,0:5,0:13,0 0,15,148:5:0:3,0:2,0:5,0 0,33,255:11:0:6,0:5,0:11,0 17 404 . G <*> 0 . DP=29;ADF=17,0;ADR=12,0;AD=29,0;I16=17,12,0,0,1074,40524,0,0,1647,96123,0,0,525,11609,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255:13:0:8,0:5,0:13,0 0,15,131:5:0:3,0:2,0:5,0 0,33,255:11:0:6,0:5,0:11,0 @@ -341,7 +340,7 @@ 17 409 . T <*> 0 . DP=29;ADF=17,0;ADR=12,0;AD=29,0;I16=17,12,0,0,1100,42734,0,0,1678,98882,0,0,525,11503,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,42,255:14:0:8,0:6,0:14,0 0,12,131:4:0:2,0:2,0:4,0 0,33,255:11:0:7,0:4,0:11,0 17 410 . T <*> 0 . DP=29;ADF=17,0;ADR=12,0;AD=29,0;I16=17,12,0,0,1035,38325,0,0,1678,98882,0,0,524,11432,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,42,255:14:0:8,0:6,0:14,0 0,12,125:4:0:2,0:2,0:4,0 0,33,255:11:0:7,0:4,0:11,0 17 411 . T <*> 0 . DP=29;ADF=17,0;ADR=12,0;AD=29,0;I16=17,12,0,0,1022,37928,0,0,1678,98882,0,0,522,11342,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,42,255:14:0:8,0:6,0:14,0 0,12,111:4:0:2,0:2,0:4,0 0,33,255:11:0:7,0:4,0:11,0 -17 412 . C T,<*> 0 . DP=30;ADF=17,1,0;ADR=12,0,0;AD=29,1,0;I16=17,12,1,0,1094,42458,14,196,1678,98882,60,3600,495,10659,25,625;QS=2.97455,0.0254545,0;SGB=-0.556633;RPBZ=-0.40473;MQBZ=0.267261;MQSBZ=-0.293785;BQBZ=-1.6942;NMBZ=-0.267102;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,255,42,255,255:15:0:8,1,0:6,0,0:14,1,0 0,12,124,12,124,124:4:0:2,0,0:2,0,0:4,0,0 0,33,255,33,255,255:11:0:7,0,0:4,0,0:11,0,0 +17 412 . C T,<*> 0 . DP=30;ADF=17,1,0;ADR=12,0,0;AD=29,1,0;I16=17,12,1,0,1094,42458,14,196,1678,98882,60,3600,495,10659,25,625;QS=2.97455,0.0254545,0;SGB=-0.556633;RPBZ=-0.40473;MQBZ=0.267261;MQSBZ=-0.293785;BQBZ=-1.6942;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,255,42,255,255:15:0:8,1,0:6,0,0:14,1,0 0,12,124,12,124,124:4:0:2,0,0:2,0,0:4,0,0 0,33,255,33,255,255:11:0:7,0,0:4,0,0:11,0,0 17 413 . A <*> 0 . DP=31;ADF=18,0;ADR=13,0;AD=31,0;I16=18,13,0,0,1189,45985,0,0,1798,106082,0,0,520,11258,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:9,0:8,0:17,0 0,9,102:3:0:2,0:1,0:3,0 0,33,255:11:0:7,0:4,0:11,0 17 414 . T <*> 0 . DP=30;ADF=18,0;ADR=12,0;AD=30,0;I16=18,12,0,0,1151,44355,0,0,1738,102482,0,0,523,11265,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:9,0:7,0:16,0 0,9,109:3:0:2,0:1,0:3,0 0,33,255:11:0:7,0:4,0:11,0 17 415 . G <*> 0 . DP=30;ADF=18,0;ADR=12,0;AD=30,0;I16=18,12,0,0,1131,43175,0,0,1738,102482,0,0,526,11306,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:9,0:7,0:16,0 0,9,110:3:0:2,0:1,0:3,0 0,33,255:11:0:7,0:4,0:11,0 @@ -366,7 +365,7 @@ 17 434 . T <*> 0 . DP=29;ADF=15,0;ADR=14,0;AD=29,0;I16=15,14,0,0,1036,37654,0,0,1647,96123,0,0,561,12567,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:8,0:8,0:16,0 0,9,98:3:0:2,0:1,0:3,0 0,30,243:10:0:5,0:5,0:10,0 17 435 . A <*> 0 . DP=29;ADF=15,0;ADR=14,0;AD=29,0;I16=15,14,0,0,1035,38091,0,0,1647,96123,0,0,562,12596,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:8,0:8,0:16,0 0,9,103:3:0:2,0:1,0:3,0 0,30,237:10:0:5,0:5,0:10,0 17 436 . T <*> 0 . DP=28;ADF=14,0;ADR=14,0;AD=28,0;I16=14,14,0,0,998,36220,0,0,1587,92523,0,0,564,12654,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:8,0:8,0:16,0 0,9,110:3:0:2,0:1,0:3,0 0,27,223:9:0:4,0:5,0:9,0 -17 437 . T G,<*> 0 . DP=28;ADF=13,1,0;ADR=14,0,0;AD=27,1,0;I16=13,14,1,0,990,36832,6,36,1558,91682,29,841,549,12435,16,256;QS=2.9781,0.0218978,0;SGB=-0.556633;RPBZ=-1.36214;MQBZ=-2.88675;MQSBZ=0.6;BQBZ=-1.67909;NMBZ=-0.19245;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255,48,255,255:16:0:8,0,0:8,0,0:16,0,0 0,9,109,9,109,109:3:0:2,0,0:1,0,0:3,0,0 0,17,200,24,203,201:9:0:3,1,0:5,0,0:8,1,0 +17 437 . T G,<*> 0 . DP=28;ADF=13,1,0;ADR=14,0,0;AD=27,1,0;I16=13,14,1,0,990,36832,6,36,1558,91682,29,841,549,12435,16,256;QS=2.9781,0.0218978,0;SGB=-0.556633;RPBZ=-1.36214;MQBZ=-2.88675;MQSBZ=0.6;BQBZ=-1.67909;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255,48,255,255:16:0:8,0,0:8,0,0:16,0,0 0,9,109,9,109,109:3:0:2,0,0:1,0,0:3,0,0 0,17,200,24,203,201:9:0:3,1,0:5,0,0:8,1,0 17 438 . A <*> 0 . DP=28;ADF=14,0;ADR=14,0;AD=28,0;I16=14,14,0,0,984,35784,0,0,1587,92523,0,0,565,12707,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:8,0:8,0:16,0 0,9,107:3:0:2,0:1,0:3,0 0,27,220:9:0:4,0:5,0:9,0 17 439 . C <*> 0 . DP=28;ADF=14,0;ADR=14,0;AD=28,0;I16=14,14,0,0,1055,40273,0,0,1587,92523,0,0,563,12649,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:8,0:8,0:16,0 0,9,107:3:0:2,0:1,0:3,0 0,27,224:9:0:4,0:5,0:9,0 17 440 . A <*> 0 . DP=28;ADF=14,0;ADR=14,0;AD=28,0;I16=14,14,0,0,1095,43251,0,0,1587,92523,0,0,561,12615,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:8,0:8,0:16,0 0,9,115:3:0:2,0:1,0:3,0 0,27,247:9:0:4,0:5,0:9,0 @@ -394,13 +393,13 @@ 17 462 . G <*> 0 . DP=32;ADF=18,0;ADR=13,0;AD=31,0;I16=18,13,0,0,1169,46001,0,0,1775,103851,0,0,577,12669,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:10,0:7,0:17,0 0,12,131:4:0:3,0:1,0:4,0 0,30,241:10:0:5,0:5,0:10,0 17 463 . G <*> 0 . DP=32;ADF=18,0;ADR=13,0;AD=31,0;I16=18,13,0,0,1095,41573,0,0,1775,103851,0,0,583,12729,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:10,0:7,0:17,0 0,12,126:4:0:3,0:1,0:4,0 0,30,221:10:0:5,0:5,0:10,0 17 464 . A <*> 0 . DP=32;ADF=18,0;ADR=13,0;AD=31,0;I16=18,13,0,0,1100,41724,0,0,1775,103851,0,0,589,12821,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:10,0:7,0:17,0 0,12,148:4:0:3,0:1,0:4,0 0,30,217:10:0:5,0:5,0:10,0 -17 465 . C T,<*> 0 . DP=33;ADF=19,0,0;ADR=12,1,0;AD=31,1,0;I16=19,12,0,1,1173,45601,4,16,1775,103851,60,3600,589,12909,6,36;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.67982;MQBZ=0.321288;MQSBZ=0.341466;BQBZ=-1.68493;NMBZ=3.21288;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255,51,255,255:17:0:10,0,0:7,0,0:17,0,0 0,15,158,15,158,158:5:0:4,0,0:1,0,0:5,0,0 0,20,224,27,227,224:10:0:5,0,0:4,1,0:9,1,0 +17 465 . C T,<*> 0 . DP=33;ADF=19,0,0;ADR=12,1,0;AD=31,1,0;I16=19,12,0,1,1173,45601,4,16,1775,103851,60,3600,589,12909,6,36;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.67982;MQBZ=0.321288;MQSBZ=0.341466;BQBZ=-1.68493;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255,51,255,255:17:0:10,0,0:7,0,0:17,0,0 0,15,158,15,158,158:5:0:4,0,0:1,0,0:5,0,0 0,20,224,27,227,224:10:0:5,0,0:4,1,0:9,1,0 17 466 . A <*> 0 . DP=34;ADF=20,0;ADR=13,0;AD=33,0;I16=20,13,0,0,1268,49686,0,0,1895,111051,0,0,602,13102,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:11,0:7,0:18,0 0,15,173:5:0:4,0:1,0:5,0 0,30,255:10:0:5,0:5,0:10,0 17 467 . A <*> 0 . DP=34;ADF=20,0;ADR=13,0;AD=33,0;I16=20,13,0,0,1246,48610,0,0,1895,111051,0,0,608,13194,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:11,0:7,0:18,0 0,15,177:5:0:4,0:1,0:5,0 0,30,251:10:0:5,0:5,0:10,0 17 468 . A <*> 0 . DP=35;ADF=21,0;ADR=13,0;AD=34,0;I16=21,13,0,0,1253,48095,0,0,1955,114651,0,0,613,13273,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:12,0:7,0:19,0 0,15,174:5:0:4,0:1,0:5,0 0,30,251:10:0:5,0:5,0:10,0 17 469 . A <*> 0 . DP=35;ADF=21,0;ADR=13,0;AD=34,0;I16=21,13,0,0,1260,49028,0,0,1955,114651,0,0,618,13340,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:12,0:7,0:19,0 0,15,165:5:0:4,0:1,0:5,0 0,30,255:10:0:5,0:5,0:10,0 17 470 . G <*> 0 . DP=35;ADF=21,0;ADR=13,0;AD=34,0;I16=21,13,0,0,1265,48879,0,0,1955,114651,0,0,623,13445,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:12,0:7,0:19,0 0,15,167:5:0:4,0:1,0:5,0 0,30,238:10:0:5,0:5,0:10,0 -17 471 . T G,C,<*> 0 . DP=36;ADF=21,0,0,0;ADR=12,1,1,0;AD=33,1,1,0;I16=21,12,0,2,1220,46380,18,162,1918,113282,97,4969,611,13281,16,256;QS=2.94529,0.0273556,0.0273556,0;VDB=0.96;SGB=0.346553;RPBZ=0.497712;MQBZ=-1.9761;MQSBZ=0.312094;BQBZ=-2.35032;NMBZ=2.19566;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255,57,255,255,57,255,255,255:19:0:12,0,0,0:7,0,0,0:19,0,0,0 0,15,169,15,169,169,15,169,169,169:5:0:4,0,0,0:1,0,0,0:5,0,0,0 0,19,219,19,221,219,27,222,222,221:11:3:5,0,0,0:4,1,1,0:9,1,1,0 +17 471 . T G,C,<*> 0 . DP=36;ADF=21,0,0,0;ADR=12,1,1,0;AD=33,1,1,0;I16=21,12,0,2,1220,46380,18,162,1918,113282,97,4969,611,13281,16,256;QS=2.94529,0.0273556,0.0273556,0;VDB=0.96;SGB=0.346553;RPBZ=0.497712;MQBZ=-1.9761;MQSBZ=0.312094;BQBZ=-2.35032;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255,57,255,255,57,255,255,255:19:0:12,0,0,0:7,0,0,0:19,0,0,0 0,15,169,15,169,169,15,169,169,169:5:0:4,0,0,0:1,0,0,0:5,0,0,0 0,19,219,19,221,219,27,222,222,221:11:3:5,0,0,0:4,1,1,0:9,1,1,0 17 472 . T <*> 0 . DP=35;ADF=21,0;ADR=13,0;AD=34,0;I16=21,13,0,0,1234,46640,0,0,1955,114651,0,0,633,13665,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:12,0:7,0:19,0 0,15,172:5:0:4,0:1,0:5,0 0,30,241:10:0:5,0:5,0:10,0 17 473 . G <*> 0 . DP=35;ADF=21,0;ADR=13,0;AD=34,0;I16=21,13,0,0,1303,51953,0,0,1955,114651,0,0,638,13780,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:12,0:7,0:19,0 0,15,159:5:0:4,0:1,0:5,0 0,30,250:10:0:5,0:5,0:10,0 17 474 . G <*> 0 . DP=36;ADF=22,0;ADR=13,0;AD=35,0;I16=22,13,0,0,1279,49235,0,0,2015,118251,0,0,642,13884,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:12,0:7,0:19,0 0,15,146:5:0:4,0:1,0:5,0 0,33,255:11:0:6,0:5,0:11,0 @@ -417,7 +416,7 @@ 17 485 . G <*> 0 . DP=35;ADF=23,0;ADR=12,0;AD=35,0;I16=23,12,0,0,1329,51411,0,0,2015,118251,0,0,669,14931,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:12,0:6,0:18,0 0,18,160:6:0:5,0:1,0:6,0 0,33,255:11:0:6,0:5,0:11,0 17 486 . A <*> 0 . DP=34;ADF=22,0;ADR=12,0;AD=34,0;I16=22,12,0,0,1313,51667,0,0,1955,114651,0,0,671,14989,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:11,0:6,0:17,0 0,18,173:6:0:5,0:1,0:6,0 0,33,255:11:0:6,0:5,0:11,0 17 487 . G <*> 0 . DP=34;ADF=22,0;ADR=12,0;AD=34,0;I16=22,12,0,0,1300,50304,0,0,1955,114651,0,0,672,15030,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:11,0:6,0:17,0 0,18,169:6:0:5,0:1,0:6,0 0,33,255:11:0:6,0:5,0:11,0 -17 488 . A G,<*> 0 . DP=35;ADF=22,1,0;ADR=12,0,0;AD=34,1,0;I16=22,12,1,0,1278,48412,4,16,1986,117410,29,841,646,14380,25,625;QS=2.98947,0.0105263,0;SGB=-0.556633;RPBZ=0.594463;MQBZ=-3.36505;MQSBZ=0.10737;BQBZ=-1.69552;NMBZ=-0.171499;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255,54,255,255:18:0:12,0,0:6,0,0:18,0,0 0,18,177,18,177,177:6:0:5,0,0:1,0,0:6,0,0 0,23,255,30,255,255:11:0:5,1,0:5,0,0:10,1,0 +17 488 . A G,<*> 0 . DP=35;ADF=22,1,0;ADR=12,0,0;AD=34,1,0;I16=22,12,1,0,1278,48412,4,16,1986,117410,29,841,646,14380,25,625;QS=2.98947,0.0105263,0;SGB=-0.556633;RPBZ=0.594463;MQBZ=-3.36505;MQSBZ=0.10737;BQBZ=-1.69552;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255,54,255,255:18:0:12,0,0:6,0,0:18,0,0 0,18,177,18,177,177:6:0:5,0,0:1,0,0:6,0,0 0,23,255,30,255,255:11:0:5,1,0:5,0,0:10,1,0 17 489 . A <*> 0 . DP=35;ADF=23,0;ADR=12,0;AD=35,0;I16=23,12,0,0,1264,46916,0,0,2015,118251,0,0,671,15015,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:12,0:6,0:18,0 0,18,175:6:0:5,0:1,0:6,0 0,33,255:11:0:6,0:5,0:11,0 17 490 . A <*> 0 . DP=36;ADF=24,0;ADR=12,0;AD=36,0;I16=24,12,0,0,1332,50280,0,0,2075,121851,0,0,671,15061,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:12,0:6,0:18,0 0,21,188:7:0:6,0:1,0:7,0 0,33,255:11:0:6,0:5,0:11,0 17 491 . T <*> 0 . DP=36;ADF=24,0;ADR=12,0;AD=36,0;I16=24,12,0,0,1284,46802,0,0,2075,121851,0,0,671,15093,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:12,0:6,0:18,0 0,21,178:7:0:6,0:1,0:7,0 0,33,255:11:0:6,0:5,0:11,0 @@ -441,9 +440,9 @@ 17 509 . C <*> 0 . DP=34;ADF=24,0;ADR=10,0;AD=34,0;I16=24,10,0,0,1272,48272,0,0,1986,117410,0,0,640,14430,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:13,0:5,0:18,0 0,21,186:7:0:6,0:1,0:7,0 0,27,241:9:0:5,0:4,0:9,0 17 510 . A <*> 0 . DP=34;ADF=23,0;ADR=11,0;AD=34,0;I16=23,11,0,0,1211,44827,0,0,1986,117410,0,0,638,14398,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:13,0:6,0:19,0 0,21,187:7:0:6,0:1,0:7,0 0,24,221:8:0:4,0:4,0:8,0 17 511 . A <*> 0 . DP=34;ADF=23,0;ADR=11,0;AD=34,0;I16=23,11,0,0,1238,46516,0,0,1986,117410,0,0,637,14395,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:13,0:6,0:19,0 0,21,195:7:0:6,0:1,0:7,0 0,24,233:8:0:4,0:4,0:8,0 -17 512 . A C,<*> 0 . DP=33;ADF=22,0,0;ADR=10,1,0;AD=32,1,0;I16=22,10,0,1,1133,41513,13,169,1866,110210,60,3600,628,14340,9,81;QS=2.97766,0.0223368,0;SGB=-0.556633;RPBZ=-1.47079;MQBZ=0.253876;MQSBZ=-0.461593;BQBZ=-1.68442;NMBZ=2.68627;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255,51,255,255:18:0:12,0,0:5,1,0:17,1,0 0,21,183,21,183,183:7:0:6,0,0:1,0,0:7,0,0 0,24,231,24,231,231:8:0:4,0,0:4,0,0:8,0,0 -17 513 . A T,<*> 0 . DP=32;ADF=21,1,0;ADR=10,0,0;AD=31,1,0;I16=21,10,1,0,1125,42283,12,144,1806,106610,60,3600,623,14249,15,225;QS=2.97966,0.020339,0;SGB=-0.556633;RPBZ=-1.24609;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.57376;NMBZ=2.63913;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,37,255,48,255,255:17:0:11,1,0:5,0,0:16,1,0 0,21,177,21,177,177:7:0:6,0,0:1,0,0:7,0,0 0,24,233,24,233,233:8:0:4,0,0:4,0,0:8,0,0 -17 514 . A T,<*> 0 . DP=32;ADF=22,0,0;ADR=9,1,0;AD=31,1,0;I16=22,9,0,1,1086,40204,16,256,1806,106610,60,3600,627,14381,11,121;QS=2.97127,0.0287253,0;SGB=-0.556633;RPBZ=-1.4628;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.46657;NMBZ=2.63913;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,34,255,48,255,255:17:0:12,0,0:4,1,0:16,1,0 0,21,172,21,172,172:7:0:6,0,0:1,0,0:7,0,0 0,24,235,24,235,235:8:0:4,0,0:4,0,0:8,0,0 +17 512 . A C,<*> 0 . DP=33;ADF=22,0,0;ADR=10,1,0;AD=32,1,0;I16=22,10,0,1,1133,41513,13,169,1866,110210,60,3600,628,14340,9,81;QS=2.97766,0.0223368,0;SGB=-0.556633;RPBZ=-1.47079;MQBZ=0.253876;MQSBZ=-0.461593;BQBZ=-1.68442;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255,51,255,255:18:0:12,0,0:5,1,0:17,1,0 0,21,183,21,183,183:7:0:6,0,0:1,0,0:7,0,0 0,24,231,24,231,231:8:0:4,0,0:4,0,0:8,0,0 +17 513 . A T,<*> 0 . DP=32;ADF=21,1,0;ADR=10,0,0;AD=31,1,0;I16=21,10,1,0,1125,42283,12,144,1806,106610,60,3600,623,14249,15,225;QS=2.97966,0.020339,0;SGB=-0.556633;RPBZ=-1.24609;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.57376;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,37,255,48,255,255:17:0:11,1,0:5,0,0:16,1,0 0,21,177,21,177,177:7:0:6,0,0:1,0,0:7,0,0 0,24,233,24,233,233:8:0:4,0,0:4,0,0:8,0,0 +17 514 . A T,<*> 0 . DP=32;ADF=22,0,0;ADR=9,1,0;AD=31,1,0;I16=22,9,0,1,1086,40204,16,256,1806,106610,60,3600,627,14381,11,121;QS=2.97127,0.0287253,0;SGB=-0.556633;RPBZ=-1.4628;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.46657;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,34,255,48,255,255:17:0:12,0,0:4,1,0:16,1,0 0,21,172,21,172,172:7:0:6,0,0:1,0,0:7,0,0 0,24,235,24,235,235:8:0:4,0,0:4,0,0:8,0,0 17 515 . C <*> 0 . DP=32;ADF=22,0;ADR=10,0;AD=32,0;I16=22,10,0,0,1050,37704,0,0,1866,110210,0,0,638,14554,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:12,0:5,0:17,0 0,21,169:7:0:6,0:1,0:7,0 0,24,211:8:0:4,0:4,0:8,0 17 516 . C <*> 0 . DP=32;ADF=22,0;ADR=10,0;AD=32,0;I16=22,10,0,0,1109,40651,0,0,1866,110210,0,0,637,14579,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:12,0:5,0:17,0 0,21,187:7:0:6,0:1,0:7,0 0,24,215:8:0:4,0:4,0:8,0 17 517 . T <*> 0 . DP=33;ADF=23,0;ADR=10,0;AD=33,0;I16=23,10,0,0,1269,49995,0,0,1926,113810,0,0,636,14626,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:13,0:5,0:18,0 0,21,201:7:0:6,0:1,0:7,0 0,24,242:8:0:4,0:4,0:8,0 @@ -452,7 +451,7 @@ 17 520 . T <*> 0 . DP=36;ADF=25,0;ADR=11,0;AD=36,0;I16=25,11,0,0,1243,45051,0,0,2106,124610,0,0,638,14818,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,63,255:21:0:15,0:6,0:21,0 0,21,180:7:0:6,0:1,0:7,0 0,24,223:8:0:4,0:4,0:8,0 17 521 . C <*> 0 . DP=34;ADF=25,0;ADR=9,0;AD=34,0;I16=25,9,0,0,1281,49527,0,0,1986,117410,0,0,641,14875,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,60,255:20:0:15,0:5,0:20,0 0,21,191:7:0:6,0:1,0:7,0 0,21,204:7:0:4,0:3,0:7,0 17 522 . A <*> 0 . DP=32;ADF=24,0;ADR=8,0;AD=32,0;I16=24,8,0,0,1158,43228,0,0,1897,112969,0,0,646,14960,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,60,255:20:0:15,0:5,0:20,0 0,21,185:7:0:6,0:1,0:7,0 0,15,170:5:0:3,0:2,0:5,0 -17 523 . T G,<*> 0 . DP=32;ADF=23,1,0;ADR=8,0,0;AD=31,1,0;I16=23,8,1,0,1184,45708,15,225,1837,109369,60,3600,626,14446,25,625;QS=2.9794,0.0206044,0;SGB=-0.556633;RPBZ=1.13742;MQBZ=0.179605;MQSBZ=-1.73205;BQBZ=-1.68805;NMBZ=2.89159;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,44,255,57,255,255:20:0:14,1,0:5,0,0:19,1,0 0,21,191,21,191,191:7:0:6,0,0:1,0,0:7,0,0 0,15,166,15,166,166:5:0:3,0,0:2,0,0:5,0,0 +17 523 . T G,<*> 0 . DP=32;ADF=23,1,0;ADR=8,0,0;AD=31,1,0;I16=23,8,1,0,1184,45708,15,225,1837,109369,60,3600,626,14446,25,625;QS=2.9794,0.0206044,0;SGB=-0.556633;RPBZ=1.13742;MQBZ=0.179605;MQSBZ=-1.73205;BQBZ=-1.68805;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,44,255,57,255,255:20:0:14,1,0:5,0,0:19,1,0 0,21,191,21,191,191:7:0:6,0,0:1,0,0:7,0,0 0,15,166,15,166,166:5:0:3,0,0:2,0,0:5,0,0 17 524 . T <*> 0 . DP=32;ADF=24,0;ADR=8,0;AD=32,0;I16=24,8,0,0,1096,39618,0,0,1897,112969,0,0,654,15108,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,60,255:20:0:15,0:5,0:20,0 0,21,194:7:0:6,0:1,0:7,0 0,15,150:5:0:3,0:2,0:5,0 17 525 . G <*> 0 . DP=32;ADF=24,0;ADR=8,0;AD=32,0;I16=24,8,0,0,1188,45718,0,0,1897,112969,0,0,656,15120,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,60,255:20:0:15,0:5,0:20,0 0,21,188:7:0:6,0:1,0:7,0 0,15,133:5:0:3,0:2,0:5,0 17 526 . C <*> 0 . DP=32;ADF=24,0;ADR=8,0;AD=32,0;I16=24,8,0,0,1154,44014,0,0,1897,112969,0,0,658,15156,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,60,255:20:0:15,0:5,0:20,0 0,21,185:7:0:6,0:1,0:7,0 0,15,137:5:0:3,0:2,0:5,0 @@ -464,7 +463,7 @@ 17 532 . T <*> 0 . DP=32;ADF=25,0;ADR=7,0;AD=32,0;I16=25,7,0,0,1161,43607,0,0,1897,112969,0,0,649,14477,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:15,0:4,0:19,0 0,21,181:7:0:6,0:1,0:7,0 0,18,192:6:0:4,0:2,0:6,0 17 533 . C <*> 0 . DP=32;ADF=25,0;ADR=7,0;AD=32,0;I16=25,7,0,0,1154,44084,0,0,1897,112969,0,0,644,14274,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:15,0:4,0:19,0 0,21,178:7:0:6,0:1,0:7,0 0,18,180:6:0:4,0:2,0:6,0 17 534 . T <*> 0 . DP=31;ADF=24,0;ADR=7,0;AD=31,0;I16=24,7,0,0,1222,49526,0,0,1837,109369,0,0,640,14104,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:14,0:4,0:18,0 0,21,205:7:0:6,0:1,0:7,0 0,18,205:6:0:4,0:2,0:6,0 -17 535 . A G,<*> 0 . DP=31;ADF=24,0,0;ADR=6,1,0;AD=30,1,0;I16=24,6,0,1,1080,39870,8,64,1777,105769,60,3600,611,13341,25,625;QS=2.98623,0.0137694,0;SGB=-0.556633;RPBZ=-0.894788;MQBZ=0.182574;MQSBZ=-1.85164;BQBZ=-1.6854;NMBZ=2.94255;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,41,255,51,255,255:18:0:14,0,0:3,1,0:17,1,0 0,21,194,21,194,194:7:0:6,0,0:1,0,0:7,0,0 0,18,189,18,189,189:6:0:4,0,0:2,0,0:6,0,0 +17 535 . A G,<*> 0 . DP=31;ADF=24,0,0;ADR=6,1,0;AD=30,1,0;I16=24,6,0,1,1080,39870,8,64,1777,105769,60,3600,611,13341,25,625;QS=2.98623,0.0137694,0;SGB=-0.556633;RPBZ=-0.894788;MQBZ=0.182574;MQSBZ=-1.85164;BQBZ=-1.6854;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,41,255,51,255,255:18:0:14,0,0:3,1,0:17,1,0 0,21,194,21,194,194:7:0:6,0,0:1,0,0:7,0,0 0,18,189,18,189,189:6:0:4,0,0:2,0,0:6,0,0 17 536 . C <*> 0 . DP=31;ADF=24,0;ADR=7,0;AD=31,0;I16=24,7,0,0,1095,40551,0,0,1837,109369,0,0,631,13809,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:14,0:4,0:18,0 0,21,184:7:0:6,0:1,0:7,0 0,18,157:6:0:4,0:2,0:6,0 17 537 . C <*> 0 . DP=31;ADF=24,0;ADR=7,0;AD=31,0;I16=24,7,0,0,1049,38677,0,0,1837,109369,0,0,626,13682,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:14,0:4,0:18,0 0,21,172:7:0:6,0:1,0:7,0 0,18,183:6:0:4,0:2,0:6,0 17 538 . A <*> 0 . DP=31;ADF=24,0;ADR=7,0;AD=31,0;I16=24,7,0,0,1138,42478,0,0,1837,109369,0,0,620,13536,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:14,0:4,0:18,0 0,21,189:7:0:6,0:1,0:7,0 0,18,181:6:0:4,0:2,0:6,0 @@ -477,8 +476,8 @@ 17 545 . A <*> 0 . DP=33;ADF=25,0;ADR=8,0;AD=33,0;I16=25,8,0,0,1197,44795,0,0,1926,113810,0,0,587,12951,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:14,0:5,0:19,0 0,24,196:8:0:7,0:1,0:8,0 0,18,184:6:0:4,0:2,0:6,0 17 546 . A <*> 0 . DP=32;ADF=24,0;ADR=8,0;AD=32,0;I16=24,8,0,0,1136,41758,0,0,1866,110210,0,0,580,12802,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:14,0:5,0:19,0 0,21,166:7:0:6,0:1,0:7,0 0,18,193:6:0:4,0:2,0:6,0 17 547 . A <*> 0 . DP=32;ADF=24,0;ADR=8,0;AD=32,0;I16=24,8,0,0,1159,43539,0,0,1866,110210,0,0,572,12634,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:14,0:5,0:19,0 0,21,180:7:0:6,0:1,0:7,0 0,18,195:6:0:4,0:2,0:6,0 -17 548 . A C,<*> 0 . DP=33;ADF=23,1,0;ADR=9,0,0;AD=32,1,0;I16=23,9,1,0,1153,42673,9,81,1866,110210,60,3600,561,12489,3,9;QS=2.98607,0.0139319,0;SGB=-0.556633;RPBZ=1.57584;MQBZ=0.253876;MQSBZ=-2.34521;BQBZ=-1.68939;NMBZ=2.40838;SCBZ=3.80814;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,44,255,54,255,255:19:0:13,1,0:5,0,0:18,1,0 0,21,181,21,181,181:7:0:6,0,0:1,0,0:7,0,0 0,21,211,21,211,211:7:0:4,0,0:3,0,0:7,0,0 -17 549 . T G,<*> 0 . DP=32;ADF=23,0,0;ADR=8,1,0;AD=31,1,0;I16=23,8,0,1,1135,42143,20,400,1806,106610,60,3600,532,11720,25,625;QS=2.96918,0.0308166,0;SGB=-0.556633;RPBZ=-0.487556;MQBZ=0.258065;MQSBZ=-2.29695;BQBZ=-1.68602;NMBZ=2.45062;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,34,255,51,255,255:18:0:13,0,0:4,1,0:17,1,0 0,21,168,21,168,168:7:0:6,0,0:1,0,0:7,0,0 0,21,208,21,208,208:7:0:4,0,0:3,0,0:7,0,0 +17 548 . A C,<*> 0 . DP=33;ADF=23,1,0;ADR=9,0,0;AD=32,1,0;I16=23,9,1,0,1153,42673,9,81,1866,110210,60,3600,561,12489,3,9;QS=2.98607,0.0139319,0;SGB=-0.556633;RPBZ=1.57584;MQBZ=0.253876;MQSBZ=-2.34521;BQBZ=-1.68939;SCBZ=3.80814;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,44,255,54,255,255:19:0:13,1,0:5,0,0:18,1,0 0,21,181,21,181,181:7:0:6,0,0:1,0,0:7,0,0 0,21,211,21,211,211:7:0:4,0,0:3,0,0:7,0,0 +17 549 . T G,<*> 0 . DP=32;ADF=23,0,0;ADR=8,1,0;AD=31,1,0;I16=23,8,0,1,1135,42143,20,400,1806,106610,60,3600,532,11720,25,625;QS=2.96918,0.0308166,0;SGB=-0.556633;RPBZ=-0.487556;MQBZ=0.258065;MQSBZ=-2.29695;BQBZ=-1.68602;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,34,255,51,255,255:18:0:13,0,0:4,1,0:17,1,0 0,21,168,21,168,168:7:0:6,0,0:1,0,0:7,0,0 0,21,208,21,208,208:7:0:4,0,0:3,0,0:7,0,0 17 550 . T <*> 0 . DP=32;ADF=23,0;ADR=9,0;AD=32,0;I16=23,9,0,0,1056,37314,0,0,1866,110210,0,0,549,12177,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:13,0:5,0:18,0 0,21,150:7:0:6,0:1,0:7,0 0,21,220:7:0:4,0:3,0:7,0 17 551 . G <*> 0 . DP=31;ADF=22,0;ADR=9,0;AD=31,0;I16=22,9,0,0,1121,41639,0,0,1806,106610,0,0,541,12045,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:12,0:5,0:17,0 0,21,172:7:0:6,0:1,0:7,0 0,21,208:7:0:4,0:3,0:7,0 17 552 . C <*> 0 . DP=30;ADF=21,0;ADR=9,0;AD=30,0;I16=21,9,0,0,1093,41365,0,0,1746,103010,0,0,535,11947,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:11,0:5,0:16,0 0,21,167:7:0:6,0:1,0:7,0 0,21,208:7:0:4,0:3,0:7,0 @@ -488,14 +487,14 @@ 17 556 . C <*> 0 . DP=29;ADF=20,0;ADR=9,0;AD=29,0;I16=20,9,0,0,1055,39195,0,0,1709,101641,0,0,509,11219,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:11,0:6,0:17,0 0,18,158:6:0:5,0:1,0:6,0 0,18,186:6:0:4,0:2,0:6,0 17 557 . A <*> 0 . DP=27;ADF=18,0;ADR=9,0;AD=27,0;I16=18,9,0,0,987,36749,0,0,1589,94441,0,0,506,11074,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,45,255:15:0:9,0:6,0:15,0 0,18,157:6:0:5,0:1,0:6,0 0,18,186:6:0:4,0:2,0:6,0 17 558 . A <*> 0 . DP=27;ADF=18,0;ADR=9,0;AD=27,0;I16=18,9,0,0,956,35872,0,0,1589,94441,0,0,502,10906,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,45,255:15:0:9,0:6,0:15,0 0,18,153:6:0:5,0:1,0:6,0 0,18,177:6:0:4,0:2,0:6,0 -17 559 . C A,<*> 0 . DP=27;ADF=18,0,0;ADR=8,1,0;AD=26,1,0;I16=18,8,0,1,915,33775,14,196,1560,93600,29,841,473,10141,25,625;QS=2.92708,0.0729167,0;SGB=-0.556633;RPBZ=-1.02726;MQBZ=-5.09902;MQSBZ=-1.41421;BQBZ=-1.54776;NMBZ=3.05941;SCBZ=5.09902;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,45,255,45,255,255:15:0:9,0,0:6,0,0:15,0,0 0,4,116,15,119,123:6:0:5,0,0:0,1,0:5,1,0 0,18,169,18,169,169:6:0:4,0,0:2,0,0:6,0,0 +17 559 . C A,<*> 0 . DP=27;ADF=18,0,0;ADR=8,1,0;AD=26,1,0;I16=18,8,0,1,915,33775,14,196,1560,93600,29,841,473,10141,25,625;QS=2.92708,0.0729167,0;SGB=-0.556633;RPBZ=-1.02726;MQBZ=-5.09902;MQSBZ=-1.41421;BQBZ=-1.54776;SCBZ=5.09902;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,45,255,45,255,255:15:0:9,0,0:6,0,0:15,0,0 0,4,116,15,119,123:6:0:5,0,0:0,1,0:5,1,0 0,18,169,18,169,169:6:0:4,0,0:2,0,0:6,0,0 17 560 . C <*> 0 . DP=28;ADF=19,0;ADR=9,0;AD=28,0;I16=19,9,0,0,992,36552,0,0,1649,98041,0,0,494,10654,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,45,255:15:0:9,0:6,0:15,0 0,18,160:6:0:5,0:1,0:6,0 0,21,181:7:0:5,0:2,0:7,0 17 561 . A <*> 0 . DP=28;ADF=19,0;ADR=9,0;AD=28,0;I16=19,9,0,0,973,35555,0,0,1649,98041,0,0,491,10571,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,45,255:15:0:9,0:6,0:15,0 0,18,158:6:0:5,0:1,0:6,0 0,21,194:7:0:5,0:2,0:7,0 17 562 . C <*> 0 . DP=28;ADF=19,0;ADR=9,0;AD=28,0;I16=19,9,0,0,1014,38392,0,0,1649,98041,0,0,488,10518,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,45,255:15:0:9,0:6,0:15,0 0,18,153:6:0:5,0:1,0:6,0 0,21,187:7:0:5,0:2,0:7,0 17 563 . A <*> 0 . DP=27;ADF=18,0;ADR=9,0;AD=27,0;I16=18,9,0,0,903,32513,0,0,1589,94441,0,0,485,10445,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,45,255:15:0:9,0:6,0:15,0 0,15,149:5:0:4,0:1,0:5,0 0,21,179:7:0:5,0:2,0:7,0 17 564 . C <*> 0 . DP=27;ADF=18,0;ADR=9,0;AD=27,0;I16=18,9,0,0,859,28747,0,0,1589,94441,0,0,482,10402,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,45,255:15:0:9,0:6,0:15,0 0,15,121:5:0:4,0:1,0:5,0 0,21,182:7:0:5,0:2,0:7,0 17 565 . G <*> 0 . DP=30;ADF=18,0;ADR=12,0;AD=30,0;I16=18,12,0,0,842,27104,0,0,1769,105241,0,0,479,10389,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:9,0:8,0:17,0 0,18,100:6:0:4,0:2,0:6,0 0,21,154:7:0:5,0:2,0:7,0 -17 566 . C A,<*> 0 . DP=29;ADF=16,1,0;ADR=12,0,0;AD=28,1,0;I16=16,12,1,0,920,33998,9,81,1649,98041,60,3600,454,9734,25,625;QS=2.98321,0.016791,0;SGB=-0.556633;RPBZ=0.239193;MQBZ=0.188982;MQSBZ=-1.19024;BQBZ=-1.43942;NMBZ=-0.339233;SCBZ=-0.188982;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,38,255,48,255,255:17:0:8,1,0:8,0,0:16,1,0 0,15,155,15,155,155:5:0:3,0,0:2,0,0:5,0,0 0,21,170,21,170,170:7:0:5,0,0:2,0,0:7,0,0 +17 566 . C A,<*> 0 . DP=29;ADF=16,1,0;ADR=12,0,0;AD=28,1,0;I16=16,12,1,0,920,33998,9,81,1649,98041,60,3600,454,9734,25,625;QS=2.98321,0.016791,0;SGB=-0.556633;RPBZ=0.239193;MQBZ=0.188982;MQSBZ=-1.19024;BQBZ=-1.43942;SCBZ=-0.188982;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,38,255,48,255,255:17:0:8,1,0:8,0,0:16,1,0 0,15,155,15,155,155:5:0:3,0,0:2,0,0:5,0,0 0,21,170,21,170,170:7:0:5,0,0:2,0,0:7,0,0 17 567 . C <*> 0 . DP=30;ADF=17,0;ADR=13,0;AD=30,0;I16=17,13,0,0,956,34312,0,0,1769,105241,0,0,496,10638,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:9,0:8,0:17,0 0,18,156:6:0:3,0:3,0:6,0 0,21,194:7:0:5,0:2,0:7,0 17 568 . C <*> 0 . DP=29;ADF=16,0;ADR=13,0;AD=29,0;I16=16,13,0,0,1060,40304,0,0,1709,101641,0,0,497,10663,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:8,0:8,0:16,0 0,18,179:6:0:3,0:3,0:6,0 0,21,193:7:0:5,0:2,0:7,0 17 569 . T <*> 0 . DP=30;ADF=16,0;ADR=13,0;AD=29,0;I16=16,13,0,0,1061,41321,0,0,1709,101641,0,0,497,10671,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:8,0:8,0:16,0 0,18,190:6:0:3,0:3,0:6,0 0,21,213:7:0:5,0:2,0:7,0 @@ -503,15 +502,15 @@ 17 571 . C <*> 0 . DP=31;ADF=17,0;ADR=13,0;AD=30,0;I16=17,13,0,0,1069,40739,0,0,1769,105241,0,0,497,10783,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:9,0:8,0:17,0 0,18,159:6:0:3,0:3,0:6,0 0,21,193:7:0:5,0:2,0:7,0 17 572 . A <*> 0 . DP=31;ADF=18,0;ADR=12,0;AD=30,0;I16=18,12,0,0,1092,41268,0,0,1769,105241,0,0,499,10887,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:9,0:8,0:17,0 0,21,204:7:0:4,0:3,0:7,0 0,18,175:6:0:5,0:1,0:6,0 17 573 . A <*> 0 . DP=31;ADF=18,0;ADR=12,0;AD=30,0;I16=18,12,0,0,1060,38698,0,0,1769,105241,0,0,501,10975,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:9,0:8,0:17,0 0,21,201:7:0:4,0:3,0:7,0 0,18,178:6:0:5,0:1,0:6,0 -17 574 . C A,<*> 0 . DP=31;ADF=18,0,0;ADR=11,1,0;AD=29,1,0;I16=18,11,0,1,1088,41328,15,225,1740,104400,29,841,478,10422,25,625;QS=2.94071,0.0592885,0;SGB=-0.556633;RPBZ=-0.173514;MQBZ=-5.38516;MQSBZ=-1.22474;BQBZ=-1.68578;NMBZ=2.63996;SCBZ=3.60588;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255,48,255,255:16:0:8,0,0:8,0,0:16,0,0 0,9,170,21,173,177:8:0:5,0,0:2,1,0:7,1,0 0,18,173,18,173,173:6:0:5,0,0:1,0,0:6,0,0 -17 575 . T C,<*> 0 . DP=30;ADF=17,0,0;ADR=11,1,0;AD=28,1,0;I16=17,11,0,1,1048,41548,9,81,1680,100800,29,841,480,10426,25,625;QS=2.96786,0.0321429,0;SGB=-0.556633;RPBZ=-0.119685;MQBZ=-5.2915;MQSBZ=-1.19024;BQBZ=-1.68121;NMBZ=2.59197;SCBZ=3.53589;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255,48,255,255:16:0:8,0,0:8,0,0:16,0,0 0,13,200,21,203,202:8:0:5,0,0:2,1,0:7,1,0 0,15,163,15,163,163:5:0:4,0,0:1,0,0:5,0,0 +17 574 . C A,<*> 0 . DP=31;ADF=18,0,0;ADR=11,1,0;AD=29,1,0;I16=18,11,0,1,1088,41328,15,225,1740,104400,29,841,478,10422,25,625;QS=2.94071,0.0592885,0;SGB=-0.556633;RPBZ=-0.173514;MQBZ=-5.38516;MQSBZ=-1.22474;BQBZ=-1.68578;SCBZ=3.60588;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255,48,255,255:16:0:8,0,0:8,0,0:16,0,0 0,9,170,21,173,177:8:0:5,0,0:2,1,0:7,1,0 0,18,173,18,173,173:6:0:5,0,0:1,0,0:6,0,0 +17 575 . T C,<*> 0 . DP=30;ADF=17,0,0;ADR=11,1,0;AD=28,1,0;I16=17,11,0,1,1048,41548,9,81,1680,100800,29,841,480,10426,25,625;QS=2.96786,0.0321429,0;SGB=-0.556633;RPBZ=-0.119685;MQBZ=-5.2915;MQSBZ=-1.19024;BQBZ=-1.68121;SCBZ=3.53589;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255,48,255,255:16:0:8,0,0:8,0,0:16,0,0 0,13,200,21,203,202:8:0:5,0,0:2,1,0:7,1,0 0,15,163,15,163,163:5:0:4,0,0:1,0,0:5,0,0 17 576 . G <*> 0 . DP=30;ADF=17,0;ADR=12,0;AD=29,0;I16=17,12,0,0,1043,39581,0,0,1709,101641,0,0,507,11087,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:8,0:8,0:16,0 0,24,208:8:0:5,0:3,0:8,0 0,15,151:5:0:4,0:1,0:5,0 17 577 . G <*> 0 . DP=30;ADF=17,0;ADR=12,0;AD=29,0;I16=17,12,0,0,997,37255,0,0,1709,101641,0,0,509,11155,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:8,0:8,0:16,0 0,24,204:8:0:5,0:3,0:8,0 0,15,146:5:0:4,0:1,0:5,0 17 578 . G <*> 0 . DP=29;ADF=16,0;ADR=13,0;AD=29,0;I16=16,13,0,0,975,34803,0,0,1709,101641,0,0,520,11286,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:7,0:9,0:16,0 0,24,198:8:0:5,0:3,0:8,0 0,15,151:5:0:4,0:1,0:5,0 17 579 . G <*> 0 . DP=30;ADF=16,0;ADR=14,0;AD=30,0;I16=16,14,0,0,1038,38820,0,0,1769,105241,0,0,523,11335,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:8,0:9,0:17,0 0,24,224:8:0:4,0:4,0:8,0 0,15,144:5:0:4,0:1,0:5,0 -17 580 . A C,<*> 0 . DP=30;ADF=15,1,0;ADR=14,0,0;AD=29,1,0;I16=15,14,1,0,1060,39178,16,256,1709,101641,60,3600,510,11078,17,289;QS=2.97338,0.0266223,0;SGB=-0.556633;RPBZ=1.32953;MQBZ=0.185695;MQSBZ=-1.06904;BQBZ=-1.69093;NMBZ=1.86885;SCBZ=-0.267102;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,34,255,48,255,255:17:0:7,1,0:9,0,0:16,1,0 0,24,221,24,221,221:8:0:4,0,0:4,0,0:8,0,0 0,15,155,15,155,155:5:0:4,0,0:1,0,0:5,0,0 +17 580 . A C,<*> 0 . DP=30;ADF=15,1,0;ADR=14,0,0;AD=29,1,0;I16=15,14,1,0,1060,39178,16,256,1709,101641,60,3600,510,11078,17,289;QS=2.97338,0.0266223,0;SGB=-0.556633;RPBZ=1.32953;MQBZ=0.185695;MQSBZ=-1.06904;BQBZ=-1.69093;SCBZ=-0.267102;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,34,255,48,255,255:17:0:7,1,0:9,0,0:16,1,0 0,24,221,24,221,221:8:0:4,0,0:4,0,0:8,0,0 0,15,155,15,155,155:5:0:4,0,0:1,0,0:5,0,0 17 581 . A <*> 0 . DP=31;ADF=16,0;ADR=15,0;AD=31,0;I16=16,15,0,0,1083,39215,0,0,1829,108841,0,0,530,11384,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:8,0:10,0:18,0 0,24,223:8:0:4,0:4,0:8,0 0,15,153:5:0:4,0:1,0:5,0 -17 582 . C G,<*> 0 . DP=31;ADF=15,1,0;ADR=15,0,0;AD=30,1,0;I16=15,15,1,0,1080,39870,8,64,1769,105241,60,3600,519,11211,15,225;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.34259;MQBZ=0.182574;MQSBZ=-1.0328;BQBZ=-1.68266;NMBZ=1.92049;SCBZ=-0.262467;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,41,255,51,255,255:18:0:7,1,0:10,0,0:17,1,0 0,24,207,24,207,207:8:0:4,0,0:4,0,0:8,0,0 0,15,151,15,151,151:5:0:4,0,0:1,0,0:5,0,0 +17 582 . C G,<*> 0 . DP=31;ADF=15,1,0;ADR=15,0,0;AD=30,1,0;I16=15,15,1,0,1080,39870,8,64,1769,105241,60,3600,519,11211,15,225;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.34259;MQBZ=0.182574;MQSBZ=-1.0328;BQBZ=-1.68266;SCBZ=-0.262467;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,41,255,51,255,255:18:0:7,1,0:10,0,0:17,1,0 0,24,207,24,207,207:8:0:4,0,0:4,0,0:8,0,0 0,15,151,15,151,151:5:0:4,0,0:1,0,0:5,0,0 17 583 . T <*> 0 . DP=30;ADF=16,0;ADR=14,0;AD=30,0;I16=16,14,0,0,1135,43913,0,0,1769,105241,0,0,539,11523,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:8,0:9,0:17,0 0,24,238:8:0:4,0:4,0:8,0 0,15,163:5:0:4,0:1,0:5,0 17 584 . C <*> 0 . DP=31;ADF=17,0;ADR=14,0;AD=31,0;I16=17,14,0,0,1069,39521,0,0,1798,106082,0,0,544,11644,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:9,0:9,0:18,0 0,24,209:8:0:4,0:4,0:8,0 0,15,157:5:0:4,0:1,0:5,0 17 585 . A <*> 0 . DP=31;ADF=17,0;ADR=14,0;AD=31,0;I16=17,14,0,0,1096,39866,0,0,1798,106082,0,0,549,11751,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:9,0:9,0:18,0 0,24,211:8:0:4,0:4,0:8,0 0,15,157:5:0:4,0:1,0:5,0 @@ -522,10 +521,10 @@ 17 590 . C <*> 0 . DP=32;ADF=17,0;ADR=15,0;AD=32,0;I16=17,15,0,0,1103,41355,0,0,1858,109682,0,0,574,12576,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:9,0:9,0:18,0 0,24,194:8:0:4,0:4,0:8,0 0,18,175:6:0:4,0:2,0:6,0 17 591 . A <*> 0 . DP=31;ADF=16,0;ADR=15,0;AD=31,0;I16=16,15,0,0,1164,44088,0,0,1798,106082,0,0,579,12695,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:9,0:9,0:18,0 0,21,209:7:0:3,0:4,0:7,0 0,18,188:6:0:4,0:2,0:6,0 17 592 . A <*> 0 . DP=31;ADF=16,0;ADR=15,0;AD=31,0;I16=16,15,0,0,1121,42193,0,0,1798,106082,0,0,583,12795,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:9,0:9,0:18,0 0,21,215:7:0:3,0:4,0:7,0 0,18,182:6:0:4,0:2,0:6,0 -17 593 . C A,<*> 0 . DP=31;ADF=16,0,0;ADR=14,1,0;AD=30,1,0;I16=16,14,0,1,1071,39925,7,49,1769,105241,29,841,561,12253,25,625;QS=2.97021,0.0297872,0;SGB=-0.556633;RPBZ=0.559355;MQBZ=-3.80789;MQSBZ=-0.0464238;BQBZ=-1.57464;NMBZ=2.13779;SCBZ=3.67454;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255,54,255,255:18:0:9,0,0:9,0,0:18,0,0 0,12,184,18,187,185:7:0:3,0,0:3,1,0:6,1,0 0,18,174,18,174,174:6:0:4,0,0:2,0,0:6,0,0 -17 594 . A G,<*> 0 . DP=33;ADF=16,1,0;ADR=16,0,0;AD=32,1,0;I16=16,16,1,0,1161,42757,4,16,1858,109682,60,3600,572,12672,15,225;QS=2.99359,0.00641026,0;SGB=-0.556633;RPBZ=-0.998367;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68954;NMBZ=1.76408;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,42,255,51,255,255:18:0:8,1,0:9,0,0:17,1,0 0,21,205,21,205,205:7:0:3,0,0:4,0,0:7,0,0 0,24,213,24,213,213:8:0:5,0,0:3,0,0:8,0,0 +17 593 . C A,<*> 0 . DP=31;ADF=16,0,0;ADR=14,1,0;AD=30,1,0;I16=16,14,0,1,1071,39925,7,49,1769,105241,29,841,561,12253,25,625;QS=2.97021,0.0297872,0;SGB=-0.556633;RPBZ=0.559355;MQBZ=-3.80789;MQSBZ=-0.0464238;BQBZ=-1.57464;SCBZ=3.67454;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255,54,255,255:18:0:9,0,0:9,0,0:18,0,0 0,12,184,18,187,185:7:0:3,0,0:3,1,0:6,1,0 0,18,174,18,174,174:6:0:4,0,0:2,0,0:6,0,0 +17 594 . A G,<*> 0 . DP=33;ADF=16,1,0;ADR=16,0,0;AD=32,1,0;I16=16,16,1,0,1161,42757,4,16,1858,109682,60,3600,572,12672,15,225;QS=2.99359,0.00641026,0;SGB=-0.556633;RPBZ=-0.998367;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68954;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,42,255,51,255,255:18:0:8,1,0:9,0,0:17,1,0 0,21,205,21,205,205:7:0:3,0,0:4,0,0:7,0,0 0,24,213,24,213,213:8:0:5,0,0:3,0,0:8,0,0 17 595 . A <*> 0 . DP=33;ADF=17,0;ADR=16,0;AD=33,0;I16=17,16,0,0,1136,40412,0,0,1918,113282,0,0,589,12905,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:9,0:9,0:18,0 0,21,198:7:0:3,0:4,0:7,0 0,24,218:8:0:5,0:3,0:8,0 -17 596 . A G,<*> 0 . DP=33;ADF=16,1,0;ADR=16,0,0;AD=32,1,0;I16=16,16,1,0,1061,37187,8,64,1858,109682,60,3600,590,12952,1,1;QS=2.98564,0.0143627,0;SGB=-0.556633;RPBZ=1.68146;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68357;NMBZ=1.61602;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,41,255,51,255,255:18:0:8,1,0:9,0,0:17,1,0 0,21,169,21,169,169:7:0:3,0,0:4,0,0:7,0,0 0,24,231,24,231,231:8:0:5,0,0:3,0,0:8,0,0 +17 596 . A G,<*> 0 . DP=33;ADF=16,1,0;ADR=16,0,0;AD=32,1,0;I16=16,16,1,0,1061,37187,8,64,1858,109682,60,3600,590,12952,1,1;QS=2.98564,0.0143627,0;SGB=-0.556633;RPBZ=1.68146;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68357;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,41,255,51,255,255:18:0:8,1,0:9,0,0:17,1,0 0,21,169,21,169,169:7:0:3,0,0:4,0,0:7,0,0 0,24,231,24,231,231:8:0:5,0,0:3,0,0:8,0,0 17 597 . C <*> 0 . DP=33;ADF=17,0;ADR=16,0;AD=33,0;I16=17,16,0,0,1196,44890,0,0,1918,113282,0,0,592,12990,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:9,0:9,0:18,0 0,21,204:7:0:3,0:4,0:7,0 0,24,220:8:0:5,0:3,0:8,0 17 598 . T <*> 0 . DP=33;ADF=16,0;ADR=17,0;AD=33,0;I16=16,17,0,0,1219,47333,0,0,1918,113282,0,0,597,13029,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:8,0:9,0:17,0 0,21,217:7:0:3,0:4,0:7,0 0,27,242:9:0:5,0:4,0:9,0 17 599 . T <*> 0 . DP=33;ADF=16,0;ADR=17,0;AD=33,0;I16=16,17,0,0,1182,43598,0,0,1918,113282,0,0,599,13095,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:8,0:9,0:17,0 0,21,197:7:0:3,0:4,0:7,0 0,27,247:9:0:5,0:4,0:9,0 diff --git a/test/mpileup/mpileup.6.out b/test/mpileup/mpileup.6.out index 21b14428d..51c080cb0 100644 --- a/test/mpileup/mpileup.6.out +++ b/test/mpileup/mpileup.6.out @@ -11,7 +11,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -25,97 +24,97 @@ ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00100 HG00101 HG00102 17 100 . C <*> . . END=102;MinDP=3;QS=3,0 PL:DP 0,27,182:9 0,9,108:3 0,15,132:5 -17 103 . T C,<*> 0 . DP=18;I16=15,1,1,0,668,28542,6,36,929,54841,29,841,323,7035,6,36;QS=2.98256,0.0174419,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64924;NMBZ=2.45514;SCBZ=4;FS=0;MQ0F=0 PL:DP:DV 0,17,184,24,187,185:9:1 0,9,118,9,118,118:3:0 0,15,147,15,147,147:5:0 -17 104 . G C,<*> 0 . DP=18;I16=15,1,1,0,601,24163,3,9,929,54841,29,841,320,6884,7,49;QS=2.98726,0.0127389,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64309;NMBZ=2.45514;SCBZ=4;FS=0;MQ0F=0 PL:DP:DV 0,18,173,24,176,173:9:1 0,9,101,9,101,101:3:0 0,15,133,15,133,133:5:0 +17 103 . T C,<*> 0 . DP=18;I16=15,1,1,0,668,28542,6,36,929,54841,29,841,323,7035,6,36;QS=2.98256,0.0174419,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64924;SCBZ=4;FS=0;MQ0F=0 PL:DP:DV 0,17,184,24,187,185:9:1 0,9,118,9,118,118:3:0 0,15,147,15,147,147:5:0 +17 104 . G C,<*> 0 . DP=18;I16=15,1,1,0,601,24163,3,9,929,54841,29,841,320,6884,7,49;QS=2.98726,0.0127389,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64309;SCBZ=4;FS=0;MQ0F=0 PL:DP:DV 0,18,173,24,176,173:9:1 0,9,101,9,101,101:3:0 0,15,133,15,133,133:5:0 17 105 . G <*> . . END=108;MinDP=3;QS=3,0 PL:DP 0,30,171:10 0,9,92:3 0,15,124:5 -17 109 . T C,<*> 0 . DP=19;I16=16,1,1,0,716,30648,2,4,989,58441,29,841,309,6415,12,144;QS=2.98922,0.0107817,0;SGB=-0.556633;RPBZ=-0.674966;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.6661;NMBZ=2.52179;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV 0,20,191,27,194,191:10:1 0,9,120,9,120,120:3:0 0,15,150,15,150,150:5:0 +17 109 . T C,<*> 0 . DP=19;I16=16,1,1,0,716,30648,2,4,989,58441,29,841,309,6415,12,144;QS=2.98922,0.0107817,0;SGB=-0.556633;RPBZ=-0.674966;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.6661;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV 0,20,191,27,194,191:10:1 0,9,120,9,120,120:3:0 0,15,150,15,150,150:5:0 17 110 . G <*> . . END=111;MinDP=3;QS=3,0 PL:DP 0,30,167:10 0,9,95:3 0,15,119:5 -17 112 . C G,<*> 0 . DP=19;I16=16,1,1,0,657,26565,2,4,989,58441,29,841,301,6277,15,225;QS=2.98907,0.010929,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65292;NMBZ=2.52179;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV 0,20,187,27,190,187:10:1 0,9,103,9,103,103:3:0 0,15,135,15,135,135:5:0 -17 113 . A G,<*> 0 . DP=19;I16=16,1,1,0,635,25055,4,16,989,58441,29,841,297,6207,16,256;QS=2.98817,0.0118343,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65205;NMBZ=2.52179;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV 0,20,172,27,175,172:10:1 0,9,102,9,102,102:3:0 0,15,139,15,139,139:5:0 +17 112 . C G,<*> 0 . DP=19;I16=16,1,1,0,657,26565,2,4,989,58441,29,841,301,6277,15,225;QS=2.98907,0.010929,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65292;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV 0,20,187,27,190,187:10:1 0,9,103,9,103,103:3:0 0,15,135,15,135,135:5:0 +17 113 . A G,<*> 0 . DP=19;I16=16,1,1,0,635,25055,4,16,989,58441,29,841,297,6207,16,256;QS=2.98817,0.0118343,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65205;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV 0,20,172,27,175,172:10:1 0,9,102,9,102,102:3:0 0,15,139,15,139,139:5:0 17 114 . C <*> . . MinDP=3;QS=3,0 PL:DP 0,30,181:10 0,9,113:3 0,15,133:5 -17 115 . C A,<*> 0 . DP=21;I16=17,2,1,0,688,27426,12,144,1078,62882,29,841,283,5827,25,625;QS=2.88785,0.11215,0;SGB=-0.556633;RPBZ=0.260329;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.47798;NMBZ=2.3712;SCBZ=-0.418446;FS=0;MQ0F=0 PL:DP:DV 0,30,189,30,189,189:10:0 3,0,86,9,89,93:3:1 0,21,153,21,153,153:7:0 -17 116 . A C,<*> 0 . DP=21;I16=17,2,1,0,705,27791,2,4,1078,62882,29,841,287,6073,19,361;QS=2.98873,0.0112676,0;SGB=-0.556633;RPBZ=0.0867763;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.65814;NMBZ=2.65016;SCBZ=2.65016;FS=0;MQ0F=0 PL:DP:DV 0,20,179,27,182,179:10:1 0,9,102,9,102,102:3:0 0,21,175,21,175,175:7:0 +17 115 . C A,<*> 0 . DP=21;I16=17,2,1,0,688,27426,12,144,1078,62882,29,841,283,5827,25,625;QS=2.88785,0.11215,0;SGB=-0.556633;RPBZ=0.260329;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.47798;SCBZ=-0.418446;FS=0;MQ0F=0 PL:DP:DV 0,30,189,30,189,189:10:0 3,0,86,9,89,93:3:1 0,21,153,21,153,153:7:0 +17 116 . A C,<*> 0 . DP=21;I16=17,2,1,0,705,27791,2,4,1078,62882,29,841,287,6073,19,361;QS=2.98873,0.0112676,0;SGB=-0.556633;RPBZ=0.0867763;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.65814;SCBZ=2.65016;FS=0;MQ0F=0 PL:DP:DV 0,20,179,27,182,179:10:1 0,9,102,9,102,102:3:0 0,21,175,21,175,175:7:0 17 117 . G <*> . . END=119;MinDP=2;QS=3,0 PL:DP 0,27,175:9 0,6,76:2 0,21,160:7 -17 120 . A G,<*> 0 . DP=19;I16=15,2,1,0,646,25392,4,16,958,55682,29,841,277,5999,23,529;QS=2.9873,0.0126984,0;SGB=-0.556633;RPBZ=0.28942;MQBZ=-2.23607;MQSBZ=-1.30384;BQBZ=-1.6486;NMBZ=3;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV 0,18,171,24,174,171:9:1 0,6,88,6,88,88:2:0 0,21,171,21,171,171:7:0 +17 120 . A G,<*> 0 . DP=19;I16=15,2,1,0,646,25392,4,16,958,55682,29,841,277,5999,23,529;QS=2.9873,0.0126984,0;SGB=-0.556633;RPBZ=0.28942;MQBZ=-2.23607;MQSBZ=-1.30384;BQBZ=-1.6486;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV 0,18,171,24,174,171:9:1 0,6,88,6,88,88:2:0 0,21,171,21,171,171:7:0 17 121 . G <*> . . END=124;MinDP=2;QS=3,0 PL:DP 0,24,170:8 0,6,84:2 0,18,154:6 -17 125 . A T,<*> 0 . DP=18;I16=14,2,1,0,589,22565,4,16,898,52082,29,841,272,5916,25,625;QS=2.98444,0.0155642,0;SGB=-0.556633;RPBZ=1.02125;MQBZ=-2.16025;MQSBZ=-1.23956;BQBZ=-1.64106;NMBZ=2.91548;SCBZ=2.91548;FS=0;MQ0F=0 PL:DP:DV 0,15,149,21,152,149:8:1 0,9,114,9,114,114:3:0 0,18,162,18,162,162:6:0 +17 125 . A T,<*> 0 . DP=18;I16=14,2,1,0,589,22565,4,16,898,52082,29,841,272,5916,25,625;QS=2.98444,0.0155642,0;SGB=-0.556633;RPBZ=1.02125;MQBZ=-2.16025;MQSBZ=-1.23956;BQBZ=-1.64106;SCBZ=2.91548;FS=0;MQ0F=0 PL:DP:DV 0,15,149,21,152,149:8:1 0,9,114,9,114,114:3:0 0,18,162,18,162,162:6:0 17 126 . A <*> . . END=158;MinDP=2;QS=3,0 PL:DP 0,18,128:6 0,6,81:2 0,15,102:5 -17 159 . A G,<*> 0 . DP=15;I16=12,2,1,0,519,19467,5,25,809,47641,60,3600,260,5880,0,0;QS=2.97076,0.0292398,0;SGB=-0.556633;RPBZ=-1.62019;MQBZ=0.267261;MQSBZ=-2.54951;BQBZ=-1.63041;NMBZ=0;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,21,157,21,157,157:7:0 0,6,83,6,83,83:2:0 0,10,129,15,132,129:6:1 +17 159 . A G,<*> 0 . DP=15;I16=12,2,1,0,519,19467,5,25,809,47641,60,3600,260,5880,0,0;QS=2.97076,0.0292398,0;SGB=-0.556633;RPBZ=-1.62019;MQBZ=0.267261;MQSBZ=-2.54951;BQBZ=-1.63041;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,21,157,21,157,157:7:0 0,6,83,6,83,83:2:0 0,10,129,15,132,129:6:1 17 160 . G <*> . . END=173;MinDP=2;QS=3,0 PL:DP 0,15,106:5 0,6,75:2 0,15,138:5 17 174 . G <*> . . END=188;MinDP=1;QS=3,0 PL:DP 0,15,111:5 0,3,27:1 0,21,116:7 17 189 . C <*> . . MinDP=2;QS=3,0 PL:DP 0,18,152:6 0,6,67:2 0,21,167:7 -17 190 . A C,<*> 0 . DP=15;I16=12,2,1,0,500,18230,5,25,778,44882,60,3600,243,5381,25,625;QS=2.97664,0.0233645,0;SGB=-0.556633;RPBZ=0;MQBZ=0.392232;MQSBZ=-3.74166;BQBZ=-1.63041;NMBZ=-0.267261;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,18,138,18,138,138:6:0 0,6,68,6,68,68:2:0 0,12,153,18,156,153:7:1 +17 190 . A C,<*> 0 . DP=15;I16=12,2,1,0,500,18230,5,25,778,44882,60,3600,243,5381,25,625;QS=2.97664,0.0233645,0;SGB=-0.556633;RPBZ=0;MQBZ=0.392232;MQSBZ=-3.74166;BQBZ=-1.63041;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,18,138,18,138,138:6:0 0,6,68,6,68,68:2:0 0,12,153,18,156,153:7:1 17 191 . T <*> . . END=222;MinDP=2;QS=3,0 PL:DP 0,18,140:6 0,6,63:2 0,12,73:4 -17 223 . G T,<*> 0 . DP=13;I16=9,3,1,0,412,14782,8,64,627,34923,60,3600,243,5657,25,625;QS=2.96596,0.0340426,0;SGB=-0.556633;RPBZ=1.07052;MQBZ=0.547723;MQSBZ=-3.4641;BQBZ=-1.60577;NMBZ=-0.288675;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,11,166,18,169,167:7:1 0,6,53,6,53,53:2:0 0,12,81,12,81,81:4:0 +17 223 . G T,<*> 0 . DP=13;I16=9,3,1,0,412,14782,8,64,627,34923,60,3600,243,5657,25,625;QS=2.96596,0.0340426,0;SGB=-0.556633;RPBZ=1.07052;MQBZ=0.547723;MQSBZ=-3.4641;BQBZ=-1.60577;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,11,166,18,169,167:7:1 0,6,53,6,53,53:2:0 0,12,81,12,81,81:4:0 17 224 . G <*> . . END=225;MinDP=2;QS=3,0 PL:DP 0,18,165:6 0,6,48:2 0,12,70:4 -17 226 . A G,C,<*> 0 . DP=13;I16=8,3,1,1,381,13669,6,18,567,31323,89,4441,248,5894,44,986;QS=2.94293,0.0392157,0.0178571,0;VDB=0.84;SGB=-2.62246;RPBZ=-0.592157;MQBZ=-0.615457;MQSBZ=-3.4641;BQBZ=-2.17723;NMBZ=2.34521;SCBZ=2.34521;FS=0;MQ0F=0 PL:DP:DV 0,18,159,12,162,159,18,159,162,159:7:1 0,6,53,6,53,53,6,53,53,53:2:0 0,5,79,9,82,80,9,82,80,80:4:1 +17 226 . A G,C,<*> 0 . DP=13;I16=8,3,1,1,381,13669,6,18,567,31323,89,4441,248,5894,44,986;QS=2.94293,0.0392157,0.0178571,0;VDB=0.84;SGB=-2.62246;RPBZ=-0.592157;MQBZ=-0.615457;MQSBZ=-3.4641;BQBZ=-2.17723;SCBZ=2.34521;FS=0;MQ0F=0 PL:DP:DV 0,18,159,12,162,159,18,159,162,159:7:1 0,6,53,6,53,53,6,53,53,53:2:0 0,5,79,9,82,80,9,82,80,80:4:1 17 227 . C <*> . . END=236;MinDP=2;QS=3,0 PL:DP 0,21,145:7 0,6,45:2 0,12,70:4 -17 237 . A C,<*> 0 . DP=14;I16=9,4,1,0,465,16877,8,64,656,35764,60,3600,266,6282,25,625;QS=2.93162,0.0683761,0;SGB=-0.556633;RPBZ=1.11754;MQBZ=0.632456;MQSBZ=-3.60555;BQBZ=-1.61959;NMBZ=-0.27735;SCBZ=-0.27735;FS=0;MQ0F=0 PL:DP:DV 0,24,206,24,206,206:8:0 0,6,53,6,53,53:2:0 0,3,84,9,87,87:4:1 +17 237 . A C,<*> 0 . DP=14;I16=9,4,1,0,465,16877,8,64,656,35764,60,3600,266,6282,25,625;QS=2.93162,0.0683761,0;SGB=-0.556633;RPBZ=1.11754;MQBZ=0.632456;MQSBZ=-3.60555;BQBZ=-1.61959;SCBZ=-0.27735;FS=0;MQ0F=0 PL:DP:DV 0,24,206,24,206,206:8:0 0,6,53,6,53,53:2:0 0,3,84,9,87,87:4:1 17 238 . C <*> . . END=255;MinDP=2;QS=3,0 PL:DP 0,24,211:8 0,6,50:2 0,12,64:4 17 256 . A <*> . . END=266;MinDP=5;QS=3,0 PL:DP 0,33,247:11 0,15,92:5 0,15,122:5 -17 267 . T G,<*> 0 . DP=21;I16=9,11,0,1,739,27465,8,64,960,50456,29,841,373,7935,25,625;QS=2.94203,0.057971,0;SGB=-0.556633;RPBZ=-0.330396;MQBZ=-1.23153;MQSBZ=-3.3021;BQBZ=-1.66282;NMBZ=2.4409;SCBZ=2.91633;FS=0;MQ0F=0 PL:DP:DV 0,33,254,33,254,254:11:0 0,6,93,12,96,96:5:1 0,15,149,15,149,149:5:0 +17 267 . T G,<*> 0 . DP=21;I16=9,11,0,1,739,27465,8,64,960,50456,29,841,373,7935,25,625;QS=2.94203,0.057971,0;SGB=-0.556633;RPBZ=-0.330396;MQBZ=-1.23153;MQSBZ=-3.3021;BQBZ=-1.66282;SCBZ=2.91633;FS=0;MQ0F=0 PL:DP:DV 0,33,254,33,254,254:11:0 0,6,93,12,96,96:5:1 0,15,149,15,149,149:5:0 17 268 . T <*> . . END=272;MinDP=5;QS=3,0 PL:DP 0,33,238:11 0,15,91:5 0,15,143:5 -17 273 . T C,<*> 0 . DP=22;I16=9,12,0,1,798,30664,5,25,989,51297,29,841,392,8620,25,625;QS=2.96094,0.0390625,0;SGB=-0.556633;RPBZ=-0.236567;MQBZ=-1.16701;MQSBZ=-3.42286;BQBZ=-1.66779;NMBZ=2.50862;SCBZ=3.00076;FS=0;MQ0F=0 PL:DP:DV 0,36,255,36,255,255:12:0 0,7,89,12,92,90:5:1 0,15,161,15,161,161:5:0 +17 273 . T C,<*> 0 . DP=22;I16=9,12,0,1,798,30664,5,25,989,51297,29,841,392,8620,25,625;QS=2.96094,0.0390625,0;SGB=-0.556633;RPBZ=-0.236567;MQBZ=-1.16701;MQSBZ=-3.42286;BQBZ=-1.66779;SCBZ=3.00076;FS=0;MQ0F=0 PL:DP:DV 0,36,255,36,255,255:12:0 0,7,89,12,92,90:5:1 0,15,161,15,161,161:5:0 17 274 . C <*> . . MinDP=5;QS=3,0 PL:DP 0,36,255:12 0,15,101:5 0,15,144:5 17 275 . C <*> . . END=277;MinDP=4;QS=3,0 PL:DP 0,33,253:11 0,15,114:5 0,12,121:4 -17 278 . A C,<*> 0 . DP=21;I16=6,14,1,0,722,26452,7,49,867,42179,60,3600,415,9521,11,121;QS=2.97935,0.020649,0;SGB=-0.556633;RPBZ=1.65198;MQBZ=1.0247;MQSBZ=-3.24037;BQBZ=-1.66667;NMBZ=-0.406816;SCBZ=-0.324037;FS=0;MQ0F=0 PL:DP:DV 0,22,231,30,234,231:11:1 0,18,123,18,123,123:6:0 0,12,121,12,121,121:4:0 +17 278 . A C,<*> 0 . DP=21;I16=6,14,1,0,722,26452,7,49,867,42179,60,3600,415,9521,11,121;QS=2.97935,0.020649,0;SGB=-0.556633;RPBZ=1.65198;MQBZ=1.0247;MQSBZ=-3.24037;BQBZ=-1.66667;SCBZ=-0.324037;FS=0;MQ0F=0 PL:DP:DV 0,22,231,30,234,231:11:1 0,18,123,18,123,123:6:0 0,12,121,12,121,121:4:0 17 279 . A <*> . . END=282;MinDP=4;QS=3,0 PL:DP 0,36,253:12 0,18,122:6 0,12,119:4 17 283 . C <*> . . END=296;MinDP=5;QS=3,0 PL:DP 0,33,240:11 0,18,119:6 0,15,122:5 -17 297 . C G,<*> 0 . DP=25;I16=9,15,1,0,901,34305,4,16,1138,59338,60,3600,445,9901,10,100;QS=2.98261,0.0173913,0;SGB=-0.556633;RPBZ=-1.24856;MQBZ=0.806872;MQSBZ=-3.22749;BQBZ=-1.67542;NMBZ=-0.434372;SCBZ=-0.368383;FS=0;MQ0F=0 PL:DP:DV 0,33,255,33,255,255:11:0 0,15,168,21,171,168:8:1 0,18,161,18,161,161:6:0 +17 297 . C G,<*> 0 . DP=25;I16=9,15,1,0,901,34305,4,16,1138,59338,60,3600,445,9901,10,100;QS=2.98261,0.0173913,0;SGB=-0.556633;RPBZ=-1.24856;MQBZ=0.806872;MQSBZ=-3.22749;BQBZ=-1.67542;SCBZ=-0.368383;FS=0;MQ0F=0 PL:DP:DV 0,33,255,33,255,255:11:0 0,15,168,21,171,168:8:1 0,18,161,18,161,161:6:0 17 298 . A <*> . . END=301;MinDP=7;QS=3,0 PL:DP 0,30,231:10 0,21,172:7 0,21,189:7 -17 302 . T TA 0 . INDEL;IDV=7;IMF=1;DP=25;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.539485,2.46052;VDB=0.241622;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.22749;BQBZ=-1.67542;NMBZ=-0.199304;SCBZ=-0.268121;FS=0;MQ0F=0 PL:DP:DV 161,0,99:11:6 158,0,14:7:6 201,21,0:7:7 +17 302 . T TA 0 . INDEL;IDV=7;IMF=1;DP=25;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.539485,2.46052;VDB=0.241622;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.22749;BQBZ=-1.67542;SCBZ=-0.268121;FS=0;MQ0F=0 PL:DP:DV 161,0,99:11:6 158,0,14:7:6 201,21,0:7:7 17 303 . G <*> . . END=334;MinDP=7;QS=3,0 PL:DP 0,30,235:10 0,21,197:7 0,21,195:7 -17 335 . A G,<*> 0 . DP=32;I16=13,18,1,0,1084,40336,4,16,1589,87297,60,3600,555,11943,0,0;QS=2.98919,0.0108108,0;SGB=-0.556633;RPBZ=-1.67936;MQBZ=0.622171;MQSBZ=-2.25492;BQBZ=-1.68602;NMBZ=-0.428353;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV 0,33,252,33,252,252:11:0 0,27,219,27,219,219:9:0 0,25,245,33,248,245:12:1 +17 335 . A G,<*> 0 . DP=32;I16=13,18,1,0,1084,40336,4,16,1589,87297,60,3600,555,11943,0,0;QS=2.98919,0.0108108,0;SGB=-0.556633;RPBZ=-1.67936;MQBZ=0.622171;MQSBZ=-2.25492;BQBZ=-1.68602;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV 0,33,252,33,252,252:11:0 0,27,219,27,219,219:9:0 0,25,245,33,248,245:12:1 17 336 . A <*> . . MinDP=9;QS=3,0 PL:DP 0,33,255:11 0,27,212:9 0,36,255:12 -17 337 . C A,<*> 0 . DP=32;I16=14,17,0,1,1125,42481,5,25,1612,89528,37,1369,536,11590,18,324;QS=2.98113,0.0188679,0;SGB=-0.556633;RPBZ=0.812593;MQBZ=-1.03695;MQSBZ=-2.25492;BQBZ=-1.68353;NMBZ=-0.376914;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV 0,33,255,33,255,255:11:0 0,17,195,24,198,195:9:1 0,36,255,36,255,255:12:0 +17 337 . C A,<*> 0 . DP=32;I16=14,17,0,1,1125,42481,5,25,1612,89528,37,1369,536,11590,18,324;QS=2.98113,0.0188679,0;SGB=-0.556633;RPBZ=0.812593;MQBZ=-1.03695;MQSBZ=-2.25492;BQBZ=-1.68353;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV 0,33,255,33,255,255:11:0 0,17,195,24,198,195:9:1 0,36,255,36,255,255:12:0 17 338 . T <*> . . END=354;MinDP=8;QS=3,0 PL:DP 0,27,225:9 0,24,185:8 0,30,255:10 -17 355 . G T,<*> 0 . DP=28;I16=14,13,0,1,1001,37907,41,1681,1442,81174,60,3600,547,12487,25,625;QS=2.875,0.125,0;SGB=-0.556633;RPBZ=0.185772;MQBZ=0.520126;MQSBZ=-1.7696;BQBZ=0.683978;NMBZ=2.33874;SCBZ=-0.27735;FS=0;MQ0F=0 PL:DP:DV 14,0,200,38,203,231:9:1 0,27,222,27,222,222:9:0 0,30,255,30,255,255:10:0 +17 355 . G T,<*> 0 . DP=28;I16=14,13,0,1,1001,37907,41,1681,1442,81174,60,3600,547,12487,25,625;QS=2.875,0.125,0;SGB=-0.556633;RPBZ=0.185772;MQBZ=0.520126;MQSBZ=-1.7696;BQBZ=0.683978;SCBZ=-0.27735;FS=0;MQ0F=0 PL:DP:DV 14,0,200,38,203,231:9:1 0,27,222,27,222,222:9:0 0,30,255,30,255,255:10:0 17 356 . G <*> . . END=358;MinDP=8;QS=3,0 PL:DP 0,27,228:9 0,24,197:8 0,30,252:10 -17 359 . G T,<*> 0 . DP=29;I16=15,13,0,1,1085,42761,10,100,1525,87005,60,3600,552,12620,25,625;QS=2.96032,0.0396825,0;SGB=-0.556633;RPBZ=-0.119611;MQBZ=0.456435;MQSBZ=-1.53333;BQBZ=-1.68246;NMBZ=3.0531;SCBZ=5.2915;FS=0;MQ0F=0 PL:DP:DV 0,30,255,30,255,255:10:0 0,13,178,21,181,180:8:1 0,33,255,33,255,255:11:0 +17 359 . G T,<*> 0 . DP=29;I16=15,13,0,1,1085,42761,10,100,1525,87005,60,3600,552,12620,25,625;QS=2.96032,0.0396825,0;SGB=-0.556633;RPBZ=-0.119611;MQBZ=0.456435;MQSBZ=-1.53333;BQBZ=-1.68246;SCBZ=5.2915;FS=0;MQ0F=0 PL:DP:DV 0,30,255,30,255,255:10:0 0,13,178,21,181,180:8:1 0,33,255,33,255,255:11:0 17 360 . A <*> . . END=368;MinDP=8;QS=3,0 PL:DP 0,30,252:10 0,24,204:8 0,30,255:10 -17 369 . T G,<*> 0 . DP=28;I16=16,11,0,1,1037,40275,6,36,1496,86164,60,3600,548,12256,25,625;QS=2.97683,0.023166,0;SGB=-0.556633;RPBZ=0.12395;MQBZ=0.408248;MQSBZ=-1.37784;BQBZ=-1.68703;NMBZ=2.99794;SCBZ=5.19615;FS=0;MQ0F=0 PL:DP:DV 0,30,250,30,250,250:10:0 0,15,189,21,192,190:8:1 0,30,255,30,255,255:10:0 +17 369 . T G,<*> 0 . DP=28;I16=16,11,0,1,1037,40275,6,36,1496,86164,60,3600,548,12256,25,625;QS=2.97683,0.023166,0;SGB=-0.556633;RPBZ=0.12395;MQBZ=0.408248;MQSBZ=-1.37784;BQBZ=-1.68703;SCBZ=5.19615;FS=0;MQ0F=0 PL:DP:DV 0,30,250,30,250,250:10:0 0,15,189,21,192,190:8:1 0,30,255,30,255,255:10:0 17 370 . C <*> . . END=374;MinDP=8;QS=3,0 PL:DP 0,30,255:10 0,24,201:8 0,30,255:10 -17 375 . A T,<*> 0 . DP=31;I16=17,13,0,1,1138,43798,14,196,1676,96964,60,3600,547,12177,4,16;QS=2.9661,0.0338983,0;SGB=-0.556633;RPBZ=-1.45432;MQBZ=0.3849;MQSBZ=-1.26404;BQBZ=-1.68488;NMBZ=2.30253;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,36,255,36,255,255:12:0 0,24,218,24,218,218:8:0 0,18,255,30,255,255:11:1 +17 375 . A T,<*> 0 . DP=31;I16=17,13,0,1,1138,43798,14,196,1676,96964,60,3600,547,12177,4,16;QS=2.9661,0.0338983,0;SGB=-0.556633;RPBZ=-1.45432;MQBZ=0.3849;MQSBZ=-1.26404;BQBZ=-1.68488;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,36,255,36,255,255:12:0 0,24,218,24,218,218:8:0 0,18,255,30,255,255:11:1 17 376 . G <*> . . END=383;MinDP=7;QS=3,0 PL:DP 0,36,255:12 0,21,172:7 0,30,255:10 -17 384 . A C,<*> 0 . DP=31;I16=19,11,0,1,1077,39885,4,16,1738,102482,60,3600,504,10988,25,625;QS=2.98419,0.0158103,0;SGB=-0.556633;RPBZ=0.615229;MQBZ=0.262613;MQSBZ=-0.333409;BQBZ=-1.68746;NMBZ=3.26825;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,39,255,39,255,255:13:0 0,15,171,21,174,171:8:1 0,30,255,30,255,255:10:0 +17 384 . A C,<*> 0 . DP=31;I16=19,11,0,1,1077,39885,4,16,1738,102482,60,3600,504,10988,25,625;QS=2.98419,0.0158103,0;SGB=-0.556633;RPBZ=0.615229;MQBZ=0.262613;MQSBZ=-0.333409;BQBZ=-1.68746;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,39,255,39,255,255:13:0 0,15,171,21,174,171:8:1 0,30,255,30,255,255:10:0 17 385 . C <*> . . END=400;MinDP=5;QS=3,0 PL:DP 0,36,255:12 0,15,133:5 0,30,255:10 -17 401 . A C,<*> 0 . DP=29;I16=17,11,0,1,1063,41001,8,64,1587,92523,60,3600,501,11113,25,625;QS=2.97985,0.0201511,0;SGB=-0.556633;RPBZ=-0.478622;MQBZ=0.339683;MQSBZ=0.29364;BQBZ=-1.68267;NMBZ=3.53589;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,39,255,39,255,255:13:0 0,15,160,15,160,160:5:0 0,22,255,30,255,255:11:1 +17 401 . A C,<*> 0 . DP=29;I16=17,11,0,1,1063,41001,8,64,1587,92523,60,3600,501,11113,25,625;QS=2.97985,0.0201511,0;SGB=-0.556633;RPBZ=-0.478622;MQBZ=0.339683;MQSBZ=0.29364;BQBZ=-1.68267;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,39,255,39,255,255:13:0 0,15,160,15,160,160:5:0 0,22,255,30,255,255:11:1 17 402 . T <*> . . END=404;MinDP=5;QS=3,0 PL:DP 0,39,255:13 0,15,131:5 0,33,255:11 17 405 . T <*> . . END=411;MinDP=4;QS=3,0 PL:DP 0,39,255:13 0,12,109:4 0,30,244:10 -17 412 . C T,<*> 0 . DP=30;I16=17,12,1,0,1094,42458,14,196,1678,98882,60,3600,495,10659,25,625;QS=2.97455,0.0254545,0;SGB=-0.556633;RPBZ=-0.40473;MQBZ=0.267261;MQSBZ=-0.293785;BQBZ=-1.6942;NMBZ=-0.267102;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,30,255,42,255,255:15:1 0,12,124,12,124,124:4:0 0,33,255,33,255,255:11:0 +17 412 . C T,<*> 0 . DP=30;I16=17,12,1,0,1094,42458,14,196,1678,98882,60,3600,495,10659,25,625;QS=2.97455,0.0254545,0;SGB=-0.556633;RPBZ=-0.40473;MQBZ=0.267261;MQSBZ=-0.293785;BQBZ=-1.6942;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,30,255,42,255,255:15:1 0,12,124,12,124,124:4:0 0,33,255,33,255,255:11:0 17 413 . A <*> . . END=436;MinDP=3;QS=3,0 PL:DP 0,45,255:15 0,9,98:3 0,27,223:9 -17 437 . T G,<*> 0 . DP=28;I16=13,14,1,0,990,36832,6,36,1558,91682,29,841,549,12435,16,256;QS=2.9781,0.0218978,0;SGB=-0.556633;RPBZ=-1.36214;MQBZ=-2.88675;MQSBZ=0.6;BQBZ=-1.67909;NMBZ=-0.19245;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,48,255,48,255,255:16:0 0,9,109,9,109,109:3:0 0,17,200,24,203,201:9:1 +17 437 . T G,<*> 0 . DP=28;I16=13,14,1,0,990,36832,6,36,1558,91682,29,841,549,12435,16,256;QS=2.9781,0.0218978,0;SGB=-0.556633;RPBZ=-1.36214;MQBZ=-2.88675;MQSBZ=0.6;BQBZ=-1.67909;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,48,255,48,255,255:16:0 0,9,109,9,109,109:3:0 0,17,200,24,203,201:9:1 17 438 . A <*> . . END=464;MinDP=2;QS=3,0 PL:DP 0,48,255:16 0,6,97:2 0,27,198:9 -17 465 . C T,<*> 0 . DP=33;I16=19,12,0,1,1173,45601,4,16,1775,103851,60,3600,589,12909,6,36;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.67982;MQBZ=0.321288;MQSBZ=0.341466;BQBZ=-1.68493;NMBZ=3.21288;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,51,255,51,255,255:17:0 0,15,158,15,158,158:5:0 0,20,224,27,227,224:10:1 +17 465 . C T,<*> 0 . DP=33;I16=19,12,0,1,1173,45601,4,16,1775,103851,60,3600,589,12909,6,36;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.67982;MQBZ=0.321288;MQSBZ=0.341466;BQBZ=-1.68493;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,51,255,51,255,255:17:0 0,15,158,15,158,158:5:0 0,20,224,27,227,224:10:1 17 466 . A <*> . . END=470;MinDP=5;QS=3,0 PL:DP 0,54,255:18 0,15,165:5 0,30,238:10 -17 471 . T G,C,<*> 0 . DP=36;I16=21,12,0,2,1220,46380,18,162,1918,113282,97,4969,611,13281,16,256;QS=2.94529,0.0273556,0.0273556,0;VDB=0.96;SGB=0.346553;RPBZ=0.497712;MQBZ=-1.9761;MQSBZ=0.312094;BQBZ=-2.35032;NMBZ=2.19566;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,57,255,57,255,255,57,255,255,255:19:0 0,15,169,15,169,169,15,169,169,169:5:0 0,19,219,19,221,219,27,222,222,221:11:2 +17 471 . T G,C,<*> 0 . DP=36;I16=21,12,0,2,1220,46380,18,162,1918,113282,97,4969,611,13281,16,256;QS=2.94529,0.0273556,0.0273556,0;VDB=0.96;SGB=0.346553;RPBZ=0.497712;MQBZ=-1.9761;MQSBZ=0.312094;BQBZ=-2.35032;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,57,255,57,255,255,57,255,255,255:19:0 0,15,169,15,169,169,15,169,169,169:5:0 0,19,219,19,221,219,27,222,222,221:11:2 17 472 . T <*> . . END=487;MinDP=5;QS=3,0 PL:DP 0,51,255:17 0,15,146:5 0,30,241:10 -17 488 . A G,<*> 0 . DP=35;I16=22,12,1,0,1278,48412,4,16,1986,117410,29,841,646,14380,25,625;QS=2.98947,0.0105263,0;SGB=-0.556633;RPBZ=0.594463;MQBZ=-3.36505;MQSBZ=0.10737;BQBZ=-1.69552;NMBZ=-0.171499;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,54,255,54,255,255:18:0 0,18,177,18,177,177:6:0 0,23,255,30,255,255:11:1 +17 488 . A G,<*> 0 . DP=35;I16=22,12,1,0,1278,48412,4,16,1986,117410,29,841,646,14380,25,625;QS=2.98947,0.0105263,0;SGB=-0.556633;RPBZ=0.594463;MQBZ=-3.36505;MQSBZ=0.10737;BQBZ=-1.69552;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,54,255,54,255,255:18:0 0,18,177,18,177,177:6:0 0,23,255,30,255,255:11:1 17 489 . A <*> . . END=511;MinDP=6;QS=3,0 PL:DP 0,51,255:17 0,18,175:6 0,24,221:8 -17 512 . A C,<*> 0 . DP=33;I16=22,10,0,1,1133,41513,13,169,1866,110210,60,3600,628,14340,9,81;QS=2.97766,0.0223368,0;SGB=-0.556633;RPBZ=-1.47079;MQBZ=0.253876;MQSBZ=-0.461593;BQBZ=-1.68442;NMBZ=2.68627;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,39,255,51,255,255:18:1 0,21,183,21,183,183:7:0 0,24,231,24,231,231:8:0 -17 513 . A T,<*> 0 . DP=32;I16=21,10,1,0,1125,42283,12,144,1806,106610,60,3600,623,14249,15,225;QS=2.97966,0.020339,0;SGB=-0.556633;RPBZ=-1.24609;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.57376;NMBZ=2.63913;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,37,255,48,255,255:17:1 0,21,177,21,177,177:7:0 0,24,233,24,233,233:8:0 -17 514 . A T,<*> 0 . DP=32;I16=22,9,0,1,1086,40204,16,256,1806,106610,60,3600,627,14381,11,121;QS=2.97127,0.0287253,0;SGB=-0.556633;RPBZ=-1.4628;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.46657;NMBZ=2.63913;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,34,255,48,255,255:17:1 0,21,172,21,172,172:7:0 0,24,235,24,235,235:8:0 +17 512 . A C,<*> 0 . DP=33;I16=22,10,0,1,1133,41513,13,169,1866,110210,60,3600,628,14340,9,81;QS=2.97766,0.0223368,0;SGB=-0.556633;RPBZ=-1.47079;MQBZ=0.253876;MQSBZ=-0.461593;BQBZ=-1.68442;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,39,255,51,255,255:18:1 0,21,183,21,183,183:7:0 0,24,231,24,231,231:8:0 +17 513 . A T,<*> 0 . DP=32;I16=21,10,1,0,1125,42283,12,144,1806,106610,60,3600,623,14249,15,225;QS=2.97966,0.020339,0;SGB=-0.556633;RPBZ=-1.24609;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.57376;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,37,255,48,255,255:17:1 0,21,177,21,177,177:7:0 0,24,233,24,233,233:8:0 +17 514 . A T,<*> 0 . DP=32;I16=22,9,0,1,1086,40204,16,256,1806,106610,60,3600,627,14381,11,121;QS=2.97127,0.0287253,0;SGB=-0.556633;RPBZ=-1.4628;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.46657;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,34,255,48,255,255:17:1 0,21,172,21,172,172:7:0 0,24,235,24,235,235:8:0 17 515 . C <*> . . END=522;MinDP=5;QS=3,0 PL:DP 0,51,255:17 0,21,169:7 0,15,170:5 -17 523 . T G,<*> 0 . DP=32;I16=23,8,1,0,1184,45708,15,225,1837,109369,60,3600,626,14446,25,625;QS=2.9794,0.0206044,0;SGB=-0.556633;RPBZ=1.13742;MQBZ=0.179605;MQSBZ=-1.73205;BQBZ=-1.68805;NMBZ=2.89159;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,44,255,57,255,255:20:1 0,21,191,21,191,191:7:0 0,15,166,15,166,166:5:0 +17 523 . T G,<*> 0 . DP=32;I16=23,8,1,0,1184,45708,15,225,1837,109369,60,3600,626,14446,25,625;QS=2.9794,0.0206044,0;SGB=-0.556633;RPBZ=1.13742;MQBZ=0.179605;MQSBZ=-1.73205;BQBZ=-1.68805;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,44,255,57,255,255:20:1 0,21,191,21,191,191:7:0 0,15,166,15,166,166:5:0 17 524 . T <*> . . END=534;MinDP=5;QS=3,0 PL:DP 0,54,255:18 0,21,172:7 0,15,133:5 -17 535 . A G,<*> 0 . DP=31;I16=24,6,0,1,1080,39870,8,64,1777,105769,60,3600,611,13341,25,625;QS=2.98623,0.0137694,0;SGB=-0.556633;RPBZ=-0.894788;MQBZ=0.182574;MQSBZ=-1.85164;BQBZ=-1.6854;NMBZ=2.94255;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,21,194,21,194,194:7:0 0,18,189,18,189,189:6:0 +17 535 . A G,<*> 0 . DP=31;I16=24,6,0,1,1080,39870,8,64,1777,105769,60,3600,611,13341,25,625;QS=2.98623,0.0137694,0;SGB=-0.556633;RPBZ=-0.894788;MQBZ=0.182574;MQSBZ=-1.85164;BQBZ=-1.6854;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,21,194,21,194,194:7:0 0,18,189,18,189,189:6:0 17 536 . C <*> . . END=547;MinDP=6;QS=3,0 PL:DP 0,54,255:18 0,21,166:7 0,18,157:6 -17 548 . A C,<*> 0 . DP=33;I16=23,9,1,0,1153,42673,9,81,1866,110210,60,3600,561,12489,3,9;QS=2.98607,0.0139319,0;SGB=-0.556633;RPBZ=1.57584;MQBZ=0.253876;MQSBZ=-2.34521;BQBZ=-1.68939;NMBZ=2.40838;SCBZ=3.80814;FS=0;MQ0F=0 PL:DP:DV 0,44,255,54,255,255:19:1 0,21,181,21,181,181:7:0 0,21,211,21,211,211:7:0 -17 549 . T G,<*> 0 . DP=32;I16=23,8,0,1,1135,42143,20,400,1806,106610,60,3600,532,11720,25,625;QS=2.96918,0.0308166,0;SGB=-0.556633;RPBZ=-0.487556;MQBZ=0.258065;MQSBZ=-2.29695;BQBZ=-1.68602;NMBZ=2.45062;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV 0,34,255,51,255,255:18:1 0,21,168,21,168,168:7:0 0,21,208,21,208,208:7:0 +17 548 . A C,<*> 0 . DP=33;I16=23,9,1,0,1153,42673,9,81,1866,110210,60,3600,561,12489,3,9;QS=2.98607,0.0139319,0;SGB=-0.556633;RPBZ=1.57584;MQBZ=0.253876;MQSBZ=-2.34521;BQBZ=-1.68939;SCBZ=3.80814;FS=0;MQ0F=0 PL:DP:DV 0,44,255,54,255,255:19:1 0,21,181,21,181,181:7:0 0,21,211,21,211,211:7:0 +17 549 . T G,<*> 0 . DP=32;I16=23,8,0,1,1135,42143,20,400,1806,106610,60,3600,532,11720,25,625;QS=2.96918,0.0308166,0;SGB=-0.556633;RPBZ=-0.487556;MQBZ=0.258065;MQSBZ=-2.29695;BQBZ=-1.68602;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV 0,34,255,51,255,255:18:1 0,21,168,21,168,168:7:0 0,21,208,21,208,208:7:0 17 550 . T <*> . . END=558;MinDP=6;QS=3,0 PL:DP 0,45,255:15 0,18,143:6 0,18,177:6 -17 559 . C A,<*> 0 . DP=27;I16=18,8,0,1,915,33775,14,196,1560,93600,29,841,473,10141,25,625;QS=2.92708,0.0729167,0;SGB=-0.556633;RPBZ=-1.02726;MQBZ=-5.09902;MQSBZ=-1.41421;BQBZ=-1.54776;NMBZ=3.05941;SCBZ=5.09902;FS=0;MQ0F=0 PL:DP:DV 0,45,255,45,255,255:15:0 0,4,116,15,119,123:6:1 0,18,169,18,169,169:6:0 +17 559 . C A,<*> 0 . DP=27;I16=18,8,0,1,915,33775,14,196,1560,93600,29,841,473,10141,25,625;QS=2.92708,0.0729167,0;SGB=-0.556633;RPBZ=-1.02726;MQBZ=-5.09902;MQSBZ=-1.41421;BQBZ=-1.54776;SCBZ=5.09902;FS=0;MQ0F=0 PL:DP:DV 0,45,255,45,255,255:15:0 0,4,116,15,119,123:6:1 0,18,169,18,169,169:6:0 17 560 . C <*> . . END=565;MinDP=5;QS=3,0 PL:DP 0,45,255:15 0,15,121:5 0,21,154:7 -17 566 . C A,<*> 0 . DP=29;I16=16,12,1,0,920,33998,9,81,1649,98041,60,3600,454,9734,25,625;QS=2.98321,0.016791,0;SGB=-0.556633;RPBZ=0.239193;MQBZ=0.188982;MQSBZ=-1.19024;BQBZ=-1.43942;NMBZ=-0.339233;SCBZ=-0.188982;FS=0;MQ0F=0 PL:DP:DV 0,38,255,48,255,255:17:1 0,15,155,15,155,155:5:0 0,21,170,21,170,170:7:0 +17 566 . C A,<*> 0 . DP=29;I16=16,12,1,0,920,33998,9,81,1649,98041,60,3600,454,9734,25,625;QS=2.98321,0.016791,0;SGB=-0.556633;RPBZ=0.239193;MQBZ=0.188982;MQSBZ=-1.19024;BQBZ=-1.43942;SCBZ=-0.188982;FS=0;MQ0F=0 PL:DP:DV 0,38,255,48,255,255:17:1 0,15,155,15,155,155:5:0 0,21,170,21,170,170:7:0 17 567 . C <*> . . END=573;MinDP=6;QS=3,0 PL:DP 0,48,255:16 0,18,156:6 0,18,175:6 -17 574 . C A,<*> 0 . DP=31;I16=18,11,0,1,1088,41328,15,225,1740,104400,29,841,478,10422,25,625;QS=2.94071,0.0592885,0;SGB=-0.556633;RPBZ=-0.173514;MQBZ=-5.38516;MQSBZ=-1.22474;BQBZ=-1.68578;NMBZ=2.63996;SCBZ=3.60588;FS=0;MQ0F=0 PL:DP:DV 0,48,255,48,255,255:16:0 0,9,170,21,173,177:8:1 0,18,173,18,173,173:6:0 -17 575 . T C,<*> 0 . DP=30;I16=17,11,0,1,1048,41548,9,81,1680,100800,29,841,480,10426,25,625;QS=2.96786,0.0321429,0;SGB=-0.556633;RPBZ=-0.119685;MQBZ=-5.2915;MQSBZ=-1.19024;BQBZ=-1.68121;NMBZ=2.59197;SCBZ=3.53589;FS=0;MQ0F=0 PL:DP:DV 0,48,255,48,255,255:16:0 0,13,200,21,203,202:8:1 0,15,163,15,163,163:5:0 +17 574 . C A,<*> 0 . DP=31;I16=18,11,0,1,1088,41328,15,225,1740,104400,29,841,478,10422,25,625;QS=2.94071,0.0592885,0;SGB=-0.556633;RPBZ=-0.173514;MQBZ=-5.38516;MQSBZ=-1.22474;BQBZ=-1.68578;SCBZ=3.60588;FS=0;MQ0F=0 PL:DP:DV 0,48,255,48,255,255:16:0 0,9,170,21,173,177:8:1 0,18,173,18,173,173:6:0 +17 575 . T C,<*> 0 . DP=30;I16=17,11,0,1,1048,41548,9,81,1680,100800,29,841,480,10426,25,625;QS=2.96786,0.0321429,0;SGB=-0.556633;RPBZ=-0.119685;MQBZ=-5.2915;MQSBZ=-1.19024;BQBZ=-1.68121;SCBZ=3.53589;FS=0;MQ0F=0 PL:DP:DV 0,48,255,48,255,255:16:0 0,13,200,21,203,202:8:1 0,15,163,15,163,163:5:0 17 576 . G <*> . . END=579;MinDP=5;QS=3,0 PL:DP 0,48,255:16 0,24,198:8 0,15,144:5 -17 580 . A C,<*> 0 . DP=30;I16=15,14,1,0,1060,39178,16,256,1709,101641,60,3600,510,11078,17,289;QS=2.97338,0.0266223,0;SGB=-0.556633;RPBZ=1.32953;MQBZ=0.185695;MQSBZ=-1.06904;BQBZ=-1.69093;NMBZ=1.86885;SCBZ=-0.267102;FS=0;MQ0F=0 PL:DP:DV 0,34,255,48,255,255:17:1 0,24,221,24,221,221:8:0 0,15,155,15,155,155:5:0 +17 580 . A C,<*> 0 . DP=30;I16=15,14,1,0,1060,39178,16,256,1709,101641,60,3600,510,11078,17,289;QS=2.97338,0.0266223,0;SGB=-0.556633;RPBZ=1.32953;MQBZ=0.185695;MQSBZ=-1.06904;BQBZ=-1.69093;SCBZ=-0.267102;FS=0;MQ0F=0 PL:DP:DV 0,34,255,48,255,255:17:1 0,24,221,24,221,221:8:0 0,15,155,15,155,155:5:0 17 581 . A <*> . . MinDP=5;QS=3,0 PL:DP 0,54,255:18 0,24,223:8 0,15,153:5 -17 582 . C G,<*> 0 . DP=31;I16=15,15,1,0,1080,39870,8,64,1769,105241,60,3600,519,11211,15,225;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.34259;MQBZ=0.182574;MQSBZ=-1.0328;BQBZ=-1.68266;NMBZ=1.92049;SCBZ=-0.262467;FS=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,24,207,24,207,207:8:0 0,15,151,15,151,151:5:0 +17 582 . C G,<*> 0 . DP=31;I16=15,15,1,0,1080,39870,8,64,1769,105241,60,3600,519,11211,15,225;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.34259;MQBZ=0.182574;MQSBZ=-1.0328;BQBZ=-1.68266;SCBZ=-0.262467;FS=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,24,207,24,207,207:8:0 0,15,151,15,151,151:5:0 17 583 . T <*> . . END=592;MinDP=5;QS=3,0 PL:DP 0,51,255:17 0,21,209:7 0,15,155:5 -17 593 . C A,<*> 0 . DP=31;I16=16,14,0,1,1071,39925,7,49,1769,105241,29,841,561,12253,25,625;QS=2.97021,0.0297872,0;SGB=-0.556633;RPBZ=0.559355;MQBZ=-3.80789;MQSBZ=-0.0464238;BQBZ=-1.57464;NMBZ=2.13779;SCBZ=3.67454;FS=0;MQ0F=0 PL:DP:DV 0,54,255,54,255,255:18:0 0,12,184,18,187,185:7:1 0,18,174,18,174,174:6:0 -17 594 . A G,<*> 0 . DP=33;I16=16,16,1,0,1161,42757,4,16,1858,109682,60,3600,572,12672,15,225;QS=2.99359,0.00641026,0;SGB=-0.556633;RPBZ=-0.998367;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68954;NMBZ=1.76408;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:DV 0,42,255,51,255,255:18:1 0,21,205,21,205,205:7:0 0,24,213,24,213,213:8:0 +17 593 . C A,<*> 0 . DP=31;I16=16,14,0,1,1071,39925,7,49,1769,105241,29,841,561,12253,25,625;QS=2.97021,0.0297872,0;SGB=-0.556633;RPBZ=0.559355;MQBZ=-3.80789;MQSBZ=-0.0464238;BQBZ=-1.57464;SCBZ=3.67454;FS=0;MQ0F=0 PL:DP:DV 0,54,255,54,255,255:18:0 0,12,184,18,187,185:7:1 0,18,174,18,174,174:6:0 +17 594 . A G,<*> 0 . DP=33;I16=16,16,1,0,1161,42757,4,16,1858,109682,60,3600,572,12672,15,225;QS=2.99359,0.00641026,0;SGB=-0.556633;RPBZ=-0.998367;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68954;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:DV 0,42,255,51,255,255:18:1 0,21,205,21,205,205:7:0 0,24,213,24,213,213:8:0 17 595 . A <*> . . MinDP=7;QS=3,0 PL:DP 0,54,255:18 0,21,198:7 0,24,218:8 -17 596 . A G,<*> 0 . DP=33;I16=16,16,1,0,1061,37187,8,64,1858,109682,60,3600,590,12952,1,1;QS=2.98564,0.0143627,0;SGB=-0.556633;RPBZ=1.68146;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68357;NMBZ=1.61602;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,21,169,21,169,169:7:0 0,24,231,24,231,231:8:0 +17 596 . A G,<*> 0 . DP=33;I16=16,16,1,0,1061,37187,8,64,1858,109682,60,3600,590,12952,1,1;QS=2.98564,0.0143627,0;SGB=-0.556633;RPBZ=1.68146;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68357;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,21,169,21,169,169:7:0 0,24,231,24,231,231:8:0 17 597 . C <*> . . END=600;MinDP=7;QS=3,0 PL:DP 0,51,255:17 0,21,194:7 0,24,220:8 diff --git a/test/mpileup/mpileup.7.out b/test/mpileup/mpileup.7.out index 256c98a55..0df1f5a8a 100644 --- a/test/mpileup/mpileup.7.out +++ b/test/mpileup/mpileup.7.out @@ -11,7 +11,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -35,7 +34,7 @@ 17 112 . C <*> 0 . DP=9;I16=7,1,0,0,295,11875,0,0,449,26041,0,0,150,3170,0,0;QS=2,0;MQ0F=0 PL 0,9,103 0,15,135 17 113 . A <*> 0 . DP=9;I16=7,1,0,0,301,12565,0,0,449,26041,0,0,147,3101,0,0;QS=2,0;MQ0F=0 PL 0,9,102 0,15,139 17 114 . C <*> 0 . DP=9;I16=7,1,0,0,306,12386,0,0,449,26041,0,0,144,3042,0,0;QS=2,0;MQ0F=0 PL 0,9,113 0,15,133 -17 115 . C A,<*> 0 . DP=11;I16=7,2,1,0,321,13261,12,144,509,29641,29,841,117,2369,25,625;QS=1.88785,0.11215,0;SGB=-0.516033;RPBZ=0.174608;MQBZ=-2;MQSBZ=-1.125;BQBZ=-1.23359;NMBZ=2.23607;SCBZ=-0.496904;FS=0;MQ0F=0 PL 3,0,86,9,89,93 0,21,153,21,153,153 +17 115 . C A,<*> 0 . DP=11;I16=7,2,1,0,321,13261,12,144,509,29641,29,841,117,2369,25,625;QS=1.88785,0.11215,0;SGB=-0.516033;RPBZ=0.174608;MQBZ=-2;MQSBZ=-1.125;BQBZ=-1.23359;SCBZ=-0.496904;FS=0;MQ0F=0 PL 3,0,86,9,89,93 0,21,153,21,153,153 17 116 . A <*> 0 . DP=11;I16=8,2,0,0,354,14068,0,0,538,30482,0,0,141,2959,0,0;QS=2,0;MQ0F=0 PL 0,9,102 0,21,175 17 117 . G <*> 0 . DP=11;I16=8,2,0,0,356,14150,0,0,538,30482,0,0,140,2938,0,0;QS=2,0;MQ0F=0 PL 0,9,97 0,21,177 17 118 . G <*> 0 . DP=11;I16=8,2,0,0,303,11685,0,0,538,30482,0,0,139,2931,0,0;QS=2,0;MQ0F=0 PL 0,9,65 0,21,162 diff --git a/test/mpileup/mpileup.8.out b/test/mpileup/mpileup.8.out index 82046fcbd..e6c16c17c 100644 --- a/test/mpileup/mpileup.8.out +++ b/test/mpileup/mpileup.8.out @@ -11,7 +11,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -23,29 +22,29 @@ 17 100 . C <*> 0 . DP=9;I16=9,0,0,0,350,14094,0,0,509,29641,0,0,159,3427,0,0;QS=1,0;MQ0F=0 PL 0,27,189 17 101 . C <*> 0 . DP=9;I16=9,0,0,0,331,12701,0,0,509,29641,0,0,159,3349,0,0;QS=1,0;MQ0F=0 PL 0,27,182 17 102 . C <*> 0 . DP=9;I16=9,0,0,0,349,13977,0,0,509,29641,0,0,159,3283,0,0;QS=1,0;MQ0F=0 PL 0,27,188 -17 103 . T C,<*> 0 . DP=9;I16=8,0,1,0,338,14304,6,36,480,28800,29,841,153,3193,6,36;QS=0.982558,0.0174419,0;SGB=-0.379885;RPBZ=-0.774597;MQBZ=-2.82843;BQBZ=-1.62549;NMBZ=2.82843;SCBZ=2.82843;FS=0;MQ0F=0 PL 0,17,184,24,187,185 -17 104 . G C,<*> 0 . DP=9;I16=8,0,1,0,310,12224,3,9,480,28800,29,841,152,3138,7,49;QS=0.987261,0.0127389,0;SGB=-0.379885;RPBZ=-0.774597;MQBZ=-2.82843;BQBZ=-1.56227;NMBZ=2.82843;SCBZ=2.82843;FS=0;MQ0F=0 PL 0,18,173,24,176,173 +17 103 . T C,<*> 0 . DP=9;I16=8,0,1,0,338,14304,6,36,480,28800,29,841,153,3193,6,36;QS=0.982558,0.0174419,0;SGB=-0.379885;RPBZ=-0.774597;MQBZ=-2.82843;BQBZ=-1.62549;SCBZ=2.82843;FS=0;MQ0F=0 PL 0,17,184,24,187,185 +17 104 . G C,<*> 0 . DP=9;I16=8,0,1,0,310,12224,3,9,480,28800,29,841,152,3138,7,49;QS=0.987261,0.0127389,0;SGB=-0.379885;RPBZ=-0.774597;MQBZ=-2.82843;BQBZ=-1.56227;SCBZ=2.82843;FS=0;MQ0F=0 PL 0,18,173,24,176,173 17 105 . G <*> 0 . DP=10;I16=10,0,0,0,318,11136,0,0,569,33241,0,0,159,3157,0,0;QS=1,0;MQ0F=0 PL 0,30,171 17 106 . G <*> 0 . DP=10;I16=10,0,0,0,372,14438,0,0,569,33241,0,0,160,3140,0,0;QS=1,0;MQ0F=0 PL 0,30,190 17 107 . C <*> 0 . DP=10;I16=10,0,0,0,372,14922,0,0,569,33241,0,0,161,3137,0,0;QS=1,0;MQ0F=0 PL 0,30,192 17 108 . C <*> 0 . DP=10;I16=10,0,0,0,367,14465,0,0,569,33241,0,0,162,3148,0,0;QS=1,0;MQ0F=0 PL 0,30,190 -17 109 . T C,<*> 0 . DP=10;I16=9,0,1,0,367,15083,2,4,540,32400,29,841,151,3029,12,144;QS=0.989218,0.0107817,0;SGB=-0.379885;RPBZ=-0.522233;MQBZ=-3;BQBZ=-1.59099;NMBZ=3;SCBZ=3;FS=0;MQ0F=0 PL 0,20,191,27,194,191 +17 109 . T C,<*> 0 . DP=10;I16=9,0,1,0,367,15083,2,4,540,32400,29,841,151,3029,12,144;QS=0.989218,0.0107817,0;SGB=-0.379885;RPBZ=-0.522233;MQBZ=-3;BQBZ=-1.59099;SCBZ=3;FS=0;MQ0F=0 PL 0,20,191,27,194,191 17 110 . G <*> 0 . DP=10;I16=10,0,0,0,376,15242,0,0,569,33241,0,0,164,3212,0,0;QS=1,0;MQ0F=0 PL 0,30,194 17 111 . G <*> 0 . DP=10;I16=10,0,0,0,316,10760,0,0,569,33241,0,0,165,3265,0,0;QS=1,0;MQ0F=0 PL 0,30,167 -17 112 . C G,<*> 0 . DP=10;I16=9,0,1,0,362,14690,2,4,540,32400,29,841,151,3107,15,225;QS=0.989071,0.010929,0;SGB=-0.379885;RPBZ=-0.174078;MQBZ=-3;BQBZ=-1.61126;NMBZ=3;SCBZ=3;FS=0;MQ0F=0 PL 0,20,187,27,190,187 -17 113 . A G,<*> 0 . DP=10;I16=9,0,1,0,334,12490,4,16,540,32400,29,841,150,3106,16,256;QS=0.988166,0.0118343,0;SGB=-0.379885;RPBZ=-0.174078;MQBZ=-3;BQBZ=-1.57628;NMBZ=3;SCBZ=3;FS=0;MQ0F=0 PL 0,20,172,27,175,172 +17 112 . C G,<*> 0 . DP=10;I16=9,0,1,0,362,14690,2,4,540,32400,29,841,151,3107,15,225;QS=0.989071,0.010929,0;SGB=-0.379885;RPBZ=-0.174078;MQBZ=-3;BQBZ=-1.61126;SCBZ=3;FS=0;MQ0F=0 PL 0,20,187,27,190,187 +17 113 . A G,<*> 0 . DP=10;I16=9,0,1,0,334,12490,4,16,540,32400,29,841,150,3106,16,256;QS=0.988166,0.0118343,0;SGB=-0.379885;RPBZ=-0.174078;MQBZ=-3;BQBZ=-1.57628;SCBZ=3;FS=0;MQ0F=0 PL 0,20,172,27,175,172 17 114 . C <*> 0 . DP=10;I16=10,0,0,0,354,13490,0,0,569,33241,0,0,166,3404,0,0;QS=1,0;MQ0F=0 PL 0,30,181 17 115 . C <*> 0 . DP=10;I16=10,0,0,0,367,14165,0,0,569,33241,0,0,166,3458,0,0;QS=1,0;MQ0F=0 PL 0,30,189 -17 116 . A C,<*> 0 . DP=10;I16=9,0,1,0,351,13723,2,4,540,32400,29,841,146,3114,19,361;QS=0.988732,0.0112676,0;SGB=-0.379885;RPBZ=0.174078;MQBZ=-3;BQBZ=-1.59099;NMBZ=3;SCBZ=3;FS=0;MQ0F=0 PL 0,20,179,27,182,179 +17 116 . A C,<*> 0 . DP=10;I16=9,0,1,0,351,13723,2,4,540,32400,29,841,146,3114,19,361;QS=0.988732,0.0112676,0;SGB=-0.379885;RPBZ=0.174078;MQBZ=-3;BQBZ=-1.59099;SCBZ=3;FS=0;MQ0F=0 PL 0,20,179,27,182,179 17 117 . G <*> 0 . DP=10;I16=10,0,0,0,359,13895,0,0,569,33241,0,0,164,3506,0,0;QS=1,0;MQ0F=0 PL 0,30,185 17 118 . G <*> 0 . DP=9;I16=9,0,0,0,317,11785,0,0,509,29641,0,0,164,3550,0,0;QS=1,0;MQ0F=0 PL 0,27,175 17 119 . G <*> 0 . DP=9;I16=9,0,0,0,320,12116,0,0,509,29641,0,0,164,3606,0,0;QS=1,0;MQ0F=0 PL 0,27,176 -17 120 . A G,<*> 0 . DP=9;I16=8,0,1,0,311,12135,4,16,480,28800,29,841,141,3145,23,529;QS=0.987302,0.0126984,0;SGB=-0.379885;RPBZ=0.387298;MQBZ=-2.82843;BQBZ=-1.55569;NMBZ=2.82843;SCBZ=2.82843;FS=0;MQ0F=0 PL 0,18,171,24,174,171 +17 120 . A G,<*> 0 . DP=9;I16=8,0,1,0,311,12135,4,16,480,28800,29,841,141,3145,23,529;QS=0.987302,0.0126984,0;SGB=-0.379885;RPBZ=0.387298;MQBZ=-2.82843;BQBZ=-1.55569;SCBZ=2.82843;FS=0;MQ0F=0 PL 0,18,171,24,174,171 17 121 . G <*> 0 . DP=9;I16=9,0,0,0,327,12691,0,0,509,29641,0,0,163,3703,0,0;QS=1,0;MQ0F=0 PL 0,27,181 17 122 . C <*> 0 . DP=9;I16=9,0,0,0,324,12880,0,0,509,29641,0,0,162,3742,0,0;QS=1,0;MQ0F=0 PL 0,27,180 17 123 . T <*> 0 . DP=8;I16=8,0,0,0,288,11074,0,0,449,26041,0,0,161,3739,0,0;QS=1,0;MQ0F=0 PL 0,24,170 17 124 . T <*> 0 . DP=9;I16=9,0,0,0,276,9034,0,0,509,29641,0,0,160,3742,0,0;QS=1,0;MQ0F=0 PL 0,27,154 -17 125 . A T,<*> 0 . DP=8;I16=7,0,1,0,253,9195,4,16,420,25200,29,841,136,3126,25,625;QS=0.984436,0.0155642,0;SGB=-0.379885;RPBZ=1.09109;MQBZ=-2.64575;BQBZ=-1.5367;NMBZ=2.64575;SCBZ=2.64575;FS=0;MQ0F=0 PL 0,15,149,21,152,149 +17 125 . A T,<*> 0 . DP=8;I16=7,0,1,0,253,9195,4,16,420,25200,29,841,136,3126,25,625;QS=0.984436,0.0155642,0;SGB=-0.379885;RPBZ=1.09109;MQBZ=-2.64575;BQBZ=-1.5367;SCBZ=2.64575;FS=0;MQ0F=0 PL 0,15,149,21,152,149 17 126 . A <*> 0 . DP=8;I16=8,0,0,0,275,9967,0,0,449,26041,0,0,162,3766,0,0;QS=1,0;MQ0F=0 PL 0,24,162 17 127 . C <*> 0 . DP=8;I16=8,0,0,0,280,10340,0,0,449,26041,0,0,163,3787,0,0;QS=1,0;MQ0F=0 PL 0,24,163 17 128 . A <*> 0 . DP=8;I16=8,0,0,0,295,11123,0,0,449,26041,0,0,164,3814,0,0;QS=1,0;MQ0F=0 PL 0,24,169 diff --git a/test/mpileup/mpileup.9.out b/test/mpileup/mpileup.9.out index 1031ac34c..42656823d 100644 --- a/test/mpileup/mpileup.9.out +++ b/test/mpileup/mpileup.9.out @@ -11,7 +11,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -35,7 +34,7 @@ 17 112 . C <*> 0 . DP=9;I16=7,1,0,0,295,11875,0,0,449,26041,0,0,150,3170,0,0;QS=2,0;MQ0F=0 PL 0,9,103 0,15,135 17 113 . A <*> 0 . DP=9;I16=7,1,0,0,301,12565,0,0,449,26041,0,0,147,3101,0,0;QS=2,0;MQ0F=0 PL 0,9,102 0,15,139 17 114 . C <*> 0 . DP=9;I16=7,1,0,0,306,12386,0,0,449,26041,0,0,144,3042,0,0;QS=2,0;MQ0F=0 PL 0,9,113 0,15,133 -17 115 . C A,<*> 0 . DP=11;I16=7,2,1,0,321,13261,12,144,509,29641,29,841,117,2369,25,625;QS=1.88785,0.11215,0;SGB=-0.516033;RPBZ=0.174608;MQBZ=-2;MQSBZ=-1.125;BQBZ=-1.23359;NMBZ=2.23607;SCBZ=-0.496904;FS=0;MQ0F=0 PL 3,0,86,9,89,93 0,21,153,21,153,153 +17 115 . C A,<*> 0 . DP=11;I16=7,2,1,0,321,13261,12,144,509,29641,29,841,117,2369,25,625;QS=1.88785,0.11215,0;SGB=-0.516033;RPBZ=0.174608;MQBZ=-2;MQSBZ=-1.125;BQBZ=-1.23359;SCBZ=-0.496904;FS=0;MQ0F=0 PL 3,0,86,9,89,93 0,21,153,21,153,153 17 116 . A <*> 0 . DP=11;I16=8,2,0,0,354,14068,0,0,538,30482,0,0,141,2959,0,0;QS=2,0;MQ0F=0 PL 0,9,102 0,21,175 17 117 . G <*> 0 . DP=11;I16=8,2,0,0,356,14150,0,0,538,30482,0,0,140,2938,0,0;QS=2,0;MQ0F=0 PL 0,9,97 0,21,177 17 118 . G <*> 0 . DP=11;I16=8,2,0,0,303,11685,0,0,538,30482,0,0,139,2931,0,0;QS=2,0;MQ0F=0 PL 0,9,65 0,21,162 diff --git a/test/test.pl b/test/test.pl index 9753264fe..f683ef391 100755 --- a/test/test.pl +++ b/test/test.pl @@ -798,9 +798,9 @@ run_test(\&test_mpileup,$opts,in=>[qw(mpileup-filter)],out=>'mpileup/mpileup-filter.1.out',ref=>'mpileup-SCR.fa',args=>q[-t 1:100 --skip-any-set READ1]); run_test(\&test_mpileup,$opts,in=>[qw(mpileup-filter)],out=>'mpileup/mpileup-filter.2.out',ref=>'mpileup-SCR.fa',args=>q[-t 1:100 --skip-all-unset READ1]); run_test(\&test_mpileup,$opts,in=>[qw(mpileup-filter)],out=>'mpileup/mpileup-filter.2.out',ref=>'mpileup-SCR.fa',args=>q[-t 1:100 --skip-any-unset READ1]); -run_test(\&test_mpileup,$opts,in=>[qw(annot-NMBZ.1)],ref=>'annot-NMBZ.1.fa',out=>'mpileup/annot-NMBZ.1.1.out',args=>q[-r chr19:69-99]); -run_test(\&test_mpileup,$opts,in=>[qw(annot-NMBZ.2)],ref=>'annot-NMBZ.2.fa',out=>'mpileup/annot-NMBZ.2.1.out',args=>q[-r chr6:75]); -run_test(\&test_mpileup,$opts,in=>[qw(annot-NMBZ.3.1 annot-NMBZ.3.2)],ref=>'annot-NMBZ.3.fa',out=>'mpileup/annot-NMBZ.3.1.out',args=>q[-r chr16:75]); +run_test(\&test_mpileup,$opts,in=>[qw(annot-NMBZ.1)],ref=>'annot-NMBZ.1.fa',out=>'mpileup/annot-NMBZ.1.1.out',args=>q[-a INFO/NMBZ -r chr19:69-99]); +run_test(\&test_mpileup,$opts,in=>[qw(annot-NMBZ.2)],ref=>'annot-NMBZ.2.fa',out=>'mpileup/annot-NMBZ.2.1.out',args=>q[-a INFO/NMBZ -r chr6:75]); +run_test(\&test_mpileup,$opts,in=>[qw(annot-NMBZ.3.1 annot-NMBZ.3.2)],ref=>'annot-NMBZ.3.fa',out=>'mpileup/annot-NMBZ.3.1.out',args=>q[-a INFO/NMBZ -r chr16:75]); run_test(\&test_csq,$opts,in=>'csq',out=>'csq.1.out',cmd=>'-f {PATH}/csq.fa -g {PATH}/csq.gff3'); run_test(\&test_csq,$opts,in=>'csq',out=>'csq.1.out',cmd=>'-f {PATH}/csq.fa -g {PATH}/csq.chr.gff3'); run_test(\&test_csq,$opts,in=>'csq.2',out=>'csq.2.out',cmd=>'-f {PATH}/csq.fa -g {PATH}/csq.2.gff',tbcsq=>1); From 9958cf464ae76bb741b22641bdb4a93e4cf50ef1 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Mon, 12 Dec 2022 16:24:03 +0100 Subject: [PATCH 58/84] Change the behavior of the `-I, --iupac-codes` option The option `-I, --iupac-codes` newly outputs IUPAC codes based on FORMAT/GT of all samples. The `-s, --samples` and `-S, --samples-file` options can be used to subset samples. In order to ignore samples and consider only the REF and ALT columns (the original behavior prior to 1.17 and this commit), run with `-s -`. Resolves #1828 --- NEWS | 7 ++ bcftools.h | 4 +- consensus.c | 184 +++++++++++++++++++++++++++-------------- doc/bcftools.txt | 16 ++-- smpl_ilist.h | 9 +- test/consensus.20.fa | 2 + test/consensus.20.vcf | 9 ++ test/consensus20.1.out | 2 + test/consensus20.2.out | 2 + test/consensus20.3.out | 2 + test/consensus20.4.out | 2 + test/test.pl | 46 ++++++----- 12 files changed, 188 insertions(+), 97 deletions(-) create mode 100644 test/consensus.20.fa create mode 100644 test/consensus.20.vcf create mode 100644 test/consensus20.1.out create mode 100644 test/consensus20.2.out create mode 100644 test/consensus20.3.out create mode 100644 test/consensus20.4.out diff --git a/NEWS b/NEWS index 88ac48870..e5e2099a9 100644 --- a/NEWS +++ b/NEWS @@ -15,6 +15,13 @@ Changes affecting specific commands: - Fix a bug where indels constrained with `-C alleles -T` would sometimes be missed (#1706) +* bcftools consensus + + - BREAKING CHANGE: the option `-I, --iupac-codes` newly outputs IUPAC codes based on FORMAT/GT + of all samples. The `-s, --samples` and `-S, --samples-file` options can be used to subset + samples. In order to ignore samples and consider only the REF and ALT columns (the original + behavior prior to 1.17), run with `-s -` (#1828) + * bcftools convert - Make variantkey conversion work for sites without an ALT allele (#1806) diff --git a/bcftools.h b/bcftools.h index a915802a8..c3f7ded16 100644 --- a/bcftools.h +++ b/bcftools.h @@ -57,8 +57,6 @@ char *init_tmp_prefix(const char *prefix); int read_AF(bcf_sr_regions_t *tgt, bcf1_t *line, double *alt_freq); int parse_overlap_option(const char *arg); -void *smalloc(size_t size); // safe malloc - static inline int iupac2bitmask(char iupac) { const int A = 1; @@ -99,7 +97,7 @@ static inline int iupac_consistent(char iupac, char nt) 13,0,0,4,11,0,0,12,0,3,15,0,0,0,5,6,8,0,7,9,0,10 }; if ( iupac > 89 ) return 0; - if ( nt > 90 ) nt -= 32; // lowercase + if ( nt > 90 ) nt -= 32; // lowercase if ( nt=='A' ) nt = 1; else if ( nt=='C' ) nt = 2; else if ( nt=='G' ) nt = 4; diff --git a/consensus.c b/consensus.c index 84ae905b7..393421eb1 100644 --- a/consensus.c +++ b/consensus.c @@ -42,6 +42,7 @@ #include "bcftools.h" #include "rbuf.h" #include "filter.h" +#include "smpl_ilist.h" // Logic of the filters: include or exclude sites which match the filters? #define FLT_INCLUDE 1 @@ -115,11 +116,12 @@ typedef struct FILE *fp_out; FILE *fp_chain; char **argv; - int argc, output_iupac, haplotype, allele, isample, napplied; - uint8_t *iupac_bitmask; - int miupac_bitmask; - char *fname, *ref_fname, *sample, *output_fname, *mask_fname, *chain_fname, missing_allele, absent_allele; + int argc, output_iupac, iupac_GTs, haplotype, allele, isample, napplied; + uint8_t *iupac_bitmask, *iupac_als; + int miupac_bitmask, miupac_als; + char *fname, *ref_fname, *sample, *sample_fname, *output_fname, *mask_fname, *chain_fname, missing_allele, absent_allele; char mark_del, mark_ins, mark_snv; + smpl_ilist_t *smpl; } args_t; @@ -226,15 +228,21 @@ static void init_data(args_t *args) if ( !bcf_sr_add_reader(args->files,args->fname) ) error("Failed to read from %s: %s\n", !strcmp("-",args->fname)?"standard input":args->fname, bcf_sr_strerror(args->files->errnum)); args->hdr = args->files->readers[0].header; args->isample = -1; - if ( args->sample ) + if ( !args->sample ) + args->smpl = smpl_ilist_init(args->hdr,NULL,0,SMPL_NONE|SMPL_VERBOSE); + else if ( args->sample && strcmp("-",args->sample) ) + args->smpl = smpl_ilist_init(args->hdr,args->sample,0,SMPL_NONE|SMPL_VERBOSE); + else if ( args->sample_fname ) + args->smpl = smpl_ilist_init(args->hdr,args->sample_fname,1,SMPL_NONE|SMPL_VERBOSE); + if ( args->smpl ) { - args->isample = bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,args->sample); - if ( args->isample<0 ) error("No such sample: %s\n", args->sample); - } - if ( (args->haplotype || args->allele) && args->isample<0 ) - { - if ( bcf_hdr_nsamples(args->hdr) > 1 ) error("The --sample option is expected with --haplotype\n"); - args->isample = 0; + if ( args->haplotype || args->allele ) + { + if ( args->smpl->n > 1 ) error("Too many samples, only one can be used with -H\n"); + args->isample = args->smpl->idx[0]; + } + else + args->iupac_GTs = 1; } int i; for (i=0; inmask; i++) @@ -258,7 +266,7 @@ static void init_data(args_t *args) if ( ! args->fp_out ) error("Failed to create %s: %s\n", args->output_fname, strerror(errno)); } else args->fp_out = stdout; - if ( args->isample<0 ) fprintf(stderr,"Note: the --sample option not given, applying all records regardless of the genotype\n"); + if ( args->isample<0 && !args->iupac_GTs ) fprintf(stderr,"Note: the --sample option not given, applying all records regardless of the genotype\n"); if ( args->filter_str ) args->filter = filter_init(args->hdr, args->filter_str); args->rid = -1; @@ -282,8 +290,10 @@ static void add_mask_with(args_t *args, char *with) } static void destroy_data(args_t *args) { + free(args->iupac_als); free(args->iupac_bitmask); if (args->filter) filter_destroy(args->filter); + if ( args->smpl ) smpl_ilist_destroy(args->smpl); bcf_sr_destroy(args->files); int i; for (i=0; ivcf_rbuf.m; i++) @@ -470,6 +480,59 @@ static void mark_snv(char *ref, char *alt, char mark) if ( tolower(ref[i])!=tolower(alt[i]) ) alt[i] = toupper(alt[i]); } } +static void iupac_init(args_t *args, bcf1_t *rec) +{ + int i; + hts_resize(uint8_t, rec->n_allele, &args->miupac_als, &args->iupac_als, 0); + for (i=0; imiupac_als; i++) args->iupac_als[i] = 0; +} +static int iupac_add_gt(args_t *args, bcf1_t *rec, uint8_t *gt, int ngt) +{ + int i, is_set = 0; + for (i=0; i= rec->n_allele ) error("Invalid VCF, too few ALT alleles at %s:%"PRId64"\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1); + args->iupac_als[ial] = 1; + is_set = 1; + } + return is_set; +} +static int iupac_set_allele(args_t *args, bcf1_t *rec) +{ + int i,j, max_len = 0, alt_len = 0, ialt = -1, fallback_alt = -1; + for (i=0; in_allele; i++) + { + if ( !args->iupac_als[i] ) continue; + if ( fallback_alt <=0 ) fallback_alt = i; + int l = strlen(rec->d.allele[i]); + for (j=0; jd.allele[i][j]) < 0 ) break; + if ( jmax_len ) + { + hts_resize(uint8_t, l, &args->miupac_bitmask, &args->iupac_bitmask, HTS_RESIZE_CLEAR); + for (j=max_len; jiupac_bitmask[j] = 0; + max_len = l; + } + if ( i>0 && l>alt_len ) + { + alt_len = l; + ialt = i; + } + for (j=0; jiupac_bitmask[j] |= iupac2bitmask(rec->d.allele[i][j]); + } + if ( alt_len > 0 ) + { + for (j=0; jd.allele[ialt][j] = bitmask2iupac(args->iupac_bitmask[j]); + return ialt; + } + if ( fallback_alt >= 0 ) return fallback_alt; + return ialt; +} static void apply_variant(args_t *args, bcf1_t *rec) { static int warned_haplotype = 0; @@ -491,7 +554,25 @@ static void apply_variant(args_t *args, bcf1_t *rec) } int ialt = 1; // the alternate allele - if ( args->isample >= 0 ) + if ( args->iupac_GTs ) + { + bcf_unpack(rec, BCF_UN_FMT); + bcf_fmt_t *fmt = bcf_get_fmt(args->hdr, rec, "GT"); + if ( !fmt ) return; + if ( fmt->type!=BCF_BT_INT8 ) + error("Todo: GT field represented with BCF_BT_INT8, too many alleles at %s:%"PRId64"?\n",bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1); + ialt = -1; + int is_set = 0; + iupac_init(args,rec); + for (i=0; ismpl->n; i++) + { + uint8_t *ptr = fmt->p + fmt->size*args->smpl->idx[i]; + is_set += iupac_add_gt(args, rec, ptr, fmt->n); + } + if ( !is_set && !args->missing_allele ) return; + if ( is_set ) ialt = iupac_set_allele(args, rec); + } + else if ( args->isample >= 0 ) { bcf_unpack(rec, BCF_UN_FMT); bcf_fmt_t *fmt = bcf_get_fmt(args->hdr, rec, "GT"); @@ -544,39 +625,10 @@ static void apply_variant(args_t *args, bcf1_t *rec) else if ( action==use_iupac ) { ialt = -1; - int is_missing = 0, alen = 0, mlen = 0, fallback_alt = -1; - for (i=0; in; i++) - { - if ( bcf_gt_is_missing(ptr[i]) ) { is_missing = 1; continue; } - if ( ptr[i]==(uint8_t)bcf_int8_vector_end ) break; - int jalt = bcf_gt_allele(ptr[i]); - if ( jalt >= rec->n_allele ) error("Invalid VCF, too few ALT alleles at %s:%"PRId64"\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1); - if ( fallback_alt <= 0 ) fallback_alt = jalt; - - int l = strlen(rec->d.allele[jalt]); - for (j=0; jd.allele[jalt][j]) < 0 ) break; - if ( j mlen ) - { - hts_expand(uint8_t,l,args->miupac_bitmask,args->iupac_bitmask); - for (j=mlen; jiupac_bitmask[j] = 0; - mlen = l; - } - if ( jalt>0 && l>alen ) - { - alen = l; - ialt = jalt; - } - for (j=0; jiupac_bitmask[j] |= iupac2bitmask(rec->d.allele[jalt][j]); - } - if ( alen > 0 ) - for (j=0; jd.allele[ialt][j] = bitmask2iupac(args->iupac_bitmask[j]); - else if ( fallback_alt >= 0 ) - ialt = fallback_alt; - else if ( is_missing && !args->missing_allele ) return; + iupac_init(args,rec); + int is_set = iupac_add_gt(args, rec, ptr, fmt->n); + if ( !is_set && !args->missing_allele ) return; + if ( is_set ) ialt = iupac_set_allele(args, rec); } else { @@ -1035,11 +1087,11 @@ static void usage(args_t *args) fprintf(stderr, " information, such as INFO/AD or FORMAT/AD.\n"); fprintf(stderr, "Usage: bcftools consensus [OPTIONS] \n"); fprintf(stderr, "Options:\n"); - fprintf(stderr, " -c, --chain FILE write a chain file for liftover\n"); - fprintf(stderr, " -a, --absent CHAR replace positions absent from VCF with CHAR\n"); - fprintf(stderr, " -e, --exclude EXPR exclude sites for which the expression is true (see man page for details)\n"); - fprintf(stderr, " -f, --fasta-ref FILE reference sequence in fasta format\n"); - fprintf(stderr, " -H, --haplotype WHICH choose which allele to use from the FORMAT/GT field, note\n"); + fprintf(stderr, " -c, --chain FILE Write a chain file for liftover\n"); + fprintf(stderr, " -a, --absent CHAR Replace positions absent from VCF with CHAR\n"); + fprintf(stderr, " -e, --exclude EXPR Exclude sites for which the expression is true (see man page for details)\n"); + fprintf(stderr, " -f, --fasta-ref FILE Reference sequence in fasta format\n"); + fprintf(stderr, " -H, --haplotype WHICH Choose which allele to use from the FORMAT/GT field, note\n"); fprintf(stderr, " the codes are case-insensitive:\n"); fprintf(stderr, " 1: first allele from GT, regardless of phasing\n"); fprintf(stderr, " 2: second allele from GT, regardless of phasing\n"); @@ -1049,17 +1101,18 @@ static void usage(args_t *args) fprintf(stderr, " LR,LA: longer allele and REF/ALT if equal length\n"); fprintf(stderr, " SR,SA: shorter allele and REF/ALT if equal length\n"); fprintf(stderr, " 1pIu,2pIu: first/second allele for phased and IUPAC code for unphased GTs\n"); - fprintf(stderr, " -i, --include EXPR select sites for which the expression is true (see man page for details)\n"); - fprintf(stderr, " -I, --iupac-codes output variants in the form of IUPAC ambiguity codes\n"); - fprintf(stderr, " --mark-del CHAR instead of removing sequence, insert CHAR for deletions\n"); - fprintf(stderr, " --mark-ins uc|lc highlight insertions in uppercase (uc) or lowercase (lc), leaving the rest as is\n"); - fprintf(stderr, " --mark-snv uc|lc highlight substitutions in uppercase (uc) or lowercase (lc), leaving the rest as is\n"); - fprintf(stderr, " -m, --mask FILE replace regions according to the next --mask-with option. The default is --mask-with N\n"); - fprintf(stderr, " --mask-with CHAR|uc|lc replace with CHAR (skips overlapping variants); change to uppercase (uc) or lowercase (lc)\n"); - fprintf(stderr, " -M, --missing CHAR output CHAR instead of skipping a missing genotype \"./.\"\n"); - fprintf(stderr, " -o, --output FILE write output to a file [standard output]\n"); - fprintf(stderr, " -p, --prefix STRING prefix to add to output sequence names\n"); - fprintf(stderr, " -s, --sample NAME apply variants of the given sample\n"); + fprintf(stderr, " -i, --include EXPR Select sites for which the expression is true (see man page for details)\n"); + fprintf(stderr, " -I, --iupac-codes Output IUPAC codes based on FORMAT/GT, use -s/-S to subset samples\n"); + fprintf(stderr, " --mark-del CHAR Instead of removing sequence, insert CHAR for deletions\n"); + fprintf(stderr, " --mark-ins uc|lc Highlight insertions in uppercase (uc) or lowercase (lc), leaving the rest as is\n"); + fprintf(stderr, " --mark-snv uc|lc Highlight substitutions in uppercase (uc) or lowercase (lc), leaving the rest as is\n"); + fprintf(stderr, " -m, --mask FILE Replace regions according to the next --mask-with option. The default is --mask-with N\n"); + fprintf(stderr, " --mask-with CHAR|uc|lc Replace with CHAR (skips overlapping variants); change to uppercase (uc) or lowercase (lc)\n"); + fprintf(stderr, " -M, --missing CHAR Output CHAR instead of skipping a missing genotype \"./.\"\n"); + fprintf(stderr, " -o, --output FILE Write output to a file [standard output]\n"); + fprintf(stderr, " -p, --prefix STRING Prefix to add to output sequence names\n"); + fprintf(stderr, " -s, --samples LIST Comma-separated list of samples to include, \"-\" to ignore samples and use REF,ALT\n"); + fprintf(stderr, " -S, --samples-file FILE File of samples to include\n"); fprintf(stderr, "Examples:\n"); fprintf(stderr, " # Get the consensus for one region. The fasta header lines are then expected\n"); fprintf(stderr, " # in the form \">chr:from-to\".\n"); @@ -1084,6 +1137,8 @@ int main_consensus(int argc, char *argv[]) {"exclude",required_argument,NULL,'e'}, {"include",required_argument,NULL,'i'}, {"sample",1,0,'s'}, + {"samples",1,0,'s'}, + {"samples-file",1,0,'S'}, {"iupac-codes",0,0,'I'}, {"haplotype",1,0,'H'}, {"output",1,0,'o'}, @@ -1096,7 +1151,7 @@ int main_consensus(int argc, char *argv[]) {0,0,0,0} }; int c; - while ((c = getopt_long(argc, argv, "h?s:1Ii:e:H:f:o:m:c:M:p:a:",loptions,NULL)) >= 0) + while ((c = getopt_long(argc, argv, "h?s:S:1Ii:e:H:f:o:m:c:M:p:a:",loptions,NULL)) >= 0) { switch (c) { @@ -1113,6 +1168,7 @@ int main_consensus(int argc, char *argv[]) break; case 'p': args->chr_prefix = optarg; break; case 's': args->sample = optarg; break; + case 'S': args->sample_fname = optarg; break; case 'o': args->output_fname = optarg; break; case 'I': args->output_iupac = 1; break; case 'e': diff --git a/doc/bcftools.txt b/doc/bcftools.txt index a147792cb..cf7d9085e 100644 --- a/doc/bcftools.txt +++ b/doc/bcftools.txt @@ -936,7 +936,10 @@ depth information, such as INFO/AD or FORMAT/AD. For that, consider using the *<>*. *-I, --iupac-codes*:: - output variants in the form of IUPAC ambiguity codes + output variants in the form of IUPAC ambiguity codes determined from FORMAT/GT fields. By default all + samples are used and can be subset with `-s, --samples` and `-S, --samples-file`. Use `-s -` to ignore + samples and use only the REF and ALT columns. NOTE: prior to version 1.17 the IUPAC codes were determined solely + from REF,ALT columns and sample genotypes were not considered. *--mark-del* 'CHAR':: instead of removing sequence, insert CHAR for deletions @@ -962,8 +965,11 @@ depth information, such as INFO/AD or FORMAT/AD. For that, consider using the *-o, --output* 'FILE':: write output to a file -*-s, --sample* 'NAME':: - apply variants of the given sample +*-s, --samples* 'LIST':: + apply variants of the listed samples. See also the option `-I, --iupac-codes` + +*-S, --samples-file* 'FILE':: + apply variants of the samples listed in the file. See also the option `-I, --iupac-codes` *Examples:* ---- @@ -971,8 +977,8 @@ depth information, such as INFO/AD or FORMAT/AD. For that, consider using the bcftools consensus -i -s NA001 -f in.fa in.vcf.gz > out.fa # Create consensus for one region. The fasta header lines are then expected - # in the form ">chr:from-to". - samtools faidx ref.fa 8:11870-11890 | bcftools consensus in.vcf.gz -o out.fa + # in the form ">chr:from-to". Ignore samples and consider only the REF and ALT columns + samtools faidx ref.fa 8:11870-11890 | bcftools consensus -s - in.vcf.gz -o out.fa # For more examples see http://samtools.github.io/bcftools/howtos/consensus-sequence.html ---- diff --git a/smpl_ilist.h b/smpl_ilist.h index 79292c3ea..e273ac417 100644 --- a/smpl_ilist.h +++ b/smpl_ilist.h @@ -1,4 +1,4 @@ -/* +/* Copyright (C) 2016-2021 Genome Research Ltd. Author: Petr Danecek @@ -9,10 +9,10 @@ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: - + The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. - + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE @@ -35,7 +35,7 @@ #define SMPL_SINGLE 2 // single sample expected #define SMPL_PAIR1 4 // two samples expected, the first is from the bcf hdr #define SMPL_PAIR2 8 // two samples expected, the second is from the bcf hdr -#define SMPL_VERBOSE 16 // print warnings +#define SMPL_VERBOSE 16 // print warnings #define SMPL_REORDER 32 // reorder samples as asked, sample_list[i] points to the VCF header index typedef struct @@ -46,6 +46,7 @@ typedef struct } smpl_ilist_t; +// Pass NULL for sample_list to get all samples smpl_ilist_t *smpl_ilist_init(bcf_hdr_t *hdr, char *sample_list, int is_file, int flags); smpl_ilist_t *smpl_ilist_map(bcf_hdr_t *hdr_a, bcf_hdr_t *hdr_b, int flags); void smpl_ilist_destroy(smpl_ilist_t *smpl); diff --git a/test/consensus.20.fa b/test/consensus.20.fa new file mode 100644 index 000000000..78de2ed5f --- /dev/null +++ b/test/consensus.20.fa @@ -0,0 +1,2 @@ +>ref +ACGTACGT diff --git a/test/consensus.20.vcf b/test/consensus.20.vcf new file mode 100644 index 000000000..71206e577 --- /dev/null +++ b/test/consensus.20.vcf @@ -0,0 +1,9 @@ +##fileformat=VCFv4.2 +##reference=file://some/path/human_g1k_v37.fasta +##contig= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT a b +ref 2 . C A . . . GT ./. 0/0 +ref 3 . G C . . . GT 0/0 0/0 +ref 4 . T C . . . GT 0/0 0/1 +ref 5 . A C . . . GT 1/1 1/1 diff --git a/test/consensus20.1.out b/test/consensus20.1.out new file mode 100644 index 000000000..db84dbc0a --- /dev/null +++ b/test/consensus20.1.out @@ -0,0 +1,2 @@ +>ref +AACCCCGT diff --git a/test/consensus20.2.out b/test/consensus20.2.out new file mode 100644 index 000000000..1e82d0427 --- /dev/null +++ b/test/consensus20.2.out @@ -0,0 +1,2 @@ +>ref +ACGYCCGT diff --git a/test/consensus20.3.out b/test/consensus20.3.out new file mode 100644 index 000000000..1e82d0427 --- /dev/null +++ b/test/consensus20.3.out @@ -0,0 +1,2 @@ +>ref +ACGYCCGT diff --git a/test/consensus20.4.out b/test/consensus20.4.out new file mode 100644 index 000000000..176a84f2a --- /dev/null +++ b/test/consensus20.4.out @@ -0,0 +1,2 @@ +>ref +A.GTCCGT diff --git a/test/test.pl b/test/test.pl index f683ef391..93c73eb6c 100755 --- a/test/test.pl +++ b/test/test.pl @@ -728,49 +728,53 @@ run_test(\&test_vcf_convert_hs2vcf,$opts,h=>'convert.hs.gt.ids.hap',s=>'convert.hs.gt.samples',out=>'convert.gt.noHead.ids.vcf',args=>'--vcf-ids --hapsample2vcf'); run_test(\&test_vcf_convert_gvcf,$opts,in=>'convert.gvcf',out=>'convert.gvcf.out',fa=>'gvcf.fa',args=>'--gvcf2vcf -i\'FILTER="PASS"\''); run_test(\&test_vcf_convert_tsv2vcf,$opts,in=>'convert.23andme',out=>'convert.23andme.vcf',args=>'-c ID,CHROM,POS,AA -s SAMPLE1',fai=>'23andme'); -run_test(\&test_vcf_consensus,$opts,in=>'consensus',out=>'consensus.1.out',fa=>'consensus.fa',mask=>'consensus.tab',args=>''); -run_test(\&test_vcf_consensus_chain,$opts,in=>'consensus',out=>'consensus.1.chain',chain=>'consensus.1.chain',fa=>'consensus.fa',mask=>'consensus.tab',args=>''); +run_test(\&test_vcf_consensus,$opts,in=>'consensus',out=>'consensus.1.out',fa=>'consensus.fa',mask=>'consensus.tab',args=>'-s -'); +run_test(\&test_vcf_consensus_chain,$opts,in=>'consensus',out=>'consensus.1.chain',chain=>'consensus.1.chain',fa=>'consensus.fa',mask=>'consensus.tab',args=>'-s -'); run_test(\&test_vcf_consensus,$opts,in=>'consensus',out=>'consensus.2.out',fa=>'consensus.fa',mask=>'consensus.tab',args=>'-H 1'); run_test(\&test_vcf_consensus_chain,$opts,in=>'consensus',out=>'consensus.2.chain',chain=>'consensus.2.chain',fa=>'consensus.fa',mask=>'consensus.tab',args=>'-H 1'); -run_test(\&test_vcf_consensus,$opts,in=>'consensus',out=>'consensus.3.out',fa=>'consensus.fa',mask=>'consensus.tab',args=>'-I'); -run_test(\&test_vcf_consensus,$opts,in=>'consensus',out=>'consensus.16.out',fa=>'consensus.fa',args=>'-I -m {PATH}/consensus.tab --mask-with X -m {PATH}/consensus.tab --mask-with lc'); +run_test(\&test_vcf_consensus,$opts,in=>'consensus',out=>'consensus.3.out',fa=>'consensus.fa',mask=>'consensus.tab',args=>'-I -s -'); +run_test(\&test_vcf_consensus,$opts,in=>'consensus',out=>'consensus.16.out',fa=>'consensus.fa',args=>'-s - -I -m {PATH}/consensus.tab --mask-with X -m {PATH}/consensus.tab --mask-with lc'); run_test(\&test_vcf_consensus_chain,$opts,in=>'consensus',out=>'consensus.3.chain',chain=>'consensus.3.chain',fa=>'consensus.fa',mask=>'consensus.tab',args=>'-I'); run_test(\&test_vcf_consensus,$opts,in=>'consensus',out=>'consensus.4.out',fa=>'consensus.fa',args=>'-H 1'); run_test(\&test_vcf_consensus_chain,$opts,in=>'consensus',out=>'consensus.4.chain',chain=>'consensus.4.chain',fa=>'consensus.fa',args=>'-H 1'); run_test(\&test_vcf_consensus,$opts,in=>'consensus2',out=>'consensus2.1.out',fa=>'consensus2.fa',args=>'-H 1'); run_test(\&test_vcf_consensus,$opts,in=>'consensus2',out=>'consensus2.2.out',fa=>'consensus2.fa',args=>'-H 2'); -run_test(\&test_vcf_consensus,$opts,in=>'empty',out=>'consensus.5.out',fa=>'consensus.fa',args=>''); +run_test(\&test_vcf_consensus,$opts,in=>'empty',out=>'consensus.5.out',fa=>'consensus.fa',args=>'-s -'); run_test(\&test_vcf_consensus,$opts,in=>'consensus3',out=>'consensus3.out',fa=>'consensus2.fa',args=>'-H 2 -M "?"'); run_test(\&test_vcf_consensus,$opts,in=>'consensus3',out=>'consensus3.2.out',fa=>'consensus2.fa',args=>'-H 2 -M "?" -p xx_'); -run_test(\&test_vcf_consensus,$opts,in=>'consensus4',out=>'consensus4.out',fa=>'consensus2.fa',args=>''); +run_test(\&test_vcf_consensus,$opts,in=>'consensus4',out=>'consensus4.out',fa=>'consensus2.fa',args=>'-s -'); run_test(\&test_vcf_consensus,$opts,in=>'consensus5',out=>'consensus5.out',fa=>'consensus5.fa',args=>'--haplotype LA'); -run_test(\&test_vcf_consensus,$opts,in=>'consensus6',out=>'consensus6.out',fa=>'consensus6.fa',args=>''); +run_test(\&test_vcf_consensus,$opts,in=>'consensus6',out=>'consensus6.out',fa=>'consensus6.fa',args=>'-s -'); run_test(\&test_vcf_consensus,$opts,in=>'consensus7',out=>'consensus7a.out',fa=>'consensus7.fa',args=>'-H 2'); run_test(\&test_vcf_consensus,$opts,in=>'consensus7',out=>'consensus7b.out',fa=>'consensus7.fa',args=>'-H 2pIu'); run_test(\&test_vcf_consensus,$opts,in=>'consensus7',out=>'consensus7c.out',fa=>'consensus7.fa',args=>'-H 1'); run_test(\&test_vcf_consensus,$opts,in=>'consensus7',out=>'consensus7d.out',fa=>'consensus7.fa',args=>'-H 1pIu'); -run_test(\&test_vcf_consensus,$opts,in=>'consensus8',out=>'consensus.8a.out',fa=>'consensus.fa',args=>''); -run_test(\&test_vcf_consensus,$opts,in=>'consensus8',out=>'consensus.8b.out',fa=>'consensus.fa',args=>'-a .'); -run_test(\&test_vcf_consensus,$opts,in=>'consensus8',out=>'consensus.8c.out',fa=>'consensus.fa',args=>q[-a . -i 'type="snp" || type="ref"']); -run_test(\&test_vcf_consensus,$opts,in=>'consensus8',out=>'consensus.8d.out',fa=>'consensus.fa',args=>q[-a . -i 'ALT!=""']); -run_test(\&test_vcf_consensus,$opts,in=>'consensus8',out=>'consensus.8e.out',fa=>'consensus.fa',args=>q[-a . -e 'MinDP>15']); -run_test(\&test_vcf_consensus,$opts,in=>'consensus8',out=>'consensus.8f.out',fa=>'consensus.fa',args=>q[-a . -e 'MinDP<15']); +run_test(\&test_vcf_consensus,$opts,in=>'consensus8',out=>'consensus.8a.out',fa=>'consensus.fa',args=>'-s -'); +run_test(\&test_vcf_consensus,$opts,in=>'consensus8',out=>'consensus.8b.out',fa=>'consensus.fa',args=>'-s - -a .'); +run_test(\&test_vcf_consensus,$opts,in=>'consensus8',out=>'consensus.8c.out',fa=>'consensus.fa',args=>q[-s - -a . -i 'type="snp" || type="ref"']); +run_test(\&test_vcf_consensus,$opts,in=>'consensus8',out=>'consensus.8d.out',fa=>'consensus.fa',args=>q[-s - -a . -i 'ALT!=""']); +run_test(\&test_vcf_consensus,$opts,in=>'consensus8',out=>'consensus.8e.out',fa=>'consensus.fa',args=>q[-s - -a . -e 'MinDP>15']); +run_test(\&test_vcf_consensus,$opts,in=>'consensus8',out=>'consensus.8f.out',fa=>'consensus.fa',args=>q[-s - -a . -e 'MinDP<15']); run_test(\&test_vcf_consensus,$opts,in=>'consensus.9',out=>'consensus.9.1.out',fa=>'consensus.9.1.fa',args=>q[-H A]); run_test(\&test_vcf_consensus,$opts,in=>'consensus.9',out=>'consensus.9.2.out',fa=>'consensus.9.2.fa',args=>q[-H A]); run_test(\&test_vcf_consensus,$opts,in=>'consensus.10',out=>'consensus.9.1.out',fa=>'consensus.9.1.fa',args=>q[-H A]); run_test(\&test_vcf_consensus,$opts,in=>'consensus.10',out=>'consensus.9.2.out',fa=>'consensus.9.2.fa',args=>q[-H A]); run_test(\&test_vcf_consensus,$opts,in=>'consensus.11',out=>'consensus.11.1.out',fa=>'consensus.11.fa',args=>q[-s smpl]); run_test(\&test_vcf_consensus,$opts,in=>'consensus.11',out=>'consensus.11.2.out',fa=>'consensus.11.fa',args=>q[-s smpl -a N]); -run_test(\&test_vcf_consensus,$opts,in=>'consensus.12',out=>'consensus.12.out',fa=>'consensus.12.fa',args=>''); -run_test(\&test_vcf_consensus,$opts,in=>'consensus.13',out=>'consensus.13.out',fa=>'consensus.13.fa',args=>''); -run_test(\&test_vcf_consensus,$opts,in=>'consensus.14',out=>'consensus.14.out',fa=>'consensus.14.fa',args=>''); -run_test(\&test_vcf_consensus,$opts,in=>'consensus.12',out=>'consensus.15.out',fa=>'consensus.12.fa',args=>'--mark-del - --mark-ins uc --mark-snv uc'); +run_test(\&test_vcf_consensus,$opts,in=>'consensus.12',out=>'consensus.12.out',fa=>'consensus.12.fa',args=>'-s -'); +run_test(\&test_vcf_consensus,$opts,in=>'consensus.13',out=>'consensus.13.out',fa=>'consensus.13.fa',args=>'-s -'); +run_test(\&test_vcf_consensus,$opts,in=>'consensus.14',out=>'consensus.14.out',fa=>'consensus.14.fa',args=>'-s -'); +run_test(\&test_vcf_consensus,$opts,in=>'consensus.12',out=>'consensus.15.out',fa=>'consensus.12.fa',args=>'-s - --mark-del - --mark-ins uc --mark-snv uc'); run_test(\&test_vcf_consensus,$opts,in=>'consensus.15',out=>'consensus.17.out',fa=>'consensus.15.fa',args=>'-H I --mark-ins lc --mark-snv lc'); -run_test(\&test_vcf_consensus,$opts,in=>'consensus.16',out=>'consensus.18.out',fa=>'consensus.fa',args=>'-I'); +run_test(\&test_vcf_consensus,$opts,in=>'consensus.16',out=>'consensus.18.out',fa=>'consensus.fa',args=>'-s - -I'); run_test(\&test_vcf_consensus,$opts,in=>'consensus.16',out=>'consensus.18.out',fa=>'consensus.fa',args=>'-H I'); -run_test(\&test_vcf_consensus,$opts,in=>'consensus.17',out=>'consensus17.1.out',fa=>'consensus2.fa',mask=>'consensus.17.bed',args=>'-M N'); -run_test(\&test_vcf_consensus,$opts,in=>'consensus.18',out=>'consensus18.1.out',fa=>'consensus.18.fa',args=>''); -run_test(\&test_vcf_consensus,$opts,in=>'consensus.19',out=>'consensus19.1.out',fa=>'consensus.19.fa',args=>''); +run_test(\&test_vcf_consensus,$opts,in=>'consensus.17',out=>'consensus17.1.out',fa=>'consensus2.fa',mask=>'consensus.17.bed',args=>'-s - -M N'); +run_test(\&test_vcf_consensus,$opts,in=>'consensus.18',out=>'consensus18.1.out',fa=>'consensus.18.fa',args=>'-s -'); +run_test(\&test_vcf_consensus,$opts,in=>'consensus.19',out=>'consensus19.1.out',fa=>'consensus.19.fa',args=>'-s - '); +run_test(\&test_vcf_consensus,$opts,in=>'consensus.20',out=>'consensus20.1.out',fa=>'consensus.20.fa',args=>'-s -'); +run_test(\&test_vcf_consensus,$opts,in=>'consensus.20',out=>'consensus20.2.out',fa=>'consensus.20.fa',args=>''); +run_test(\&test_vcf_consensus,$opts,in=>'consensus.20',out=>'consensus20.3.out',fa=>'consensus.20.fa',args=>'-M . -s b'); +run_test(\&test_vcf_consensus,$opts,in=>'consensus.20',out=>'consensus20.4.out',fa=>'consensus.20.fa',args=>'-M . -s a'); run_test(\&test_mpileup,$opts,in=>[qw(mpileup.1 mpileup.2 mpileup.3)],out=>'mpileup/mpileup.1.out',args=>q[-r17:100-150],test_list=>1); run_test(\&test_mpileup,$opts,in=>[qw(mpileup.1 mpileup.2 mpileup.3)],out=>'mpileup/mpileup.2.out',args=>q[-a DP,DV -r17:100-600]); # test files from samtools mpileup test suite run_test(\&test_mpileup,$opts,in=>[qw(mpileup.1)],out=>'mpileup/mpileup.3.out',args=>q[-B --ff 0x14 -r17:1050-1060]); # test file converted to vcf from samtools mpileup test suite From 16b187454a7b672eb23eeab9227335ebb0c6d43f Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Tue, 13 Dec 2022 08:28:27 +0100 Subject: [PATCH 59/84] Refer to the correct option --samples, rather than --sample --- consensus.c | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/consensus.c b/consensus.c index 393421eb1..e48d5123f 100644 --- a/consensus.c +++ b/consensus.c @@ -266,7 +266,7 @@ static void init_data(args_t *args) if ( ! args->fp_out ) error("Failed to create %s: %s\n", args->output_fname, strerror(errno)); } else args->fp_out = stdout; - if ( args->isample<0 && !args->iupac_GTs ) fprintf(stderr,"Note: the --sample option not given, applying all records regardless of the genotype\n"); + if ( args->isample<0 && !args->iupac_GTs ) fprintf(stderr,"Note: the --samples option not given, applying all records regardless of the genotype\n"); if ( args->filter_str ) args->filter = filter_init(args->hdr, args->filter_str); args->rid = -1; @@ -1082,7 +1082,7 @@ static void usage(args_t *args) fprintf(stderr, "\n"); fprintf(stderr, "About: Create consensus sequence by applying VCF variants to a reference fasta\n"); fprintf(stderr, " file. By default, the program will apply all ALT variants. Using the\n"); - fprintf(stderr, " --sample (and, optionally, --haplotype) option will apply genotype\n"); + fprintf(stderr, " --samples (and, optionally, --haplotype) option will apply genotype\n"); fprintf(stderr, " (or haplotype) calls from FORMAT/GT. The program ignores allelic depth\n"); fprintf(stderr, " information, such as INFO/AD or FORMAT/AD.\n"); fprintf(stderr, "Usage: bcftools consensus [OPTIONS] \n"); From 8d77f8d264a74891d7a30e3331b0b5020821b7dc Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Tue, 13 Dec 2022 09:16:21 +0000 Subject: [PATCH 60/84] New option `-d, --direction` to choose the directionality: fwd,rev,nearest,both Resolves #1829 --- NEWS | 7 +++- plugins/variant-distance.c | 78 ++++++++++++++++++++++++++----------- test/test.pl | 4 ++ test/variant-distance.1.out | 5 ++- test/variant-distance.2.out | 16 ++++++++ test/variant-distance.3.out | 16 ++++++++ test/variant-distance.4.out | 16 ++++++++ test/variant-distance.vcf | 3 ++ 8 files changed, 121 insertions(+), 24 deletions(-) create mode 100644 test/variant-distance.2.out create mode 100644 test/variant-distance.3.out create mode 100644 test/variant-distance.4.out diff --git a/NEWS b/NEWS index e5e2099a9..005a2f24f 100644 --- a/NEWS +++ b/NEWS @@ -84,12 +84,17 @@ Changes affecting specific commands: * bcftools +trio-dnm2 - - New -n, --strictly-novel option to downplay alleles which violate Mendelian + - New `-n, --strictly-novel` option to downplay alleles which violate Mendelian inheritance but are not novel - Allow to set the `--pn` and `--pns` options separately for SNVs and indels and make the indel settings more strict by default +* bcftools +variant-distance + + - New option `-d, --direction` to choose the directionality: forward, reverse, nearest (the default) + or both (#1829) + ## Release 1.16 (18th August 2022) diff --git a/plugins/variant-distance.c b/plugins/variant-distance.c index a4b8a5198..a1aeb9aef 100644 --- a/plugins/variant-distance.c +++ b/plugins/variant-distance.c @@ -44,12 +44,17 @@ #define FLT_INCLUDE 1 #define FLT_EXCLUDE 2 +#define DIR_NEAREST 0 +#define DIR_FWD 1 +#define DIR_REV 2 +#define DIR_BOTH 3 + typedef struct { char *tag; int argc, region_is_file, target_is_file, output_type, clevel; - int regions_overlap, targets_overlap; - int32_t prev_dist; + int regions_overlap, targets_overlap, direction; + int32_t fwd_dist, rev_dist; char **argv, *region, *target, *fname, *output_fname; char *filter_str; filter_t *filter; @@ -73,18 +78,19 @@ static const char *usage_text(void) "About: Annotate sites with distance to the nearest variant\n" "Usage: bcftools +variant-distance [Options]\n" "Options:\n" - " -n, --tag-name STR The tag name to be added [DIST]\n" + " -d, --direction DIRECTION Directionality: nearest, fwd, rev, both (adds a Number=2 tag) [nearest]\n" + " -n, --tag-name STR The tag name to be added [DIST]\n" "Common options:\n" - " -e, --exclude EXPR Exclude sites for which the expression is true\n" - " -i, --include EXPR Include only sites for which the expression is true\n" - " -o, --output FILE Write output to the FILE [standard output]\n" - " -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n" - " -r, --regions REGION Restrict to comma-separated list of regions\n" - " -R, --regions-file FILE Restrict to regions listed in a file\n" - " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n" - " -t, --targets REGION Similar to -r but streams rather than index-jumps\n" - " -T, --targets-file FILE Similar to -R but streams rather than index-jumps\n" - " --targets-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n" + " -e, --exclude EXPR Exclude sites for which the expression is true\n" + " -i, --include EXPR Include only sites for which the expression is true\n" + " -o, --output FILE Write output to the FILE [standard output]\n" + " -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n" + " -r, --regions REGION Restrict to comma-separated list of regions\n" + " -R, --regions-file FILE Restrict to regions listed in a file\n" + " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n" + " -t, --targets REGION Similar to -r but streams rather than index-jumps\n" + " -T, --targets-file FILE Similar to -R but streams rather than index-jumps\n" + " --targets-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n" "Examples:\n" " bcftools +variant-distance input.bcf -Ob -o output.bcf\n" "\n"; @@ -106,7 +112,13 @@ static void init_data(args_t *args) args->filter = filter_init(args->hdr, args->filter_str); if ( !args->tag ) args->tag = strdup("DIST"); - bcf_hdr_printf(args->hdr,"##INFO=",args->tag); + int nval = 1; + const char *desc = NULL; + if ( args->direction==DIR_FWD ) desc = "next"; + else if ( args->direction==DIR_REV ) desc = "previous"; + else if ( args->direction==DIR_NEAREST) desc = "nearest"; + else desc = "previous and next", nval = 2; + bcf_hdr_printf(args->hdr,"##INFO=",args->tag,nval,desc); char wmode[8]; set_wmode(wmode,args->output_type,args->output_fname,args->clevel); @@ -130,14 +142,26 @@ static void destroy_data(args_t *args) } static void flush(args_t *args, int n) { - int i; + int32_t val[2]; + int nval = 0, i; + if ( args->direction==DIR_FWD && args->fwd_dist ) nval = 1, val[0] = args->fwd_dist; + else if ( args->direction==DIR_REV && args->rev_dist ) nval = 1, val[0] = args->rev_dist; + else if ( args->direction==DIR_BOTH && (args->fwd_dist||args->rev_dist) ) nval = 2, val[0] = args->rev_dist, val[1] = args->fwd_dist; + else if ( args->direction==DIR_NEAREST && (args->fwd_dist||args->rev_dist) ) + { + if ( !args->fwd_dist ) val[0] = args->rev_dist; + else if ( !args->rev_dist ) val[0] = args->fwd_dist; + else if ( args->rev_dist < args->fwd_dist ) val[0] = args->rev_dist; + else val[0] = args->fwd_dist; + nval = 1; + } for (i=0; ibuf, 1); - if ( args->prev_dist ) + if ( nval ) { - if ( bcf_update_info_int32(args->hdr,rec,args->tag,&args->prev_dist,1)!=0 ) - error("[%s] Error: failed to update INFO/%s=%d\n",__func__,args->tag,args->prev_dist); + if ( bcf_update_info_int32(args->hdr,rec,args->tag,val,nval)!=0 ) + error("[%s] Error: failed to update INFO/%s at %s:%"PRIhts_pos"\n",__func__,args->tag,bcf_seqname(args->hdr,rec),rec->pos+1); } if ( bcf_write(args->out_fh,args->hdr,rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname); } @@ -148,6 +172,7 @@ static void process(args_t *args, int done) { // If the buffer is not empty, all records must be duplicate positions and // the previous site may or may not be set + args->fwd_dist = 0; flush(args, vcfbuf_nsites(args->buf)); return; } @@ -175,15 +200,16 @@ static void process(args_t *args, int done) if ( i==n ) return; // cannot flush yet, either a single record or all duplicates if ( rec->rid != rec0->rid ) // the new record is a different chr { + args->fwd_dist = 0; flush(args, i); - args->prev_dist = 0; + args->rev_dist = 0; return; } // the new record is a different pos - if ( !args->prev_dist || args->prev_dist > rec->pos - rec0->pos ) args->prev_dist = rec->pos - rec0->pos; + args->fwd_dist = rec->pos - rec0->pos; flush(args, i); - args->prev_dist = rec->pos - rec0->pos; + args->rev_dist = args->fwd_dist; } int run(int argc, char **argv) @@ -195,6 +221,7 @@ int run(int argc, char **argv) args->clevel = -1; static struct option loptions[] = { + {"direction",required_argument,NULL,'d'}, {"tag-name",required_argument,NULL,'n'}, {"exclude",required_argument,NULL,'e'}, {"include",required_argument,NULL,'i'}, @@ -210,10 +237,17 @@ int run(int argc, char **argv) }; int c; char *tmp; - while ((c = getopt_long(argc, argv, "r:R:t:T:o:O:n:",loptions,NULL)) >= 0) + while ((c = getopt_long(argc, argv, "r:R:t:T:o:O:n:d:",loptions,NULL)) >= 0) { switch (c) { + case 'd': + if ( !strcasecmp("nearest",optarg) ) args->direction = DIR_NEAREST; + else if ( !strcasecmp("fwd",optarg) ) args->direction = DIR_FWD; + else if ( !strcasecmp("rev",optarg) ) args->direction = DIR_REV; + else if ( !strcasecmp("both",optarg) ) args->direction = DIR_BOTH; + else error("Unknown argument to --direction: %s\n",optarg); + break; case 'n': args->tag = strdup(optarg); break; case 'e': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); diff --git a/test/test.pl b/test/test.pl index 93c73eb6c..75559e1be 100755 --- a/test/test.pl +++ b/test/test.pl @@ -664,6 +664,10 @@ run_test(\&test_vcf_plugin,$opts,in=>'prune.1',out=>'prune.1.6.out',cmd=>'+prune -w 2bp -n 1 -N 1st'); run_test(\&test_vcf_plugin,$opts,in=>'prune.1',out=>'prune.1.7.out',cmd=>'+prune -w 2bp -n 1 -N rand --random-seed 1'); run_test(\&test_vcf_plugin,$opts,in=>'variant-distance',out=>'variant-distance.1.out',cmd=>'+variant-distance'); +run_test(\&test_vcf_plugin,$opts,in=>'variant-distance',out=>'variant-distance.1.out',cmd=>'+variant-distance -d nearest'); +run_test(\&test_vcf_plugin,$opts,in=>'variant-distance',out=>'variant-distance.2.out',cmd=>'+variant-distance -d fwd'); +run_test(\&test_vcf_plugin,$opts,in=>'variant-distance',out=>'variant-distance.3.out',cmd=>'+variant-distance -d rev'); +run_test(\&test_vcf_plugin,$opts,in=>'variant-distance',out=>'variant-distance.4.out',cmd=>'+variant-distance -d both'); run_test(\&test_plugin_split,$opts,in=>'split.1',out=>'split.1.1.out',tmp=>'split.1.1'); run_test(\&test_plugin_split,$opts,in=>'split.1',out=>'split.1.2.out',tmp=>'split.1.2',args=>'-S {PATH}/split.smpl.1.2.txt'); run_test(\&test_plugin_split,$opts,in=>'split.1',out=>'split.1.3.out',tmp=>'split.1.3',args=>'-S {PATH}/split.smpl.1.3.txt'); diff --git a/test/variant-distance.1.out b/test/variant-distance.1.out index 2b3c23ad3..21d206127 100644 --- a/test/variant-distance.1.out +++ b/test/variant-distance.1.out @@ -2,7 +2,8 @@ ##FILTER= ##reference=file://some/path/human_g1k_v37.fasta ##contig= -##INFO= +##contig= +##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO 1 101 . T A . . DIST=3 1 101 . T C . . DIST=3 @@ -11,3 +12,5 @@ 1 108 . T A . . DIST=4 1 108 . T C . . DIST=4 1 115 . T A . . DIST=7 +2 120 . T A . . DIST=10 +2 130 . T A . . DIST=10 diff --git a/test/variant-distance.2.out b/test/variant-distance.2.out new file mode 100644 index 000000000..da6f0748d --- /dev/null +++ b/test/variant-distance.2.out @@ -0,0 +1,16 @@ +##fileformat=VCFv4.2 +##FILTER= +##reference=file://some/path/human_g1k_v37.fasta +##contig= +##contig= +##INFO= +#CHROM POS ID REF ALT QUAL FILTER INFO +1 101 . T A . . DIST=3 +1 101 . T C . . DIST=3 +1 104 . T A . . DIST=4 +1 104 . T C . . DIST=4 +1 108 . T A . . DIST=7 +1 108 . T C . . DIST=7 +1 115 . T A . . . +2 120 . T A . . DIST=10 +2 130 . T A . . . diff --git a/test/variant-distance.3.out b/test/variant-distance.3.out new file mode 100644 index 000000000..3423b97d2 --- /dev/null +++ b/test/variant-distance.3.out @@ -0,0 +1,16 @@ +##fileformat=VCFv4.2 +##FILTER= +##reference=file://some/path/human_g1k_v37.fasta +##contig= +##contig= +##INFO= +#CHROM POS ID REF ALT QUAL FILTER INFO +1 101 . T A . . . +1 101 . T C . . . +1 104 . T A . . DIST=3 +1 104 . T C . . DIST=3 +1 108 . T A . . DIST=4 +1 108 . T C . . DIST=4 +1 115 . T A . . DIST=7 +2 120 . T A . . . +2 130 . T A . . DIST=10 diff --git a/test/variant-distance.4.out b/test/variant-distance.4.out new file mode 100644 index 000000000..3e7695ea0 --- /dev/null +++ b/test/variant-distance.4.out @@ -0,0 +1,16 @@ +##fileformat=VCFv4.2 +##FILTER= +##reference=file://some/path/human_g1k_v37.fasta +##contig= +##contig= +##INFO= +#CHROM POS ID REF ALT QUAL FILTER INFO +1 101 . T A . . DIST=0,3 +1 101 . T C . . DIST=0,3 +1 104 . T A . . DIST=3,4 +1 104 . T C . . DIST=3,4 +1 108 . T A . . DIST=4,7 +1 108 . T C . . DIST=4,7 +1 115 . T A . . DIST=7,0 +2 120 . T A . . DIST=0,10 +2 130 . T A . . DIST=10,0 diff --git a/test/variant-distance.vcf b/test/variant-distance.vcf index 2f7eef1e0..ad4cd4524 100644 --- a/test/variant-distance.vcf +++ b/test/variant-distance.vcf @@ -1,6 +1,7 @@ ##fileformat=VCFv4.2 ##reference=file://some/path/human_g1k_v37.fasta ##contig= +##contig= #CHROM POS ID REF ALT QUAL FILTER INFO 1 101 . T A . . . 1 101 . T C . . . @@ -9,3 +10,5 @@ 1 108 . T A . . . 1 108 . T C . . . 1 115 . T A . . . +2 120 . T A . . . +2 130 . T A . . . From d80a35fd68e11fbd9b80c4a7bb356dec98ba90e3 Mon Sep 17 00:00:00 2001 From: Rob Davies Date: Tue, 13 Dec 2022 11:38:16 +0000 Subject: [PATCH 61/84] Switch MacOS CI tests to an ARM-based image Before x86-64 is phased out at the end of the year. Uses cirrus-ci recommended container, see: https://cirrus-ci.org/guide/macOS/ --- .cirrus.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.cirrus.yml b/.cirrus.yml index 0961666db..a5b08ebce 100644 --- a/.cirrus.yml +++ b/.cirrus.yml @@ -139,8 +139,8 @@ rockylinux_task: macosx_task: name: macosx + clang - osx_instance: - image: catalina-base + macos_instance: + image: ghcr.io/cirruslabs/macos-ventura-base:latest environment: CC: clang From 83dba37e8ad552c7b53a8f2d218b1148e6f870f3 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Thu, 15 Dec 2022 16:32:57 +0100 Subject: [PATCH 62/84] Make the INFO/FS annotation functional and remove it from the default annotations. Resolves #1834 --- NEWS | 3 + bam2bcf.c | 5 + mpileup.c | 6 +- test/mpileup/annot-NMBZ.1.1.out | 13 +- test/mpileup/annot-NMBZ.2.1.out | 3 +- test/mpileup/annot-NMBZ.3.1.out | 5 +- test/mpileup/indel-AD.1.out | 225 +++++++++++++++--------------- test/mpileup/indel-AD.2.out | 3 +- test/mpileup/indel-AD.3.out | 3 +- test/mpileup/indel-AD.4.out | 3 +- test/mpileup/mpileup-SCR.out | 3 +- test/mpileup/mpileup-filter.1.out | 1 - test/mpileup/mpileup-filter.2.out | 1 - test/mpileup/mpileup.1.out | 19 ++- test/mpileup/mpileup.10.out | 19 ++- test/mpileup/mpileup.11.out | 177 ++++++++++++----------- test/mpileup/mpileup.2.out | 97 +++++++------ test/mpileup/mpileup.3.out | 1 - test/mpileup/mpileup.4.out | 97 +++++++------ test/mpileup/mpileup.5.out | 97 +++++++------ test/mpileup/mpileup.6.out | 97 +++++++------ test/mpileup/mpileup.7.out | 3 +- test/mpileup/mpileup.8.out | 17 ++- test/mpileup/mpileup.9.out | 3 +- 24 files changed, 444 insertions(+), 457 deletions(-) diff --git a/NEWS b/NEWS index 005a2f24f..455a6b827 100644 --- a/NEWS +++ b/NEWS @@ -57,6 +57,9 @@ Changes affecting specific commands: it uses diploid reference consensus sequence. Note that in the current version it has the potential to increase sensitivity but at the cost of decreased specificity. + - Make the FS annotation (Fisher exact test strand bias) functional and remove it + from the default annotations + * bcftools norm - New --multi-overlaps option allows to set overlapping alleles either to the diff --git a/bam2bcf.c b/bam2bcf.c index 08fb5cdd4..88e25de1f 100644 --- a/bam2bcf.c +++ b/bam2bcf.c @@ -1040,6 +1040,11 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, bcf_callaux_t *bca, int // No need to calculate MWU tests when there is no ALT allele, this should speed up things slightly if ( !has_alt ) return 0; + if ( bca->fmt_flag & B2B_INFO_FS ) + { + double left,right,two; + call->strand_bias = kt_fisher_exact(call->anno[0], call->anno[1], call->anno[2], call->anno[3], &left, &right, &two); + } if ( bca->fmt_flag & B2B_INFO_SGB ) calc_SegBias(calls, call); // calc_chisq_bias("XPOS", call->bcf_hdr->id[BCF_DT_CTG][call->tid].key, call->pos, bca->ref_pos, bca->alt_pos, bca->npos); diff --git a/mpileup.c b/mpileup.c index e06ecd2d8..9b21b1873 100644 --- a/mpileup.c +++ b/mpileup.c @@ -803,7 +803,7 @@ static int mpileup(mplp_conf_t *conf) if ( conf->fmt_flag&B2B_INFO_SCBZ ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_FS ) - bcf_hdr_append(conf->bcf_hdr,"##INFO="); + bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_SGB ) bcf_hdr_append(conf->bcf_hdr,"##INFO="); if ( conf->fmt_flag&B2B_INFO_MQ0F ) @@ -1147,7 +1147,7 @@ static void list_annotations(FILE *fp) " INFO/ADF .. Total allelic depths on the forward strand (Number=R,Type=Integer)\n" " INFO/ADR .. Total allelic depths on the reverse strand (Number=R,Type=Integer)\n" "* INFO/BQBZ .. Mann-Whitney U test of Base Quality Bias (Number=1,Type=Float)\n" - "* INFO/FS .. Phred-scaled p-value using Fisher's exact test to detect strand bias (Number=1,Type=Float)\n" + " INFO/FS .. Fisher's exact test P-value to detect strand bias (Number=1,Type=Float)\n" "* INFO/IDV .. Maximum number of raw reads supporting an indel (Number=1,Type=Integer)\n" "* INFO/IMF .. Maximum fraction of raw reads supporting an indel (Number=1,Type=Float)\n" " INFO/MIN_PL_SUM\n" @@ -1300,7 +1300,7 @@ int main_mpileup(int argc, char *argv[]) mplp.n_threads = 0; mplp.bsmpl = bam_smpl_init(); // the default to be changed in future, see also parse_format_flag() - mplp.fmt_flag = B2B_INFO_BQBZ|B2B_INFO_FS|B2B_INFO_IDV|B2B_INFO_IMF|B2B_INFO_MQ0F|B2B_INFO_MQBZ|B2B_INFO_MQSBZ|B2B_INFO_RPBZ|B2B_INFO_SCBZ|B2B_INFO_SGB|B2B_INFO_VDB; + mplp.fmt_flag = B2B_INFO_BQBZ|B2B_INFO_IDV|B2B_INFO_IMF|B2B_INFO_MQ0F|B2B_INFO_MQBZ|B2B_INFO_MQSBZ|B2B_INFO_RPBZ|B2B_INFO_SCBZ|B2B_INFO_SGB|B2B_INFO_VDB; mplp.max_read_len = 500; mplp.ambig_reads = B2B_DROP; mplp.indel_win_size = 110; diff --git a/test/mpileup/annot-NMBZ.1.1.out b/test/mpileup/annot-NMBZ.1.1.out index a82d31a6c..1ac755e6e 100644 --- a/test/mpileup/annot-NMBZ.1.1.out +++ b/test/mpileup/annot-NMBZ.1.1.out @@ -13,23 +13,22 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample -chr19 69 . G C,<*> 0 . DP=46;I16=18,21,2,3,1377,50689,217,10339,2340,140400,266,14324,759,16653,92,1754;QS=0.868222,0.131778,0;VDB=0.216674;SGB=-0.590765;RPBZ=0.0924924;MQBZ=-4.95028;MQSBZ=-0.485415;BQBZ=-0.0931785;NMBZ=6.54221;SCBZ=6.54221;FS=0;MQ0F=0 PL 60,0,255,177,255,255 +chr19 69 . G C,<*> 0 . DP=46;I16=18,21,2,3,1377,50689,217,10339,2340,140400,266,14324,759,16653,92,1754;QS=0.868222,0.131778,0;VDB=0.216674;SGB=-0.590765;RPBZ=0.0924924;MQBZ=-4.95028;MQSBZ=-0.485415;BQBZ=-0.0931785;NMBZ=6.54221;SCBZ=6.54221;MQ0F=0 PL 60,0,255,177,255,255 chr19 70 . G <*> 0 . DP=47;I16=19,25,0,0,1638,63732,0,0,2606,154724,0,0,829,18007,0,0;QS=1,0;MQ0F=0 PL 0,132,255 chr19 71 . T <*> 0 . DP=47;I16=19,25,0,0,1488,54040,0,0,2606,154724,0,0,827,17989,0,0;QS=1,0;MQ0F=0 PL 0,132,255 -chr19 72 . G A,<*> 0 . DP=48;I16=18,22,2,3,1377,49347,203,9477,2400,144000,266,14324,733,16223,92,1796;QS=0.874841,0.125159,0;VDB=0.206846;SGB=-0.590765;RPBZ=0.415523;MQBZ=-5.01073;MQSBZ=-0.448951;BQBZ=0.145086;NMBZ=6.61856;SCBZ=6.61856;FS=0;MQ0F=0 PL 48,0,255,169,255,255 +chr19 72 . G A,<*> 0 . DP=48;I16=18,22,2,3,1377,49347,203,9477,2400,144000,266,14324,733,16223,92,1796;QS=0.874841,0.125159,0;VDB=0.206846;SGB=-0.590765;RPBZ=0.415523;MQBZ=-5.01073;MQSBZ=-0.448951;BQBZ=0.145086;NMBZ=6.61856;SCBZ=6.61856;MQ0F=0 PL 48,0,255,169,255,255 chr19 73 . G <*> 0 . DP=48;I16=20,25,0,0,1608,61094,0,0,2666,158324,0,0,823,18049,0,0;QS=1,0;MQ0F=0 PL 0,135,255 chr19 74 . T <*> 0 . DP=48;I16=20,25,0,0,1478,53810,0,0,2666,158324,0,0,820,18080,0,0;QS=1,0;MQ0F=0 PL 0,135,255 chr19 75 . G <*> 0 . DP=48;I16=20,25,0,0,1617,61719,0,0,2666,158324,0,0,813,17961,0,0;QS=1,0;MQ0F=0 PL 0,135,255 -chr19 76 . A C,<*> 0 . DP=47;I16=18,21,2,3,1383,50589,220,10546,2340,140400,266,14324,715,15927,92,1964;QS=0.867085,0.132915,0;VDB=0.187998;SGB=-0.590765;RPBZ=0.573514;MQBZ=-4.95028;MQSBZ=-0.485415;BQBZ=0.556487;NMBZ=6.54221;SCBZ=5.78316;FS=0;MQ0F=0 PL 63,0,255,180,255,255 +chr19 76 . A C,<*> 0 . DP=47;I16=18,21,2,3,1383,50589,220,10546,2340,140400,266,14324,715,15927,92,1964;QS=0.867085,0.132915,0;VDB=0.187998;SGB=-0.590765;RPBZ=0.573514;MQBZ=-4.95028;MQSBZ=-0.485415;BQBZ=0.556487;NMBZ=6.54221;SCBZ=5.78316;MQ0F=0 PL 63,0,255,180,255,255 chr19 77 . G <*> 0 . DP=47;I16=20,24,0,0,1639,63567,0,0,2606,154724,0,0,799,17769,0,0;QS=1,0;MQ0F=0 PL 0,132,255 -chr19 78 . G C,<*> 0 . DP=46;I16=17,21,2,3,1392,52920,202,9494,2280,136800,266,14324,702,15700,88,1896;QS=0.87768,0.12232,0;VDB=0.181959;SGB=-0.590765;RPBZ=0.739183;MQBZ=-4.88906;MQSBZ=-0.44293;BQBZ=-0.380581;NMBZ=6.46493;SCBZ=5.71324;FS=0;MQ0F=0 PL 51,0,255,166,255,255 +chr19 78 . G C,<*> 0 . DP=46;I16=17,21,2,3,1392,52920,202,9494,2280,136800,266,14324,702,15700,88,1896;QS=0.87768,0.12232,0;VDB=0.181959;SGB=-0.590765;RPBZ=0.739183;MQBZ=-4.88906;MQSBZ=-0.44293;BQBZ=-0.380581;NMBZ=6.46493;SCBZ=5.71324;MQ0F=0 PL 51,0,255,166,255,255 chr19 79 . G <*> 0 . DP=45;I16=18,24,0,0,1560,60778,0,0,2486,147524,0,0,780,17370,0,0;QS=1,0;MQ0F=0 PL 0,126,255 chr19 80 . G <*> 0 . DP=43;I16=17,23,0,0,1448,55202,0,0,2366,140324,0,0,771,17137,0,0;QS=1,0;MQ0F=0 PL 0,120,255 chr19 81 . C <*> 0 . DP=43;I16=17,23,0,0,1493,58329,0,0,2366,140324,0,0,762,16946,0,0;QS=1,0;MQ0F=0 PL 0,120,255 @@ -42,7 +41,7 @@ chr19 87 . C <*> 0 . DP=39;I16=15,22,0,0,1325,50283,0,0,2186,129524,0,0,724,1610 chr19 88 . C <*> 0 . DP=38;I16=14,23,0,0,1377,52341,0,0,2186,129524,0,0,735,16311,0,0;QS=1,0;MQ0F=0 PL 0,111,255 chr19 89 . G <*> 0 . DP=37;I16=13,23,0,0,1343,51159,0,0,2126,125924,0,0,720,15832,0,0;QS=1,0;MQ0F=0 PL 0,108,255 chr19 90 . C <*> 0 . DP=37;I16=13,23,0,0,1311,49173,0,0,2126,125924,0,0,704,15346,0,0;QS=1,0;MQ0F=0 PL 0,108,255 -chr19 91 . A G,<*> 0 . DP=37;I16=13,18,0,5,1128,42894,164,5518,1860,111600,266,14324,579,12347,107,2459;QS=0.873065,0.126935,0;VDB=0.0081677;SGB=-0.590765;RPBZ=1.60224;MQBZ=-4.43656;MQSBZ=-1.33955;BQBZ=-1.63294;NMBZ=5.89499;SCBZ=5.1969;FS=0;MQ0F=0 PL 27,0,255,121,255,255 +chr19 91 . A G,<*> 0 . DP=37;I16=13,18,0,5,1128,42894,164,5518,1860,111600,266,14324,579,12347,107,2459;QS=0.873065,0.126935,0;VDB=0.0081677;SGB=-0.590765;RPBZ=1.60224;MQBZ=-4.43656;MQSBZ=-1.33955;BQBZ=-1.63294;NMBZ=5.89499;SCBZ=5.1969;MQ0F=0 PL 27,0,255,121,255,255 chr19 92 . T <*> 0 . DP=36;I16=13,23,0,0,1262,45858,0,0,2126,125924,0,0,668,14314,0,0;QS=1,0;MQ0F=0 PL 0,108,255 chr19 93 . C <*> 0 . DP=36;I16=13,23,0,0,1250,44748,0,0,2126,125924,0,0,649,13819,0,0;QS=1,0;MQ0F=0 PL 0,108,255 chr19 94 . G <*> 0 . DP=35;I16=12,23,0,0,1262,46192,0,0,2066,122324,0,0,631,13369,0,0;QS=1,0;MQ0F=0 PL 0,105,255 @@ -50,4 +49,4 @@ chr19 95 . T <*> 0 . DP=35;I16=12,23,0,0,1163,41003,0,0,2066,122324,0,0,610,1281 chr19 96 . G <*> 0 . DP=34;I16=11,23,0,0,1178,41726,0,0,2006,118724,0,0,589,12261,0,0;QS=1,0;MQ0F=0 PL 0,102,255 chr19 97 . C <*> 0 . DP=34;I16=11,23,0,0,1191,42673,0,0,2006,118724,0,0,568,11752,0,0;QS=1,0;MQ0F=0 PL 0,102,255 chr19 98 . C <*> 0 . DP=33;I16=11,22,0,0,1153,41759,0,0,1946,115124,0,0,546,11188,0,0;QS=1,0;MQ0F=0 PL 0,99,255 -chr19 99 . C G,<*> 0 . DP=33;I16=11,17,0,5,1016,37202,178,6402,1680,100800,266,14324,436,8720,86,1850;QS=0.850921,0.149079,0;VDB=0.00429937;SGB=-0.590765;RPBZ=2.38675;MQBZ=-4.22751;MQSBZ=-1.26321;BQBZ=-0.583488;NMBZ=5.63252;SCBZ=4.95871;FS=0;MQ0F=0 PL 45,0,255,129,255,255 +chr19 99 . C G,<*> 0 . DP=33;I16=11,17,0,5,1016,37202,178,6402,1680,100800,266,14324,436,8720,86,1850;QS=0.850921,0.149079,0;VDB=0.00429937;SGB=-0.590765;RPBZ=2.38675;MQBZ=-4.22751;MQSBZ=-1.26321;BQBZ=-0.583488;NMBZ=5.63252;SCBZ=4.95871;MQ0F=0 PL 45,0,255,129,255,255 diff --git a/test/mpileup/annot-NMBZ.2.1.out b/test/mpileup/annot-NMBZ.2.1.out index 211ff1d2e..ccd3d62e1 100644 --- a/test/mpileup/annot-NMBZ.2.1.out +++ b/test/mpileup/annot-NMBZ.2.1.out @@ -13,11 +13,10 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample -chr6 75 . G A,<*> 0 . DP=283;I16=131,25,98,28,5557,200289,4591,168791,9360,561600,7560,453600,2484,51052,2121,45743;QS=0.547596,0.452404,0;VDB=3.5699e-10;SGB=-0.693147;RPBZ=-0.269598;MQBZ=0;MQSBZ=0;BQBZ=1.5258;NMBZ=-2.02395;SCBZ=-1.56217;FS=0;MQ0F=0 PL 255,0,255,255,255,255 +chr6 75 . G A,<*> 0 . DP=283;I16=131,25,98,28,5557,200289,4591,168791,9360,561600,7560,453600,2484,51052,2121,45743;QS=0.547596,0.452404,0;VDB=3.5699e-10;SGB=-0.693147;RPBZ=-0.269598;MQBZ=0;MQSBZ=0;BQBZ=1.5258;NMBZ=-2.02395;SCBZ=-1.56217;MQ0F=0 PL 255,0,255,255,255,255 diff --git a/test/mpileup/annot-NMBZ.3.1.out b/test/mpileup/annot-NMBZ.3.1.out index 73e2937e3..6d32e8d00 100644 --- a/test/mpileup/annot-NMBZ.3.1.out +++ b/test/mpileup/annot-NMBZ.3.1.out @@ -13,12 +13,11 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample sample2 -chr16 75 . C T,<*> 0 . DP=246;I16=114,125,1,0,8929,339403,8,64,14340,860400,40,1600,3901,80155,11,121;QS=1.99845,0.00154859,0;SGB=-0.516033;RPBZ=-1.14044;MQBZ=-15.4596;MQSBZ=1.04257;BQBZ=-1.74564;NMBZ=7.74597;SCBZ=10.8628;FS=0;MQ0F=0 PL 0,255,255,255,255,255 0,255,255,255,255,255 -chr16 75 . CTTTTTTTT CTTTTTTTTT,CTTTTTTTTTT 0 . INDEL;IDV=38;IMF=0.368932;DP=246;I16=92,109,23,16,8040,321600,1580,64400,12040,721600,2340,140400,3237,66777,675,13499;QS=1.43466,0.548367,0.0169779;VDB=0.506381;SGB=-13.9289;RPBZ=-1.68678;MQBZ=0.434057;MQSBZ=1.04257;BQBZ=-1.74564;NMBZ=-0.886523;SCBZ=-0.615101;FS=0;MQ0F=0 PL 255,0,116,255,195,255 0,255,198,255,201,210 +chr16 75 . C T,<*> 0 . DP=246;I16=114,125,1,0,8929,339403,8,64,14340,860400,40,1600,3901,80155,11,121;QS=1.99845,0.00154859,0;SGB=-0.516033;RPBZ=-1.14044;MQBZ=-15.4596;MQSBZ=1.04257;BQBZ=-1.74564;NMBZ=7.74597;SCBZ=10.8628;MQ0F=0 PL 0,255,255,255,255,255 0,255,255,255,255,255 +chr16 75 . CTTTTTTTT CTTTTTTTTT,CTTTTTTTTTT 0 . INDEL;IDV=38;IMF=0.368932;DP=246;I16=92,109,23,16,8040,321600,1580,64400,12040,721600,2340,140400,3237,66777,675,13499;QS=1.43466,0.548367,0.0169779;VDB=0.506381;SGB=-13.9289;RPBZ=-1.68678;MQBZ=0.434057;MQSBZ=1.04257;BQBZ=-1.74564;NMBZ=-0.886523;SCBZ=-0.615101;MQ0F=0 PL 255,0,116,255,195,255 0,255,198,255,201,210 diff --git a/test/mpileup/indel-AD.1.out b/test/mpileup/indel-AD.1.out index 196bad1eb..c3e657d03 100644 --- a/test/mpileup/indel-AD.1.out +++ b/test/mpileup/indel-AD.1.out @@ -12,7 +12,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -28,47 +27,47 @@ 000000F 397 . A <*> 0 . DP=3;I16=1,2,0,0,80,2554,0,0,180,10800,0,0,9,33,0,0;QS=1,0;MQ0F=0 PL:AD 0,9,77:3,0 000000F 398 . C <*> 0 . DP=3;I16=1,2,0,0,75,2309,0,0,180,10800,0,0,12,54,0,0;QS=1,0;MQ0F=0 PL:AD 0,9,72:3,0 000000F 399 . T <*> 0 . DP=3;I16=1,2,0,0,86,2582,0,0,180,10800,0,0,15,81,0,0;QS=1,0;MQ0F=0 PL:AD 0,9,82:3,0 -000000F 400 . C T,<*> 0 . DP=3;I16=1,1,0,1,63,2165,12,144,120,7200,60,3600,13,89,5,25;QS=0.84,0.16,0;SGB=-0.379885;RPBZ=-0.707107;MQBZ=0;MQSBZ=0;BQBZ=-1.22474;SCBZ=0;FS=0;MQ0F=0 PL:AD 3,0,54,9,57,61:2,1,0 +000000F 400 . C T,<*> 0 . DP=3;I16=1,1,0,1,63,2165,12,144,120,7200,60,3600,13,89,5,25;QS=0.84,0.16,0;SGB=-0.379885;RPBZ=-0.707107;MQBZ=0;MQSBZ=0;BQBZ=-1.22474;SCBZ=0;MQ0F=0 PL:AD 3,0,54,9,57,61:2,1,0 000000F 401 . G <*> 0 . DP=3;I16=1,2,0,0,65,1969,0,0,180,10800,0,0,21,153,0,0;QS=1,0;MQ0F=0 PL:AD 0,9,62:3,0 000000F 402 . C <*> 0 . DP=5;I16=1,3,0,0,83,2041,0,0,240,14400,0,0,24,198,0,0;QS=1,0;MQ0F=0 PL:AD 0,12,75:4,0 000000F 403 . A <*> 0 . DP=5;I16=2,3,0,0,102,2818,0,0,300,18000,0,0,29,251,0,0;QS=1,0;MQ0F=0 PL:AD 0,15,91:5,0 000000F 404 . T <*> 0 . DP=5;I16=2,3,0,0,141,4875,0,0,300,18000,0,0,34,314,0,0;QS=1,0;MQ0F=0 PL:AD 0,15,127:5,0 000000F 405 . G <*> 0 . DP=6;I16=3,3,0,0,175,6043,0,0,360,21600,0,0,39,387,0,0;QS=1,0;MQ0F=0 PL:AD 0,18,150:6,0 -000000F 406 . A T,<*> 0 . DP=6;I16=3,2,0,1,143,5019,12,144,300,18000,60,3600,34,350,11,121;QS=0.922581,0.0774194,0;SGB=-0.379885;RPBZ=0.603023;MQBZ=0;MQSBZ=0;BQBZ=-0.948683;SCBZ=-0.447214;FS=0;MQ0F=0 PL:AD 0,5,117,15,120,122:5,1,0 +000000F 406 . A T,<*> 0 . DP=6;I16=3,2,0,1,143,5019,12,144,300,18000,60,3600,34,350,11,121;QS=0.922581,0.0774194,0;SGB=-0.379885;RPBZ=0.603023;MQBZ=0;MQSBZ=0;BQBZ=-0.948683;SCBZ=-0.447214;MQ0F=0 PL:AD 0,5,117,15,120,122:5,1,0 000000F 407 . G <*> 0 . DP=6;I16=3,3,0,0,170,5748,0,0,360,21600,0,0,51,567,0,0;QS=1,0;MQ0F=0 PL:AD 0,18,148:6,0 000000F 408 . A <*> 0 . DP=6;I16=3,3,0,0,150,4818,0,0,360,21600,0,0,57,675,0,0;QS=1,0;MQ0F=0 PL:AD 0,18,130:6,0 000000F 409 . G <*> 0 . DP=6;I16=3,3,0,0,194,6940,0,0,360,21600,0,0,63,795,0,0;QS=1,0;MQ0F=0 PL:AD 0,18,166:6,0 000000F 410 . T <*> 0 . DP=7;I16=4,3,0,0,157,4587,0,0,420,25200,0,0,88,1288,0,0;QS=1,0;MQ0F=0 PL:AD 0,21,132:7,0 000000F 411 . T <*> 0 . DP=8;I16=5,3,0,0,255,8901,0,0,480,28800,0,0,115,1871,0,0;QS=1,0;MQ0F=0 PL:AD 0,24,196:8,0 -000000F 412 . A G,<*> 0 . DP=8;I16=5,2,0,1,235,8721,8,64,420,25200,60,3600,113,2009,10,100;QS=0.967078,0.0329218,0;SGB=-0.379885;RPBZ=0;MQBZ=0;MQSBZ=0;BQBZ=-1.62747;SCBZ=-0.75;FS=0;MQ0F=0 PL:AD 0,14,175,21,178,176:7,1,0 +000000F 412 . A G,<*> 0 . DP=8;I16=5,2,0,1,235,8721,8,64,420,25200,60,3600,113,2009,10,100;QS=0.967078,0.0329218,0;SGB=-0.379885;RPBZ=0;MQBZ=0;MQSBZ=0;BQBZ=-1.62747;SCBZ=-0.75;MQ0F=0 PL:AD 0,14,175,21,178,176:7,1,0 000000F 413 . T <*> 0 . DP=9;I16=5,4,0,0,288,10546,0,0,540,32400,0,0,131,2363,0,0;QS=1,0;MQ0F=0 PL:AD 0,27,214:9,0 000000F 414 . G <*> 0 . DP=9;I16=5,4,0,0,317,12083,0,0,540,32400,0,0,140,2634,0,0;QS=1,0;MQ0F=0 PL:AD 0,27,236:9,0 -000000F 415 . T G,<*> 0 . DP=9;I16=5,3,0,1,291,10937,22,484,480,28800,60,3600,136,2754,13,169;QS=0.929712,0.0702875,0;SGB=-0.379885;RPBZ=0.195283;MQBZ=0;MQSBZ=0;BQBZ=-1.5;SCBZ=-0.690269;FS=0;MQ0F=0 PL:AD 0,5,202,24,205,214:8,1,0 -000000F 416 . G C,<*> 0 . DP=10;I16=6,3,0,1,324,11944,12,144,540,32400,60,3600,144,3034,14,196;QS=0.964286,0.0357143,0;SGB=-0.379885;RPBZ=0.350285;MQBZ=0;MQSBZ=0;BQBZ=-1.62698;SCBZ=-0.642529;FS=0;MQ0F=0 PL:AD 0,17,225,27,228,228:9,1,0 +000000F 415 . T G,<*> 0 . DP=9;I16=5,3,0,1,291,10937,22,484,480,28800,60,3600,136,2754,13,169;QS=0.929712,0.0702875,0;SGB=-0.379885;RPBZ=0.195283;MQBZ=0;MQSBZ=0;BQBZ=-1.5;SCBZ=-0.690269;MQ0F=0 PL:AD 0,5,202,24,205,214:8,1,0 +000000F 416 . G C,<*> 0 . DP=10;I16=6,3,0,1,324,11944,12,144,540,32400,60,3600,144,3034,14,196;QS=0.964286,0.0357143,0;SGB=-0.379885;RPBZ=0.350285;MQBZ=0;MQSBZ=0;BQBZ=-1.62698;SCBZ=-0.642529;MQ0F=0 PL:AD 0,17,225,27,228,228:9,1,0 000000F 417 . T <*> 0 . DP=10;I16=6,4,0,0,364,13992,0,0,600,36000,0,0,166,3454,0,0;QS=1,0;MQ0F=0 PL:AD 0,30,255:10,0 000000F 418 . A <*> 0 . DP=10;I16=6,4,0,0,360,13680,0,0,600,36000,0,0,173,3643,0,0;QS=1,0;MQ0F=0 PL:AD 0,30,254:10,0 000000F 419 . A <*> 0 . DP=10;I16=6,4,0,0,344,13112,0,0,600,36000,0,0,180,3846,0,0;QS=1,0;MQ0F=0 PL:AD 0,30,242:10,0 -000000F 420 . A C,<*> 0 . DP=11;I16=7,3,0,1,306,11440,12,144,600,36000,60,3600,190,4180,18,324;QS=0.962382,0.0376176,0;SGB=-0.379885;RPBZ=0.476513;MQBZ=0;MQSBZ=0;BQBZ=-1.00766;SCBZ=-0.73252;FS=0;MQ0F=0 PL:AD 0,20,212,30,215,215:10,1,0 +000000F 420 . A C,<*> 0 . DP=11;I16=7,3,0,1,306,11440,12,144,600,36000,60,3600,190,4180,18,324;QS=0.962382,0.0376176,0;SGB=-0.379885;RPBZ=0.476513;MQBZ=0;MQSBZ=0;BQBZ=-1.00766;SCBZ=-0.73252;MQ0F=0 PL:AD 0,20,212,30,215,215:10,1,0 000000F 421 . A <*> 0 . DP=12;I16=8,4,0,0,388,13950,0,0,720,43200,0,0,236,5160,0,0;QS=1,0;MQ0F=0 PL:AD 0,36,255:12,0 000000F 422 . C <*> 0 . DP=13;I16=8,5,0,0,484,18266,0,0,780,46800,0,0,243,5389,0,0;QS=1,0;MQ0F=0 PL:AD 0,39,255:13,0 000000F 423 . A <*> 0 . DP=15;I16=9,6,0,0,509,18579,0,0,900,54000,0,0,266,5858,0,0;QS=1,0;MQ0F=0 PL:AD 0,45,255:15,0 000000F 424 . G <*> 0 . DP=15;I16=9,6,0,0,516,19368,0,0,900,54000,0,0,276,6150,0,0;QS=1,0;MQ0F=0 PL:AD 0,45,255:15,0 000000F 425 . A <*> 0 . DP=15;I16=9,6,0,0,516,19668,0,0,900,54000,0,0,284,6360,0,0;QS=1,0;MQ0F=0 PL:AD 0,45,255:15,0 -000000F 426 . G T,<*> 0 . DP=15;I16=9,5,0,1,519,20109,12,144,840,50400,60,3600,288,6570,4,16;QS=0.977401,0.0225989,0;SGB=-0.379885;RPBZ=-1.28103;MQBZ=0;MQSBZ=0;BQBZ=-1.70698;SCBZ=-0.879593;FS=0;MQ0F=0 PL:AD 0,31,255,42,255,255:14,1,0 +000000F 426 . G T,<*> 0 . DP=15;I16=9,5,0,1,519,20109,12,144,840,50400,60,3600,288,6570,4,16;QS=0.977401,0.0225989,0;SGB=-0.379885;RPBZ=-1.28103;MQBZ=0;MQSBZ=0;BQBZ=-1.70698;SCBZ=-0.879593;MQ0F=0 PL:AD 0,31,255,42,255,255:14,1,0 000000F 427 . C <*> 0 . DP=15;I16=9,6,0,0,550,21100,0,0,900,54000,0,0,300,6828,0,0;QS=1,0;MQ0F=0 PL:AD 0,45,255:15,0 000000F 428 . T <*> 0 . DP=15;I16=9,6,0,0,521,19363,0,0,900,54000,0,0,306,6984,0,0;QS=1,0;MQ0F=0 PL:AD 0,45,255:15,0 -000000F 429 . C A,<*> 0 . DP=17;I16=10,6,0,1,533,19507,12,144,960,57600,60,3600,287,6527,25,625;QS=0.977982,0.0220183,0;SGB=-0.379885;RPBZ=1.33584;MQBZ=0;MQSBZ=0;BQBZ=-1.55274;SCBZ=-0.887279;FS=0;MQ0F=0 PL:AD 0,37,255,48,255,255:16,1,0 +000000F 429 . C A,<*> 0 . DP=17;I16=10,6,0,1,533,19507,12,144,960,57600,60,3600,287,6527,25,625;QS=0.977982,0.0220183,0;SGB=-0.379885;RPBZ=1.33584;MQBZ=0;MQSBZ=0;BQBZ=-1.55274;SCBZ=-0.887279;MQ0F=0 PL:AD 0,37,255,48,255,255:16,1,0 000000F 430 . A <*> 0 . DP=18;I16=10,8,0,0,583,20803,0,0,1080,64800,0,0,320,7334,0,0;QS=1,0;MQ0F=0 PL:AD 0,54,255:18,0 000000F 431 . A <*> 0 . DP=19;I16=10,8,0,0,616,23012,0,0,1080,64800,0,0,328,7482,0,0;QS=1,0;MQ0F=0 PL:AD 0,54,255:18,0 000000F 432 . T <*> 0 . DP=19;I16=11,8,0,0,682,26264,0,0,1140,68400,0,0,337,7647,0,0;QS=1,0;MQ0F=0 PL:AD 0,57,255:19,0 000000F 433 . T <*> 0 . DP=19;I16=11,8,0,0,696,26452,0,0,1140,68400,0,0,346,7830,0,0;QS=1,0;MQ0F=0 PL:AD 0,57,255:19,0 000000F 434 . T <*> 0 . DP=19;I16=11,8,0,0,678,25728,0,0,1140,68400,0,0,354,7980,0,0;QS=1,0;MQ0F=0 PL:AD 0,57,255:19,0 000000F 435 . T <*> 0 . DP=20;I16=11,9,0,0,717,26931,0,0,1200,72000,0,0,362,8146,0,0;QS=1,0;MQ0F=0 PL:AD 0,60,255:20,0 -000000F 436 . A C,<*> 0 . DP=21;I16=11,9,0,1,728,28034,12,144,1200,72000,60,3600,346,7704,25,625;QS=0.983784,0.0162162,0;SGB=-0.379885;RPBZ=0.909477;MQBZ=0;MQSBZ=0;BQBZ=-1.66309;SCBZ=-0.82685;FS=0;MQ0F=0 PL:AD 0,49,255,60,255,255:20,1,0 +000000F 436 . A C,<*> 0 . DP=21;I16=11,9,0,1,728,28034,12,144,1200,72000,60,3600,346,7704,25,625;QS=0.983784,0.0162162,0;SGB=-0.379885;RPBZ=0.909477;MQBZ=0;MQSBZ=0;BQBZ=-1.66309;SCBZ=-0.82685;MQ0F=0 PL:AD 0,49,255,60,255,255:20,1,0 000000F 437 . T <*> 0 . DP=21;I16=11,10,0,0,770,29698,0,0,1260,75600,0,0,381,8531,0,0;QS=1,0;MQ0F=0 PL:AD 0,63,255:21,0 000000F 438 . T <*> 0 . DP=22;I16=11,10,0,0,726,26976,0,0,1260,75600,0,0,391,8753,0,0;QS=1,0;MQ0F=0 PL:AD 0,63,255:21,0 000000F 439 . T <*> 0 . DP=25;I16=14,10,0,0,804,30038,0,0,1440,86400,0,0,444,9912,0,0;QS=1,0;MQ0F=0 PL:AD 0,72,255:24,0 -000000F 440 . T A,<*> 0 . DP=27;I16=15,11,1,0,896,33856,12,144,1560,93600,60,3600,455,10163,25,625;QS=0.986784,0.0132159,0;SGB=-0.379885;RPBZ=1.28585;MQBZ=0;MQSBZ=0;BQBZ=-1.41134;SCBZ=0.48519;FS=0;MQ0F=0 PL:AD 0,66,255,78,255,255:26,1,0 +000000F 440 . T A,<*> 0 . DP=27;I16=15,11,1,0,896,33856,12,144,1560,93600,60,3600,455,10163,25,625;QS=0.986784,0.0132159,0;SGB=-0.379885;RPBZ=1.28585;MQBZ=0;MQSBZ=0;BQBZ=-1.41134;SCBZ=0.48519;MQ0F=0 PL:AD 0,66,255,78,255,255:26,1,0 000000F 441 . G <*> 0 . DP=29;I16=17,11,0,0,1033,39137,0,0,1680,100800,0,0,495,11163,0,0;QS=1,0;MQ0F=0 PL:AD 0,84,255:28,0 000000F 442 . T <*> 0 . DP=29;I16=18,11,0,0,1067,41223,0,0,1740,104400,0,0,531,11951,0,0;QS=1,0;MQ0F=0 PL:AD 0,87,255:29,0 000000F 443 . A <*> 0 . DP=31;I16=20,11,0,0,1078,40562,0,0,1860,111600,0,0,544,12226,0,0;QS=1,0;MQ0F=0 PL:AD 0,93,255:31,0 @@ -79,45 +78,45 @@ 000000F 448 . T <*> 0 . DP=35;I16=23,12,0,0,1220,45736,0,0,2100,126000,0,0,667,15037,0,0;QS=1,0;MQ0F=0 PL:AD 0,105,255:35,0 000000F 449 . T <*> 0 . DP=35;I16=23,12,0,0,1249,47703,0,0,2100,126000,0,0,679,15245,0,0;QS=1,0;MQ0F=0 PL:AD 0,105,255:35,0 000000F 450 . G <*> 0 . DP=38;I16=25,13,0,0,1449,56453,0,0,2280,136800,0,0,715,16059,0,0;QS=1,0;MQ0F=0 PL:AD 0,114,255:38,0 -000000F 451 . T A,<*> 0 . DP=43;I16=24,16,0,1,1485,57079,12,144,2400,144000,60,3600,708,15882,0,0;QS=0.991984,0.00801603,0;SGB=-0.379885;RPBZ=-1.56545;MQBZ=0;MQSBZ=0;BQBZ=-1.91213;SCBZ=-0.839032;FS=0;MQ0F=0 PL:AD 0,107,255,120,255,255:40,1,0 -000000F 452 . G T,<*> 0 . DP=45;I16=24,18,0,1,1541,58723,12,144,2520,151200,60,3600,707,15841,23,529;QS=0.992273,0.00772698,0;SGB=-0.379885;RPBZ=0.645561;MQBZ=0;MQSBZ=0;BQBZ=-1.75577;SCBZ=0.629801;FS=0;MQ0F=0 PL:AD 0,113,255,126,255,255:42,1,0 +000000F 451 . T A,<*> 0 . DP=43;I16=24,16,0,1,1485,57079,12,144,2400,144000,60,3600,708,15882,0,0;QS=0.991984,0.00801603,0;SGB=-0.379885;RPBZ=-1.56545;MQBZ=0;MQSBZ=0;BQBZ=-1.91213;SCBZ=-0.839032;MQ0F=0 PL:AD 0,107,255,120,255,255:40,1,0 +000000F 452 . G T,<*> 0 . DP=45;I16=24,18,0,1,1541,58723,12,144,2520,151200,60,3600,707,15841,23,529;QS=0.992273,0.00772698,0;SGB=-0.379885;RPBZ=0.645561;MQBZ=0;MQSBZ=0;BQBZ=-1.75577;SCBZ=0.629801;MQ0F=0 PL:AD 0,113,255,126,255,255:42,1,0 000000F 453 . C <*> 0 . DP=45;I16=24,19,0,0,1623,65335,0,0,2580,154800,0,0,753,16853,0,0;QS=1,0;MQ0F=0 PL:AD 0,129,255:43,0 -000000F 454 . A C,<*> 0 . DP=47;I16=24,20,1,0,1699,68295,12,144,2640,158400,60,3600,774,17286,25,625;QS=0.992987,0.00701344,0;SGB=-0.379885;RPBZ=1.46482;MQBZ=0;MQSBZ=0;BQBZ=-1.87433;SCBZ=0.550575;FS=0;MQ0F=0 PL:AD 0,119,255,132,255,255:44,1,0 +000000F 454 . A C,<*> 0 . DP=47;I16=24,20,1,0,1699,68295,12,144,2640,158400,60,3600,774,17286,25,625;QS=0.992987,0.00701344,0;SGB=-0.379885;RPBZ=1.46482;MQBZ=0;MQSBZ=0;BQBZ=-1.87433;SCBZ=0.550575;MQ0F=0 PL:AD 0,119,255,132,255,255:44,1,0 000000F 455 . G <*> 0 . DP=48;I16=26,20,0,0,1807,74553,0,0,2760,165600,0,0,823,18385,0,0;QS=1,0;MQ0F=0 PL:AD 0,138,255:46,0 000000F 456 . T <*> 0 . DP=49;I16=26,21,0,0,1757,69583,0,0,2820,169200,0,0,845,18853,0,0;QS=1,0;MQ0F=0 PL:AD 0,141,255:47,0 000000F 457 . T <*> 0 . DP=49;I16=26,21,0,0,1836,73528,0,0,2820,169200,0,0,866,19264,0,0;QS=1,0;MQ0F=0 PL:AD 0,141,255:47,0 000000F 458 . A <*> 0 . DP=50;I16=26,22,0,0,1817,72337,0,0,2880,172800,0,0,887,19717,0,0;QS=1,0;MQ0F=0 PL:AD 0,144,255:48,0 000000F 459 . G <*> 0 . DP=50;I16=26,22,0,0,1791,70171,0,0,2880,172800,0,0,909,20213,0,0;QS=1,0;MQ0F=0 PL:AD 0,144,255:48,0 000000F 460 . A <*> 0 . DP=49;I16=26,22,0,0,1675,63873,0,0,2880,172800,0,0,923,20689,0,0;QS=1,0;MQ0F=0 PL:AD 0,144,255:48,0 -000000F 461 . A T,C,<*> 0 . DP=52;I16=25,22,1,1,1650,63298,24,288,2820,169200,120,7200,927,21061,17,145;QS=0.985663,0.00716846,0.00716846,0;VDB=0.06;SGB=-0.453602;RPBZ=-1.92231;MQBZ=0;MQSBZ=0;BQBZ=-2.2578;SCBZ=-0.055422;FS=0;MQ0F=0 PL:AD 0,128,255,128,255,255,141,255,255,255:47,1,1,0 -000000F 462 . A T,<*> 0 . DP=52;I16=26,22,0,1,1705,65163,12,144,2880,172800,60,3600,955,21615,10,100;QS=0.993011,0.00698893,0;SGB=-0.379885;RPBZ=-1.09702;MQBZ=0;MQSBZ=0;BQBZ=-1.74927;SCBZ=-0.853241;FS=0;MQ0F=0 PL:AD 0,130,255,144,255,255:48,1,0 +000000F 461 . A T,C,<*> 0 . DP=52;I16=25,22,1,1,1650,63298,24,288,2820,169200,120,7200,927,21061,17,145;QS=0.985663,0.00716846,0.00716846,0;VDB=0.06;SGB=-0.453602;RPBZ=-1.92231;MQBZ=0;MQSBZ=0;BQBZ=-2.2578;SCBZ=-0.055422;MQ0F=0 PL:AD 0,128,255,128,255,255,141,255,255,255:47,1,1,0 +000000F 462 . A T,<*> 0 . DP=52;I16=26,22,0,1,1705,65163,12,144,2880,172800,60,3600,955,21615,10,100;QS=0.993011,0.00698893,0;SGB=-0.379885;RPBZ=-1.09702;MQBZ=0;MQSBZ=0;BQBZ=-1.74927;SCBZ=-0.853241;MQ0F=0 PL:AD 0,130,255,144,255,255:48,1,0 000000F 463 . A <*> 0 . DP=52;I16=26,24,0,0,1836,71956,0,0,3000,180000,0,0,996,22366,0,0;QS=1,0;MQ0F=0 PL:AD 0,151,255:50,0 -000000F 464 . T G,<*> 0 . DP=52;I16=26,23,0,1,1873,73813,12,144,2940,176400,60,3600,993,22355,25,625;QS=0.993634,0.00636605,0;SGB=-0.379885;RPBZ=0.173386;MQBZ=0;MQSBZ=0;BQBZ=-1.93908;SCBZ=-0.840331;FS=0;MQ0F=0 PL:AD 0,133,255,148,255,255:49,1,0 +000000F 464 . T G,<*> 0 . DP=52;I16=26,23,0,1,1873,73813,12,144,2940,176400,60,3600,993,22355,25,625;QS=0.993634,0.00636605,0;SGB=-0.379885;RPBZ=0.173386;MQBZ=0;MQSBZ=0;BQBZ=-1.93908;SCBZ=-0.840331;MQ0F=0 PL:AD 0,133,255,148,255,255:49,1,0 000000F 465 . A <*> 0 . DP=52;I16=26,24,0,0,1950,78232,0,0,3000,180000,0,0,1039,23587,0,0;QS=1,0;MQ0F=0 PL:AD 0,151,255:50,0 -000000F 466 . A C,<*> 0 . DP=52;I16=25,24,1,0,1858,74740,12,144,2940,176400,60,3600,1033,23509,25,625;QS=0.993583,0.00641711,0;SGB=-0.379885;RPBZ=-1.24865;MQBZ=0;MQSBZ=0;BQBZ=-1.79438;SCBZ=1.87165;FS=0;MQ0F=0 PL:AD 0,133,255,148,255,255:49,1,0 +000000F 466 . A C,<*> 0 . DP=52;I16=25,24,1,0,1858,74740,12,144,2940,176400,60,3600,1033,23509,25,625;QS=0.993583,0.00641711,0;SGB=-0.379885;RPBZ=-1.24865;MQBZ=0;MQSBZ=0;BQBZ=-1.79438;SCBZ=1.87165;MQ0F=0 PL:AD 0,133,255,148,255,255:49,1,0 000000F 467 . T <*> 0 . DP=53;I16=26,25,0,0,1890,74962,0,0,3060,183600,0,0,1076,24668,0,0;QS=1,0;MQ0F=0 PL:AD 0,154,255:51,0 000000F 468 . A <*> 0 . DP=54;I16=27,25,0,0,1967,78281,0,0,3120,187200,0,0,1095,25239,0,0;QS=1,0;MQ0F=0 PL:AD 0,157,255:52,0 000000F 469 . T <*> 0 . DP=54;I16=27,25,0,0,2046,83348,0,0,3120,187200,0,0,1113,25747,0,0;QS=1,0;MQ0F=0 PL:AD 0,157,255:52,0 000000F 470 . G <*> 0 . DP=55;I16=28,25,0,0,2047,81939,0,0,3180,190800,0,0,1131,26291,0,0;QS=1,0;MQ0F=0 PL:AD 0,160,255:53,0 000000F 471 . A <*> 0 . DP=56;I16=28,26,0,0,2028,80100,0,0,3240,194400,0,0,1150,26872,0,0;QS=1,0;MQ0F=0 PL:AD 0,163,255:54,0 000000F 472 . T <*> 0 . DP=59;I16=29,28,0,0,2122,83726,0,0,3420,205200,0,0,1191,27925,0,0;QS=1,0;MQ0F=0 PL:AD 0,172,255:57,0 -000000F 473 . C A,G,<*> 0 . DP=63;I16=19,15,12,13,1263,49285,963,39221,2040,122400,1500,90000,705,16449,548,12960;QS=0.567385,0.427224,0.00539084,0;VDB=1.64281e-06;SGB=-0.692914;RPBZ=1.05908;MQBZ=0;MQSBZ=0;BQBZ=1.40915;SCBZ=0.597801;FS=0;MQ0F=0 PL:AD 255,0,255,255,255,255,255,255,255,255:34,24,1,0 +000000F 473 . C A,G,<*> 0 . DP=63;I16=19,15,12,13,1263,49285,963,39221,2040,122400,1500,90000,705,16449,548,12960;QS=0.567385,0.427224,0.00539084,0;VDB=1.64281e-06;SGB=-0.692914;RPBZ=1.05908;MQBZ=0;MQSBZ=0;BQBZ=1.40915;SCBZ=0.597801;MQ0F=0 PL:AD 255,0,255,255,255,255,255,255,255,255:34,24,1,0 000000F 474 . A <*> 0 . DP=64;I16=33,28,0,0,2172,84276,0,0,3660,219600,0,0,1296,30488,0,0;QS=1,0;MQ0F=0 PL:AD 0,184,255:61,0 000000F 475 . A <*> 0 . DP=64;I16=34,28,0,0,2092,79478,0,0,3720,223200,0,0,1322,31258,0,0;QS=1,0;MQ0F=0 PL:AD 0,187,255:62,0 -000000F 476 . A G,<*> 0 . DP=65;I16=34,28,0,1,2176,83678,12,144,3720,223200,60,3600,1319,31299,25,625;QS=0.994516,0.00548446,0;SGB=-0.379885;RPBZ=1.04564;MQBZ=0;MQSBZ=0;BQBZ=-1.59705;SCBZ=0.713967;FS=0;MQ0F=0 PL:AD 0,172,255,187,255,255:62,1,0 -000000F 477 . T G,<*> 0 . DP=65;I16=34,28,0,1,2352,93436,12,144,3720,223200,60,3600,1338,31806,25,625;QS=0.994924,0.00507614,0;SGB=-0.379885;RPBZ=-0.687896;MQBZ=0;MQSBZ=0;BQBZ=-1.84472;SCBZ=-0.892396;FS=0;MQ0F=0 PL:AD 0,172,255,187,255,255:62,1,0 +000000F 476 . A G,<*> 0 . DP=65;I16=34,28,0,1,2176,83678,12,144,3720,223200,60,3600,1319,31299,25,625;QS=0.994516,0.00548446,0;SGB=-0.379885;RPBZ=1.04564;MQBZ=0;MQSBZ=0;BQBZ=-1.59705;SCBZ=0.713967;MQ0F=0 PL:AD 0,172,255,187,255,255:62,1,0 +000000F 477 . T G,<*> 0 . DP=65;I16=34,28,0,1,2352,93436,12,144,3720,223200,60,3600,1338,31806,25,625;QS=0.994924,0.00507614,0;SGB=-0.379885;RPBZ=-0.687896;MQBZ=0;MQSBZ=0;BQBZ=-1.84472;SCBZ=-0.892396;MQ0F=0 PL:AD 0,172,255,187,255,255:62,1,0 000000F 478 . C <*> 0 . DP=65;I16=34,29,0,0,2376,94566,0,0,3780,226800,0,0,1381,32925,0,0;QS=1,0;MQ0F=0 PL:AD 0,190,255:63,0 -000000F 479 . T G,<*> 0 . DP=68;I16=36,29,0,1,2467,98357,12,144,3900,234000,60,3600,1416,33712,21,441;QS=0.995159,0.00484066,0;SGB=-0.379885;RPBZ=-0.787962;MQBZ=0;MQSBZ=0;BQBZ=-1.86106;SCBZ=-0.927153;FS=0;MQ0F=0 PL:AD 0,180,255,196,255,255:65,1,0 +000000F 479 . T G,<*> 0 . DP=68;I16=36,29,0,1,2467,98357,12,144,3900,234000,60,3600,1416,33712,21,441;QS=0.995159,0.00484066,0;SGB=-0.379885;RPBZ=-0.787962;MQBZ=0;MQSBZ=0;BQBZ=-1.86106;SCBZ=-0.927153;MQ0F=0 PL:AD 0,180,255,196,255,255:65,1,0 000000F 480 . G <*> 0 . DP=70;I16=38,30,0,0,2563,101527,0,0,4080,244800,0,0,1495,35435,0,0;QS=1,0;MQ0F=0 PL:AD 0,205,255:68,0 000000F 481 . T <*> 0 . DP=70;I16=38,30,0,0,2521,98551,0,0,4080,244800,0,0,1514,35994,0,0;QS=1,0;MQ0F=0 PL:AD 0,205,255:68,0 -000000F 482 . T G,<*> 0 . DP=70;I16=37,30,1,0,2575,103005,12,144,4020,241200,60,3600,1518,36344,14,196;QS=0.995361,0.00463858,0;SGB=-0.379885;RPBZ=-0.892198;MQBZ=0;MQSBZ=0;BQBZ=-1.93937;SCBZ=-0.948507;FS=0;MQ0F=0 PL:AD 0,186,255,202,255,255:67,1,0 +000000F 482 . T G,<*> 0 . DP=70;I16=37,30,1,0,2575,103005,12,144,4020,241200,60,3600,1518,36344,14,196;QS=0.995361,0.00463858,0;SGB=-0.379885;RPBZ=-0.892198;MQBZ=0;MQSBZ=0;BQBZ=-1.93937;SCBZ=-0.948507;MQ0F=0 PL:AD 0,186,255,202,255,255:67,1,0 000000F 483 . T <*> 0 . DP=70;I16=38,30,0,0,2646,106206,0,0,4080,244800,0,0,1549,37071,0,0;QS=1,0;MQ0F=0 PL:AD 0,205,255:68,0 000000F 484 . G <*> 0 . DP=70;I16=38,30,0,0,2659,107225,0,0,4080,244800,0,0,1565,37585,0,0;QS=1,0;MQ0F=0 PL:AD 0,205,255:68,0 000000F 485 . T <*> 0 . DP=70;I16=38,30,0,0,2618,104932,0,0,4080,244800,0,0,1578,37978,0,0;QS=1,0;MQ0F=0 PL:AD 0,205,255:68,0 000000F 486 . T <*> 0 . DP=70;I16=38,30,0,0,2589,103545,0,0,4080,244800,0,0,1589,38295,0,0;QS=1,0;MQ0F=0 PL:AD 0,205,255:68,0 000000F 487 . T <*> 0 . DP=73;I16=38,33,0,0,2694,107284,0,0,4260,255600,0,0,1599,38583,0,0;QS=1,0;MQ0F=0 PL:AD 0,214,255:71,0 -000000F 488 . A G,<*> 0 . DP=76;I16=41,32,0,1,2640,102296,8,64,4380,262800,60,3600,1679,40447,1,1;QS=0.996979,0.00302115,0;SGB=-0.379885;RPBZ=-1.52228;MQBZ=0;MQSBZ=0;BQBZ=-1.89405;SCBZ=-0.946449;FS=0;MQ0F=0 PL:AD 0,204,255,220,255,255:73,1,0 -000000F 489 . C A,<*> 0 . DP=79;I16=43,33,0,1,2694,103126,12,144,4560,273600,60,3600,1715,41273,25,625;QS=0.995565,0.00443459,0;SGB=-0.379885;RPBZ=-0.495167;MQBZ=0;MQSBZ=0;BQBZ=-1.58784;SCBZ=-0.974263;FS=0;MQ0F=0 PL:AD 0,213,255,229,255,255:76,1,0 +000000F 488 . A G,<*> 0 . DP=76;I16=41,32,0,1,2640,102296,8,64,4380,262800,60,3600,1679,40447,1,1;QS=0.996979,0.00302115,0;SGB=-0.379885;RPBZ=-1.52228;MQBZ=0;MQSBZ=0;BQBZ=-1.89405;SCBZ=-0.946449;MQ0F=0 PL:AD 0,204,255,220,255,255:73,1,0 +000000F 489 . C A,<*> 0 . DP=79;I16=43,33,0,1,2694,103126,12,144,4560,273600,60,3600,1715,41273,25,625;QS=0.995565,0.00443459,0;SGB=-0.379885;RPBZ=-0.495167;MQBZ=0;MQSBZ=0;BQBZ=-1.58784;SCBZ=-0.974263;MQ0F=0 PL:AD 0,213,255,229,255,255:76,1,0 000000F 490 . C <*> 0 . DP=80;I16=43,35,0,0,2796,107040,0,0,4680,280800,0,0,1782,43020,0,0;QS=1,0;MQ0F=0 PL:AD 0,235,255:78,0 000000F 491 . T <*> 0 . DP=80;I16=43,35,0,0,2910,113818,0,0,4680,280800,0,0,1798,43500,0,0;QS=1,0;MQ0F=0 PL:AD 0,235,255:78,0 000000F 492 . G <*> 0 . DP=81;I16=43,35,0,0,3089,125687,0,0,4680,280800,0,0,1814,44012,0,0;QS=1,0;MQ0F=0 PL:AD 0,235,255:78,0 @@ -127,83 +126,83 @@ 000000F 496 . T <*> 0 . DP=87;I16=47,37,0,0,3238,128760,0,0,5040,302400,0,0,1917,46777,0,0;QS=1,0;MQ0F=0 PL:AD 0,253,255:84,0 000000F 497 . G <*> 0 . DP=87;I16=47,37,0,0,3280,132640,0,0,5040,302400,0,0,1933,47227,0,0;QS=1,0;MQ0F=0 PL:AD 0,253,255:84,0 000000F 498 . T <*> 0 . DP=88;I16=48,37,0,0,3081,120187,0,0,5100,306000,0,0,1971,48181,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:85,0 -000000F 499 . T C,<*> 0 . DP=89;I16=48,36,0,1,3190,126958,8,64,5040,302400,60,3600,1957,47809,25,625;QS=0.997498,0.00250156,0;SGB=-0.379885;RPBZ=-0.305833;MQBZ=0;MQSBZ=0;BQBZ=-1.95559;SCBZ=-1.05778;FS=0;MQ0F=0 PL:AD 0,237,255,253,255,255:84,1,0 -000000F 500 . T G,A,<*> 0 . DP=92;I16=50,37,1,1,3308,133104,24,288,5220,313200,120,7200,1986,48376,50,1250;QS=0.992797,0.00360144,0.00360144,0;VDB=0.32;SGB=-0.453602;RPBZ=0.41539;MQBZ=0;MQSBZ=0;BQBZ=-2.60206;SCBZ=-1.0009;FS=0;MQ0F=0 PL:AD 0,245,255,245,255,255,255,255,255,255:87,1,1,0 +000000F 499 . T C,<*> 0 . DP=89;I16=48,36,0,1,3190,126958,8,64,5040,302400,60,3600,1957,47809,25,625;QS=0.997498,0.00250156,0;SGB=-0.379885;RPBZ=-0.305833;MQBZ=0;MQSBZ=0;BQBZ=-1.95559;SCBZ=-1.05778;MQ0F=0 PL:AD 0,237,255,253,255,255:84,1,0 +000000F 500 . T G,A,<*> 0 . DP=92;I16=50,37,1,1,3308,133104,24,288,5220,313200,120,7200,1986,48376,50,1250;QS=0.992797,0.00360144,0.00360144,0;VDB=0.32;SGB=-0.453602;RPBZ=0.41539;MQBZ=0;MQSBZ=0;BQBZ=-2.60206;SCBZ=-1.0009;MQ0F=0 PL:AD 0,245,255,245,255,255,255,255,255,255:87,1,1,0 000000F 501 . G <*> 0 . DP=97;I16=53,40,0,0,3485,138049,0,0,5580,334800,0,0,2050,49962,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:93,0 -000000F 502 . T A,<*> 0 . DP=98;I16=53,40,1,0,3391,132771,12,144,5580,334800,60,3600,2065,50183,25,625;QS=0.996476,0.00352423,0;SGB=-0.379885;RPBZ=1.67751;MQBZ=0;MQSBZ=0;BQBZ=-1.7355;SCBZ=0.856937;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:93,1,0 +000000F 502 . T A,<*> 0 . DP=98;I16=53,40,1,0,3391,132771,12,144,5580,334800,60,3600,2065,50183,25,625;QS=0.996476,0.00352423,0;SGB=-0.379885;RPBZ=1.67751;MQBZ=0;MQSBZ=0;BQBZ=-1.7355;SCBZ=0.856937;MQ0F=0 PL:AD 0,255,255,255,255,255:93,1,0 000000F 503 . G <*> 0 . DP=98;I16=54,40,0,0,3540,140610,0,0,5640,338400,0,0,2108,51206,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:94,0 -000000F 504 . T C,A,<*> 0 . DP=102;I16=53,42,1,1,3464,137680,20,208,5700,342000,120,7200,2099,50913,25,625;QS=0.994259,0.00344432,0.00229621,0;VDB=0.92;SGB=-0.453602;RPBZ=0.0126977;MQBZ=0;MQSBZ=0;BQBZ=-2.43319;SCBZ=0.512446;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:95,1,1,0 +000000F 504 . T C,A,<*> 0 . DP=102;I16=53,42,1,1,3464,137680,20,208,5700,342000,120,7200,2099,50913,25,625;QS=0.994259,0.00344432,0.00229621,0;VDB=0.92;SGB=-0.453602;RPBZ=0.0126977;MQBZ=0;MQSBZ=0;BQBZ=-2.43319;SCBZ=0.512446;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:95,1,1,0 000000F 505 . G <*> 0 . DP=102;I16=54,43,0,0,3640,144678,0,0,5820,349200,0,0,2141,51803,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:97,0 -000000F 506 . C G,<*> 0 . DP=103;I16=54,43,0,1,3621,145273,12,144,5820,349200,60,3600,2138,51502,25,625;QS=0.996697,0.00330306,0;SGB=-0.379885;RPBZ=0.194473;MQBZ=0;MQSBZ=0;BQBZ=-1.75415;SCBZ=-1.07827;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:97,1,0 +000000F 506 . C G,<*> 0 . DP=103;I16=54,43,0,1,3621,145273,12,144,5820,349200,60,3600,2138,51502,25,625;QS=0.996697,0.00330306,0;SGB=-0.379885;RPBZ=0.194473;MQBZ=0;MQSBZ=0;BQBZ=-1.75415;SCBZ=-1.07827;MQ0F=0 PL:AD 0,255,255,255,255,255:97,1,0 000000F 507 . T <*> 0 . DP=103;I16=54,44,0,0,3520,139202,0,0,5880,352800,0,0,2181,52471,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:98,0 -000000F 508 . C T,<*> 0 . DP=103;I16=54,43,0,1,3476,137498,12,144,5820,349200,60,3600,2174,52226,25,625;QS=0.99656,0.00344037,0;SGB=-0.379885;RPBZ=0.265217;MQBZ=0;MQSBZ=0;BQBZ=-1.63996;SCBZ=-1.07818;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:97,1,0 +000000F 508 . C T,<*> 0 . DP=103;I16=54,43,0,1,3476,137498,12,144,5820,349200,60,3600,2174,52226,25,625;QS=0.99656,0.00344037,0;SGB=-0.379885;RPBZ=0.265217;MQBZ=0;MQSBZ=0;BQBZ=-1.63996;SCBZ=-1.07818;MQ0F=0 PL:AD 0,255,255,255,255,255:97,1,0 000000F 509 . C <*> 0 . DP=103;I16=54,44,0,0,3580,142206,0,0,5880,352800,0,0,2217,53267,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:98,0 -000000F 510 . C A,G,<*> 0 . DP=106;I16=54,43,1,2,3646,145190,42,692,5820,349200,180,10800,2189,52645,67,1515;QS=0.988612,0.00921909,0.0021692,0;VDB=0.401962;SGB=-0.511536;RPBZ=-0.707412;MQBZ=0;MQSBZ=0;BQBZ=-3.02794;SCBZ=-0.99293;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:97,2,1,0 -000000F 511 . T A,<*> 0 . DP=107;I16=55,45,0,1,3663,144413,12,144,6000,360000,60,3600,2251,54067,25,625;QS=0.996735,0.00326531,0;SGB=-0.379885;RPBZ=-0.0343102;MQBZ=0;MQSBZ=0;BQBZ=-1.71065;SCBZ=-1.08137;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:100,1,0 -000000F 512 . C A,G,<*> 0 . DP=107;I16=55,43,1,3,3657,146609,54,836,5880,352800,240,14400,2238,53902,83,1939;QS=0.985449,0.0123956,0.00215575,0;VDB=0.681156;SGB=-0.556411;RPBZ=-0.465574;MQBZ=0;MQSBZ=0;BQBZ=-3.45917;SCBZ=-0.667699;FS=0;MQ0F=0 PL:AD 0,248,255,255,255,255,255,255,255,255:98,3,1,0 -000000F 513 . T G,<*> 0 . DP=108;I16=56,46,0,1,3774,150038,7,49,6120,367200,60,3600,2340,56352,0,0;QS=0.998149,0.00185136,0;SGB=-0.379885;RPBZ=-1.71577;MQBZ=0;MQSBZ=0;BQBZ=-1.90666;SCBZ=-1.07835;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:102,1,0 -000000F 514 . G T,<*> 0 . DP=110;I16=56,47,1,1,3763,148539,20,208,6180,370800,120,7200,2348,56422,25,625;QS=0.994713,0.00528681,0;VDB=0.44;SGB=-0.453602;RPBZ=-1.58286;MQBZ=0;MQSBZ=0;BQBZ=-2.48498;SCBZ=0.0121282;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:103,2,0 -000000F 515 . C G,<*> 0 . DP=110;I16=57,47,0,1,3848,153002,12,144,6240,374400,60,3600,2367,56887,25,625;QS=0.996891,0.00310881,0;SGB=-0.379885;RPBZ=0.263997;MQBZ=0;MQSBZ=0;BQBZ=-1.75323;SCBZ=-1.07538;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:104,1,0 -000000F 516 . G T,<*> 0 . DP=111;I16=57,48,0,1,3969,158573,12,144,6300,378000,60,3600,2411,58015,0,0;QS=0.996986,0.00301432,0;SGB=-0.379885;RPBZ=-1.71626;MQBZ=0;MQSBZ=0;BQBZ=-1.8341;SCBZ=-1.06697;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:105,1,0 -000000F 517 . T C,<*> 0 . DP=112;I16=56,50,1,0,3850,151946,12,144,6360,381600,60,3600,2408,58016,21,441;QS=0.996893,0.0031072,0;SGB=-0.379885;RPBZ=-0.7772;MQBZ=0;MQSBZ=0;BQBZ=-1.67048;SCBZ=0.856997;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:106,1,0 +000000F 510 . C A,G,<*> 0 . DP=106;I16=54,43,1,2,3646,145190,42,692,5820,349200,180,10800,2189,52645,67,1515;QS=0.988612,0.00921909,0.0021692,0;VDB=0.401962;SGB=-0.511536;RPBZ=-0.707412;MQBZ=0;MQSBZ=0;BQBZ=-3.02794;SCBZ=-0.99293;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:97,2,1,0 +000000F 511 . T A,<*> 0 . DP=107;I16=55,45,0,1,3663,144413,12,144,6000,360000,60,3600,2251,54067,25,625;QS=0.996735,0.00326531,0;SGB=-0.379885;RPBZ=-0.0343102;MQBZ=0;MQSBZ=0;BQBZ=-1.71065;SCBZ=-1.08137;MQ0F=0 PL:AD 0,255,255,255,255,255:100,1,0 +000000F 512 . C A,G,<*> 0 . DP=107;I16=55,43,1,3,3657,146609,54,836,5880,352800,240,14400,2238,53902,83,1939;QS=0.985449,0.0123956,0.00215575,0;VDB=0.681156;SGB=-0.556411;RPBZ=-0.465574;MQBZ=0;MQSBZ=0;BQBZ=-3.45917;SCBZ=-0.667699;MQ0F=0 PL:AD 0,248,255,255,255,255,255,255,255,255:98,3,1,0 +000000F 513 . T G,<*> 0 . DP=108;I16=56,46,0,1,3774,150038,7,49,6120,367200,60,3600,2340,56352,0,0;QS=0.998149,0.00185136,0;SGB=-0.379885;RPBZ=-1.71577;MQBZ=0;MQSBZ=0;BQBZ=-1.90666;SCBZ=-1.07835;MQ0F=0 PL:AD 0,255,255,255,255,255:102,1,0 +000000F 514 . G T,<*> 0 . DP=110;I16=56,47,1,1,3763,148539,20,208,6180,370800,120,7200,2348,56422,25,625;QS=0.994713,0.00528681,0;VDB=0.44;SGB=-0.453602;RPBZ=-1.58286;MQBZ=0;MQSBZ=0;BQBZ=-2.48498;SCBZ=0.0121282;MQ0F=0 PL:AD 0,255,255,255,255,255:103,2,0 +000000F 515 . C G,<*> 0 . DP=110;I16=57,47,0,1,3848,153002,12,144,6240,374400,60,3600,2367,56887,25,625;QS=0.996891,0.00310881,0;SGB=-0.379885;RPBZ=0.263997;MQBZ=0;MQSBZ=0;BQBZ=-1.75323;SCBZ=-1.07538;MQ0F=0 PL:AD 0,255,255,255,255,255:104,1,0 +000000F 516 . G T,<*> 0 . DP=111;I16=57,48,0,1,3969,158573,12,144,6300,378000,60,3600,2411,58015,0,0;QS=0.996986,0.00301432,0;SGB=-0.379885;RPBZ=-1.71626;MQBZ=0;MQSBZ=0;BQBZ=-1.8341;SCBZ=-1.06697;MQ0F=0 PL:AD 0,255,255,255,255,255:105,1,0 +000000F 517 . T C,<*> 0 . DP=112;I16=56,50,1,0,3850,151946,12,144,6360,381600,60,3600,2408,58016,21,441;QS=0.996893,0.0031072,0;SGB=-0.379885;RPBZ=-0.7772;MQBZ=0;MQSBZ=0;BQBZ=-1.67048;SCBZ=0.856997;MQ0F=0 PL:AD 0,255,255,255,255,255:106,1,0 000000F 518 . G <*> 0 . DP=115;I16=59,50,0,0,3977,155237,0,0,6540,392400,0,0,2447,58891,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:109,0 -000000F 519 . C A,<*> 0 . DP=116;I16=60,49,0,1,4018,159736,12,144,6540,392400,60,3600,2443,58747,25,625;QS=0.997022,0.00297767,0;SGB=-0.379885;RPBZ=0.110257;MQBZ=0;MQSBZ=0;BQBZ=-1.72465;SCBZ=-1.03419;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:109,1,0 -000000F 520 . T G,C,A 0 . DP=116;I16=59,48,1,2,4046,162680,48,1152,6420,385200,180,10800,2436,58644,53,1259;QS=0.988276,0.00781632,0.00195408,0.00195408;VDB=0.913952;SGB=-0.511536;RPBZ=0.578224;MQBZ=0;MQSBZ=0;BQBZ=-2.88822;SCBZ=-0.373153;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:107,1,1,1 -000000F 521 . G A,T,<*> 0 . DP=118;I16=61,48,1,2,4131,166701,36,432,6540,392400,180,10800,2454,59246,53,1089;QS=0.991361,0.00575954,0.00287977,0;VDB=0.251321;SGB=-0.511536;RPBZ=-1.60419;MQBZ=0;MQSBZ=0;BQBZ=-3.05428;SCBZ=-0.836529;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:109,2,1,0 +000000F 519 . C A,<*> 0 . DP=116;I16=60,49,0,1,4018,159736,12,144,6540,392400,60,3600,2443,58747,25,625;QS=0.997022,0.00297767,0;SGB=-0.379885;RPBZ=0.110257;MQBZ=0;MQSBZ=0;BQBZ=-1.72465;SCBZ=-1.03419;MQ0F=0 PL:AD 0,255,255,255,255,255:109,1,0 +000000F 520 . T G,C,A 0 . DP=116;I16=59,48,1,2,4046,162680,48,1152,6420,385200,180,10800,2436,58644,53,1259;QS=0.988276,0.00781632,0.00195408,0.00195408;VDB=0.913952;SGB=-0.511536;RPBZ=0.578224;MQBZ=0;MQSBZ=0;BQBZ=-2.88822;SCBZ=-0.373153;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:107,1,1,1 +000000F 521 . G A,T,<*> 0 . DP=118;I16=61,48,1,2,4131,166701,36,432,6540,392400,180,10800,2454,59246,53,1089;QS=0.991361,0.00575954,0.00287977,0;VDB=0.251321;SGB=-0.511536;RPBZ=-1.60419;MQBZ=0;MQSBZ=0;BQBZ=-3.05428;SCBZ=-0.836529;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:109,2,1,0 000000F 522 . G <*> 0 . DP=118;I16=62,50,0,0,4076,161128,0,0,6720,403200,0,0,2525,60719,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:112,0 -000000F 523 . C A,<*> 0 . DP=119;I16=63,49,0,1,4174,166860,12,144,6720,403200,60,3600,2518,60530,25,625;QS=0.997133,0.0028667,0;SGB=-0.379885;RPBZ=-0.13799;MQBZ=0;MQSBZ=0;BQBZ=-1.80506;SCBZ=-1.02482;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:112,1,0 -000000F 524 . T G,<*> 0 . DP=119;I16=62,50,1,0,4191,166163,27,729,6720,403200,60,3600,2537,61019,25,625;QS=0.993599,0.00640114,0;SGB=-0.379885;RPBZ=-0.82791;MQBZ=0;MQSBZ=0;BQBZ=-1.39926;SCBZ=0.0480382;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:112,1,0 -000000F 525 . A C,G,<*> 0 . DP=119;I16=62,48,1,2,4098,163296,36,432,6600,396000,180,10800,2509,60447,71,1691;QS=0.991292,0.00580552,0.00290276,0;VDB=0.199299;SGB=-0.511536;RPBZ=-1.60781;MQBZ=0;MQSBZ=0;BQBZ=-2.97339;SCBZ=1.45142;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:110,2,1,0 -000000F 526 . T A,<*> 0 . DP=120;I16=63,49,0,1,4180,166064,12,144,6720,403200,60,3600,2570,61910,25,625;QS=0.997137,0.0028626,0;SGB=-0.379885;RPBZ=-1.2266;MQBZ=0;MQSBZ=0;BQBZ=-1.74833;SCBZ=0.367327;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:112,1,0 -000000F 527 . C G,A,<*> 0 . DP=120;I16=62,49,1,1,4246,172572,24,288,6660,399600,120,7200,2557,61573,48,1154;QS=0.994379,0.0028103,0.0028103,0;VDB=0.18;SGB=-0.453602;RPBZ=-1.28504;MQBZ=0;MQSBZ=0;BQBZ=-2.51884;SCBZ=1.10043;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:111,1,1,0 -000000F 528 . A G,<*> 0 . DP=121;I16=62,51,1,0,4295,173733,12,144,6780,406800,60,3600,2588,62236,25,625;QS=0.997214,0.00278616,0;SGB=-0.379885;RPBZ=-0.805477;MQBZ=0;MQSBZ=0;BQBZ=-1.82642;SCBZ=0.0634184;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:113,1,0 -000000F 529 . T C,<*> 0 . DP=123;I16=65,50,0,1,4363,176845,8,64,6900,414000,60,3600,2639,63305,25,625;QS=0.99817,0.00183024,0;SGB=-0.379885;RPBZ=-1.04546;MQBZ=0;MQSBZ=0;BQBZ=-1.9592;SCBZ=-1.04156;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:115,1,0 +000000F 523 . C A,<*> 0 . DP=119;I16=63,49,0,1,4174,166860,12,144,6720,403200,60,3600,2518,60530,25,625;QS=0.997133,0.0028667,0;SGB=-0.379885;RPBZ=-0.13799;MQBZ=0;MQSBZ=0;BQBZ=-1.80506;SCBZ=-1.02482;MQ0F=0 PL:AD 0,255,255,255,255,255:112,1,0 +000000F 524 . T G,<*> 0 . DP=119;I16=62,50,1,0,4191,166163,27,729,6720,403200,60,3600,2537,61019,25,625;QS=0.993599,0.00640114,0;SGB=-0.379885;RPBZ=-0.82791;MQBZ=0;MQSBZ=0;BQBZ=-1.39926;SCBZ=0.0480382;MQ0F=0 PL:AD 0,255,255,255,255,255:112,1,0 +000000F 525 . A C,G,<*> 0 . DP=119;I16=62,48,1,2,4098,163296,36,432,6600,396000,180,10800,2509,60447,71,1691;QS=0.991292,0.00580552,0.00290276,0;VDB=0.199299;SGB=-0.511536;RPBZ=-1.60781;MQBZ=0;MQSBZ=0;BQBZ=-2.97339;SCBZ=1.45142;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:110,2,1,0 +000000F 526 . T A,<*> 0 . DP=120;I16=63,49,0,1,4180,166064,12,144,6720,403200,60,3600,2570,61910,25,625;QS=0.997137,0.0028626,0;SGB=-0.379885;RPBZ=-1.2266;MQBZ=0;MQSBZ=0;BQBZ=-1.74833;SCBZ=0.367327;MQ0F=0 PL:AD 0,255,255,255,255,255:112,1,0 +000000F 527 . C G,A,<*> 0 . DP=120;I16=62,49,1,1,4246,172572,24,288,6660,399600,120,7200,2557,61573,48,1154;QS=0.994379,0.0028103,0.0028103,0;VDB=0.18;SGB=-0.453602;RPBZ=-1.28504;MQBZ=0;MQSBZ=0;BQBZ=-2.51884;SCBZ=1.10043;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:111,1,1,0 +000000F 528 . A G,<*> 0 . DP=121;I16=62,51,1,0,4295,173733,12,144,6780,406800,60,3600,2588,62236,25,625;QS=0.997214,0.00278616,0;SGB=-0.379885;RPBZ=-0.805477;MQBZ=0;MQSBZ=0;BQBZ=-1.82642;SCBZ=0.0634184;MQ0F=0 PL:AD 0,255,255,255,255,255:113,1,0 +000000F 529 . T C,<*> 0 . DP=123;I16=65,50,0,1,4363,176845,8,64,6900,414000,60,3600,2639,63305,25,625;QS=0.99817,0.00183024,0;SGB=-0.379885;RPBZ=-1.04546;MQBZ=0;MQSBZ=0;BQBZ=-1.9592;SCBZ=-1.04156;MQ0F=0 PL:AD 0,255,255,255,255,255:115,1,0 000000F 530 . G <*> 0 . DP=123;I16=65,51,0,0,4357,176035,0,0,6960,417600,0,0,2672,64088,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:116,0 -000000F 531 . T A,G,<*> 0 . DP=123;I16=63,49,2,2,4199,169729,48,576,6720,403200,240,14400,2579,61741,100,2500;QS=0.988698,0.00847657,0.00282552,0;VDB=0.0550934;SGB=-0.556411;RPBZ=-0.650816;MQBZ=0;MQSBZ=0;BQBZ=-3.46139;SCBZ=-0.463641;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:112,3,1,0 -000000F 532 . C A,G,<*> 0 . DP=124;I16=65,49,0,3,4352,176182,36,432,6840,410400,180,10800,2640,63492,45,897;QS=0.991796,0.00546946,0.00273473,0;VDB=0.588406;SGB=-0.511536;RPBZ=-1.58686;MQBZ=0;MQSBZ=0;BQBZ=-3.10955;SCBZ=-1.82952;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:114,2,1,0 +000000F 531 . T A,G,<*> 0 . DP=123;I16=63,49,2,2,4199,169729,48,576,6720,403200,240,14400,2579,61741,100,2500;QS=0.988698,0.00847657,0.00282552,0;VDB=0.0550934;SGB=-0.556411;RPBZ=-0.650816;MQBZ=0;MQSBZ=0;BQBZ=-3.46139;SCBZ=-0.463641;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:112,3,1,0 +000000F 532 . C A,G,<*> 0 . DP=124;I16=65,49,0,3,4352,176182,36,432,6840,410400,180,10800,2640,63492,45,897;QS=0.991796,0.00546946,0.00273473,0;VDB=0.588406;SGB=-0.511536;RPBZ=-1.58686;MQBZ=0;MQSBZ=0;BQBZ=-3.10955;SCBZ=-1.82952;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:114,2,1,0 000000F 533 . A <*> 0 . DP=124;I16=65,52,0,0,4235,168199,0,0,7020,421200,0,0,2692,64582,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:117,0 -000000F 534 . G A,<*> 0 . DP=124;I16=65,51,0,1,4319,173543,12,144,6960,417600,60,3600,2677,64331,21,441;QS=0.997229,0.00277072,0;SGB=-0.379885;RPBZ=-1.3327;MQBZ=0;MQSBZ=0;BQBZ=-1.72023;SCBZ=-1.04702;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:116,1,0 -000000F 535 . G A,<*> 0 . DP=125;I16=65,52,0,1,4309,171791,12,144,7020,421200,60,3600,2679,64385,25,625;QS=0.997223,0.00277713,0;SGB=-0.379885;RPBZ=-1.10121;MQBZ=0;MQSBZ=0;BQBZ=-1.74874;SCBZ=0.0762649;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:117,1,0 -000000F 536 . T G,A,<*> 0 . DP=125;I16=65,51,0,2,4274,171298,24,288,6960,417600,120,7200,2661,64041,48,1154;QS=0.994416,0.002792,0.002792,0;VDB=0.1;SGB=-0.453602;RPBZ=-1.74128;MQBZ=0;MQSBZ=0;BQBZ=-2.39373;SCBZ=-0.693187;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:116,1,1,0 +000000F 534 . G A,<*> 0 . DP=124;I16=65,51,0,1,4319,173543,12,144,6960,417600,60,3600,2677,64331,21,441;QS=0.997229,0.00277072,0;SGB=-0.379885;RPBZ=-1.3327;MQBZ=0;MQSBZ=0;BQBZ=-1.72023;SCBZ=-1.04702;MQ0F=0 PL:AD 0,255,255,255,255,255:116,1,0 +000000F 535 . G A,<*> 0 . DP=125;I16=65,52,0,1,4309,171791,12,144,7020,421200,60,3600,2679,64385,25,625;QS=0.997223,0.00277713,0;SGB=-0.379885;RPBZ=-1.10121;MQBZ=0;MQSBZ=0;BQBZ=-1.74874;SCBZ=0.0762649;MQ0F=0 PL:AD 0,255,255,255,255,255:117,1,0 +000000F 536 . T G,A,<*> 0 . DP=125;I16=65,51,0,2,4274,171298,24,288,6960,417600,120,7200,2661,64041,48,1154;QS=0.994416,0.002792,0.002792,0;VDB=0.1;SGB=-0.453602;RPBZ=-1.74128;MQBZ=0;MQSBZ=0;BQBZ=-2.39373;SCBZ=-0.693187;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:116,1,1,0 000000F 537 . A <*> 0 . DP=125;I16=65,53,0,0,4390,175290,0,0,7080,424800,0,0,2713,65375,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:118,0 -000000F 537 . AC A 0 . INDEL;IDV=60;IMF=0.48;DP=125;I16=36,26,30,27,2480,99200,2280,91200,3720,223200,3420,205200,1433,34549,1298,31150;QS=0.263673,0.736327;VDB=0.383756;SGB=-0.693147;RPBZ=-0.543708;MQBZ=0;MQSBZ=0;BQBZ=-2.39373;SCBZ=0.641853;FS=0;MQ0F=0 PL:AD 255,0,28:62,57 +000000F 537 . AC A 0 . INDEL;IDV=60;IMF=0.48;DP=125;I16=36,26,30,27,2480,99200,2280,91200,3720,223200,3420,205200,1433,34549,1298,31150;QS=0.263673,0.736327;VDB=0.383756;SGB=-0.693147;RPBZ=-0.543708;MQBZ=0;MQSBZ=0;BQBZ=-2.39373;SCBZ=0.641853;MQ0F=0 PL:AD 255,0,28:62,57 000000F 538 . C <*> 0 . DP=65;I16=36,26,0,0,2195,86349,0,0,3720,223200,0,0,1432,34600,0,0;QS=1,0;MQ0F=0 PL:AD 0,187,255:62,0 -000000F 538 . CT C 0 . INDEL;IDV=64;IMF=0.512;DP=125;I16=30,26,36,25,2240,89600,2440,97600,3360,201600,3660,219600,1277,30663,1380,33214;QS=0.22136,0.77864;VDB=0.00357075;SGB=-0.693147;RPBZ=0.242079;MQBZ=0;MQSBZ=0;BQBZ=-2.39373;SCBZ=-0.994262;FS=0;MQ0F=0 PL:AD 255,0,28:56,61 +000000F 538 . CT C 0 . INDEL;IDV=64;IMF=0.512;DP=125;I16=30,26,36,25,2240,89600,2440,97600,3360,201600,3660,219600,1277,30663,1380,33214;QS=0.22136,0.77864;VDB=0.00357075;SGB=-0.693147;RPBZ=0.242079;MQBZ=0;MQSBZ=0;BQBZ=-2.39373;SCBZ=-0.994262;MQ0F=0 PL:AD 255,0,28:56,61 000000F 539 . T <*> 0 . DP=60;I16=29,26,0,0,2120,86238,0,0,3300,198000,0,0,1260,30374,0,0;QS=1,0;MQ0F=0 PL:AD 0,166,255:55,0 000000F 540 . G <*> 0 . DP=124;I16=64,53,0,0,4130,161310,0,0,7020,421200,0,0,2703,65511,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:117,0 000000F 541 . G <*> 0 . DP=124;I16=64,53,0,0,4143,160525,0,0,7020,421200,0,0,2705,65703,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:117,0 -000000F 542 . T G,A,<*> 0 . DP=124;I16=63,52,1,1,4035,156631,24,288,6900,414000,120,7200,2657,64685,50,1250;QS=0.994087,0.00295639,0.00295639,0;VDB=0.26;SGB=-0.453602;RPBZ=-1.44078;MQBZ=0;MQSBZ=0;BQBZ=-2.25702;SCBZ=-0.906022;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:115,1,1,0 -000000F 543 . C G,A,<*> 0 . DP=122;I16=62,53,1,1,4006,154170,24,288,6900,414000,120,7200,2673,65063,50,1250;QS=0.994045,0.00297767,0.00297767,0;VDB=0.22;SGB=-0.453602;RPBZ=-0.483734;MQBZ=0;MQSBZ=0;BQBZ=-2.21926;SCBZ=0.31726;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:115,1,1,0 -000000F 544 . T A,<*> 0 . DP=121;I16=62,53,0,1,4151,162625,12,144,6900,414000,60,3600,2697,65733,25,625;QS=0.997117,0.00288254,0;SGB=-0.379885;RPBZ=0.238977;MQBZ=0;MQSBZ=0;BQBZ=-1.67238;SCBZ=-1.05505;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:115,1,0 -000000F 545 . G A,<*> 0 . DP=121;I16=62,53,0,1,4078,158586,12,144,6900,414000,60,3600,2710,66228,8,64;QS=0.997066,0.00293399,0;SGB=-0.379885;RPBZ=1.6131;MQBZ=0;MQSBZ=0;BQBZ=-1.61213;SCBZ=-1.05503;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:115,1,0 -000000F 546 . G A,<*> 0 . DP=121;I16=62,53,0,1,4230,164790,12,144,6900,414000,60,3600,2689,65637,25,625;QS=0.997171,0.00282885,0;SGB=-0.379885;RPBZ=-0.97077;MQBZ=0;MQSBZ=0;BQBZ=-1.77555;SCBZ=-1.0549;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:115,1,0 -000000F 547 . A C,<*> 0 . DP=119;I16=62,51,0,1,4105,158737,12,144,6780,406800,60,3600,2686,65592,25,625;QS=0.997085,0.00291474,0;SGB=-0.379885;RPBZ=-0.896646;MQBZ=0;MQSBZ=0;BQBZ=-1.70779;SCBZ=0.0314879;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:113,1,0 -000000F 548 . C G,<*> 0 . DP=119;I16=62,51,0,1,4014,154686,12,144,6780,406800,60,3600,2681,65479,25,625;QS=0.997019,0.00298063,0;SGB=-0.379885;RPBZ=-0.896728;MQBZ=0;MQSBZ=0;BQBZ=-1.67128;SCBZ=0.0314876;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:113,1,0 -000000F 549 . C A,<*> 0 . DP=117;I16=33,29,29,22,2214,83510,1893,75363,3720,223200,3060,183600,1463,35977,1212,29370;QS=0.53908,0.46092,0;VDB=0.0978768;SGB=-0.693147;RPBZ=-0.600202;MQBZ=0;MQSBZ=0;BQBZ=1.17837;SCBZ=0.928426;FS=0;MQ0F=0 PL:AD 255,0,255,255,255,255:62,51,0 -000000F 550 . G T,<*> 0 . DP=117;I16=62,50,0,1,4113,161301,22,484,6720,403200,60,3600,2641,64473,25,625;QS=0.99468,0.00532044,0;SGB=-0.379885;RPBZ=-0.950536;MQBZ=0;MQSBZ=0;BQBZ=-1.55326;SCBZ=-1.07862;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:112,1,0 -000000F 551 . G T,A,<*> 0 . DP=116;I16=60,50,1,1,4131,164089,24,288,6600,396000,120,7200,2607,63583,50,1250;QS=0.994224,0.00288809,0.00288809,0;VDB=0.32;SGB=-0.453602;RPBZ=-1.01088;MQBZ=0;MQSBZ=0;BQBZ=-2.59034;SCBZ=0.329971;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:110,1,1,0 -000000F 552 . A C,<*> 0 . DP=116;I16=60,50,1,1,3927,151331,24,288,6600,396000,120,7200,2598,63352,50,1250;QS=0.993926,0.00607441,0;VDB=0.1;SGB=-0.453602;RPBZ=-1.12079;MQBZ=0;MQSBZ=0;BQBZ=-2.37929;SCBZ=-0.136538;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:110,2,0 -000000F 553 . G T,<*> 0 . DP=116;I16=60,51,1,0,4046,158108,12,144,6660,399600,60,3600,2613,63729,25,625;QS=0.997043,0.00295712,0;SGB=-0.379885;RPBZ=-0.35579;MQBZ=0;MQSBZ=0;BQBZ=-1.77886;SCBZ=0.688792;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:111,1,0 +000000F 542 . T G,A,<*> 0 . DP=124;I16=63,52,1,1,4035,156631,24,288,6900,414000,120,7200,2657,64685,50,1250;QS=0.994087,0.00295639,0.00295639,0;VDB=0.26;SGB=-0.453602;RPBZ=-1.44078;MQBZ=0;MQSBZ=0;BQBZ=-2.25702;SCBZ=-0.906022;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:115,1,1,0 +000000F 543 . C G,A,<*> 0 . DP=122;I16=62,53,1,1,4006,154170,24,288,6900,414000,120,7200,2673,65063,50,1250;QS=0.994045,0.00297767,0.00297767,0;VDB=0.22;SGB=-0.453602;RPBZ=-0.483734;MQBZ=0;MQSBZ=0;BQBZ=-2.21926;SCBZ=0.31726;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:115,1,1,0 +000000F 544 . T A,<*> 0 . DP=121;I16=62,53,0,1,4151,162625,12,144,6900,414000,60,3600,2697,65733,25,625;QS=0.997117,0.00288254,0;SGB=-0.379885;RPBZ=0.238977;MQBZ=0;MQSBZ=0;BQBZ=-1.67238;SCBZ=-1.05505;MQ0F=0 PL:AD 0,255,255,255,255,255:115,1,0 +000000F 545 . G A,<*> 0 . DP=121;I16=62,53,0,1,4078,158586,12,144,6900,414000,60,3600,2710,66228,8,64;QS=0.997066,0.00293399,0;SGB=-0.379885;RPBZ=1.6131;MQBZ=0;MQSBZ=0;BQBZ=-1.61213;SCBZ=-1.05503;MQ0F=0 PL:AD 0,255,255,255,255,255:115,1,0 +000000F 546 . G A,<*> 0 . DP=121;I16=62,53,0,1,4230,164790,12,144,6900,414000,60,3600,2689,65637,25,625;QS=0.997171,0.00282885,0;SGB=-0.379885;RPBZ=-0.97077;MQBZ=0;MQSBZ=0;BQBZ=-1.77555;SCBZ=-1.0549;MQ0F=0 PL:AD 0,255,255,255,255,255:115,1,0 +000000F 547 . A C,<*> 0 . DP=119;I16=62,51,0,1,4105,158737,12,144,6780,406800,60,3600,2686,65592,25,625;QS=0.997085,0.00291474,0;SGB=-0.379885;RPBZ=-0.896646;MQBZ=0;MQSBZ=0;BQBZ=-1.70779;SCBZ=0.0314879;MQ0F=0 PL:AD 0,255,255,255,255,255:113,1,0 +000000F 548 . C G,<*> 0 . DP=119;I16=62,51,0,1,4014,154686,12,144,6780,406800,60,3600,2681,65479,25,625;QS=0.997019,0.00298063,0;SGB=-0.379885;RPBZ=-0.896728;MQBZ=0;MQSBZ=0;BQBZ=-1.67128;SCBZ=0.0314876;MQ0F=0 PL:AD 0,255,255,255,255,255:113,1,0 +000000F 549 . C A,<*> 0 . DP=117;I16=33,29,29,22,2214,83510,1893,75363,3720,223200,3060,183600,1463,35977,1212,29370;QS=0.53908,0.46092,0;VDB=0.0978768;SGB=-0.693147;RPBZ=-0.600202;MQBZ=0;MQSBZ=0;BQBZ=1.17837;SCBZ=0.928426;MQ0F=0 PL:AD 255,0,255,255,255,255:62,51,0 +000000F 550 . G T,<*> 0 . DP=117;I16=62,50,0,1,4113,161301,22,484,6720,403200,60,3600,2641,64473,25,625;QS=0.99468,0.00532044,0;SGB=-0.379885;RPBZ=-0.950536;MQBZ=0;MQSBZ=0;BQBZ=-1.55326;SCBZ=-1.07862;MQ0F=0 PL:AD 0,255,255,255,255,255:112,1,0 +000000F 551 . G T,A,<*> 0 . DP=116;I16=60,50,1,1,4131,164089,24,288,6600,396000,120,7200,2607,63583,50,1250;QS=0.994224,0.00288809,0.00288809,0;VDB=0.32;SGB=-0.453602;RPBZ=-1.01088;MQBZ=0;MQSBZ=0;BQBZ=-2.59034;SCBZ=0.329971;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:110,1,1,0 +000000F 552 . A C,<*> 0 . DP=116;I16=60,50,1,1,3927,151331,24,288,6600,396000,120,7200,2598,63352,50,1250;QS=0.993926,0.00607441,0;VDB=0.1;SGB=-0.453602;RPBZ=-1.12079;MQBZ=0;MQSBZ=0;BQBZ=-2.37929;SCBZ=-0.136538;MQ0F=0 PL:AD 0,255,255,255,255,255:110,2,0 +000000F 553 . G T,<*> 0 . DP=116;I16=60,51,1,0,4046,158108,12,144,6660,399600,60,3600,2613,63729,25,625;QS=0.997043,0.00295712,0;SGB=-0.379885;RPBZ=-0.35579;MQBZ=0;MQSBZ=0;BQBZ=-1.77886;SCBZ=0.688792;MQ0F=0 PL:AD 0,255,255,255,255,255:111,1,0 000000F 554 . A <*> 0 . DP=113;I16=60,50,0,0,4046,159278,0,0,6600,396000,0,0,2629,64087,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:110,0 000000F 555 . G <*> 0 . DP=112;I16=60,49,0,0,4016,156988,0,0,6540,392400,0,0,2600,63438,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:109,0 000000F 556 . A <*> 0 . DP=112;I16=60,49,0,0,3915,151463,0,0,6540,392400,0,0,2588,63068,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:109,0 000000F 557 . A <*> 0 . DP=112;I16=60,49,0,0,3957,151889,0,0,6540,392400,0,0,2575,62681,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:109,0 -000000F 558 . A G,<*> 0 . DP=112;I16=60,47,0,2,3726,140280,24,288,6420,385200,120,7200,2510,60980,50,1250;QS=0.9936,0.0064,0;VDB=0.22;SGB=-0.453602;RPBZ=-1.14043;MQBZ=0;MQSBZ=0;BQBZ=-2.29525;SCBZ=-0.444037;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:107,2,0 -000000F 559 . C T,<*> 0 . DP=112;I16=59,49,1,0,3985,155617,12,144,6480,388800,60,3600,2518,61092,25,625;QS=0.996998,0.00300225,0;SGB=-0.379885;RPBZ=0.731168;MQBZ=0;MQSBZ=0;BQBZ=-1.78272;SCBZ=-1.08527;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:108,1,0 +000000F 558 . A G,<*> 0 . DP=112;I16=60,47,0,2,3726,140280,24,288,6420,385200,120,7200,2510,60980,50,1250;QS=0.9936,0.0064,0;VDB=0.22;SGB=-0.453602;RPBZ=-1.14043;MQBZ=0;MQSBZ=0;BQBZ=-2.29525;SCBZ=-0.444037;MQ0F=0 PL:AD 0,255,255,255,255,255:107,2,0 +000000F 559 . C T,<*> 0 . DP=112;I16=59,49,1,0,3985,155617,12,144,6480,388800,60,3600,2518,61092,25,625;QS=0.996998,0.00300225,0;SGB=-0.379885;RPBZ=0.731168;MQBZ=0;MQSBZ=0;BQBZ=-1.78272;SCBZ=-1.08527;MQ0F=0 PL:AD 0,255,255,255,255,255:108,1,0 000000F 560 . T <*> 0 . DP=110;I16=59,48,0,0,3896,150870,0,0,6420,385200,0,0,2507,60841,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:107,0 000000F 561 . G <*> 0 . DP=110;I16=59,48,0,0,3921,153367,0,0,6420,385200,0,0,2492,60440,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:107,0 -000000F 562 . T C,A,<*> 0 . DP=110;I16=58,47,1,1,3748,143542,24,288,6300,378000,120,7200,2425,58723,50,1250;QS=0.993637,0.00318134,0.00318134,0;VDB=0.32;SGB=-0.453602;RPBZ=1.03535;MQBZ=0;MQSBZ=0;BQBZ=-2.35872;SCBZ=-0.452888;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:105,1,1,0 -000000F 563 . G A,<*> 0 . DP=109;I16=59,45,0,2,3881,153011,24,288,6240,374400,120,7200,2384,57712,50,1250;QS=0.993854,0.00614597,0;VDB=0.06;SGB=-0.453602;RPBZ=-1.81161;MQBZ=0;MQSBZ=0;BQBZ=-2.59069;SCBZ=-0.927311;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:104,2,0 +000000F 562 . T C,A,<*> 0 . DP=110;I16=58,47,1,1,3748,143542,24,288,6300,378000,120,7200,2425,58723,50,1250;QS=0.993637,0.00318134,0.00318134,0;VDB=0.32;SGB=-0.453602;RPBZ=1.03535;MQBZ=0;MQSBZ=0;BQBZ=-2.35872;SCBZ=-0.452888;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:105,1,1,0 +000000F 563 . G A,<*> 0 . DP=109;I16=59,45,0,2,3881,153011,24,288,6240,374400,120,7200,2384,57712,50,1250;QS=0.993854,0.00614597,0;VDB=0.06;SGB=-0.453602;RPBZ=-1.81161;MQBZ=0;MQSBZ=0;BQBZ=-2.59069;SCBZ=-0.927311;MQ0F=0 PL:AD 0,255,255,255,255,255:104,2,0 000000F 564 . G <*> 0 . DP=109;I16=59,47,0,0,3954,155218,0,0,6360,381600,0,0,2417,58561,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:106,0 -000000F 565 . A G,<*> 0 . DP=108;I16=59,44,0,2,3818,150006,24,288,6180,370800,120,7200,2351,56943,50,1250;QS=0.993753,0.00624675,0;VDB=0.52;SGB=-0.453602;RPBZ=-0.0703536;MQBZ=0;MQSBZ=0;BQBZ=-2.43017;SCBZ=-0.752998;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:103,2,0 +000000F 565 . A G,<*> 0 . DP=108;I16=59,44,0,2,3818,150006,24,288,6180,370800,120,7200,2351,56943,50,1250;QS=0.993753,0.00624675,0;VDB=0.52;SGB=-0.453602;RPBZ=-0.0703536;MQBZ=0;MQSBZ=0;BQBZ=-2.43017;SCBZ=-0.752998;MQ0F=0 PL:AD 0,255,255,255,255,255:103,2,0 000000F 566 . T <*> 0 . DP=108;I16=59,46,0,0,3981,157549,0,0,6300,378000,0,0,2384,57808,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:105,0 -000000F 567 . G T,C,<*> 0 . DP=108;I16=57,46,2,0,3847,151871,20,208,6180,370800,120,7200,2318,56254,48,1154;QS=0.994828,0.00310318,0.00206879,0;VDB=0.7;SGB=-0.453602;RPBZ=0.128964;MQBZ=0;MQSBZ=0;BQBZ=-2.74966;SCBZ=-0.146119;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:103,1,1,0 -000000F 568 . T C,<*> 0 . DP=106;I16=56,47,1,0,3763,145559,8,64,6180,370800,60,3600,2349,56993,25,625;QS=0.997879,0.00212145,0;SGB=-0.379885;RPBZ=0.983018;MQBZ=0;MQSBZ=0;BQBZ=-1.93576;SCBZ=-1.05631;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:103,1,0 -000000F 569 . C G,A,<*> 0 . DP=104;I16=55,45,0,2,3734,146948,24,288,6000,360000,120,7200,2309,55985,50,1250;QS=0.993614,0.00319319,0.00319319,0;VDB=0.58;SGB=-0.453602;RPBZ=-0.543243;MQBZ=0;MQSBZ=0;BQBZ=-2.54989;SCBZ=-1.48352;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:100,1,1,0 +000000F 567 . G T,C,<*> 0 . DP=108;I16=57,46,2,0,3847,151871,20,208,6180,370800,120,7200,2318,56254,48,1154;QS=0.994828,0.00310318,0.00206879,0;VDB=0.7;SGB=-0.453602;RPBZ=0.128964;MQBZ=0;MQSBZ=0;BQBZ=-2.74966;SCBZ=-0.146119;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:103,1,1,0 +000000F 568 . T C,<*> 0 . DP=106;I16=56,47,1,0,3763,145559,8,64,6180,370800,60,3600,2349,56993,25,625;QS=0.997879,0.00212145,0;SGB=-0.379885;RPBZ=0.983018;MQBZ=0;MQSBZ=0;BQBZ=-1.93576;SCBZ=-1.05631;MQ0F=0 PL:AD 0,255,255,255,255,255:103,1,0 +000000F 569 . C G,A,<*> 0 . DP=104;I16=55,45,0,2,3734,146948,24,288,6000,360000,120,7200,2309,55985,50,1250;QS=0.993614,0.00319319,0.00319319,0;VDB=0.58;SGB=-0.453602;RPBZ=-0.543243;MQBZ=0;MQSBZ=0;BQBZ=-2.54989;SCBZ=-1.48352;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:100,1,1,0 000000F 570 . T <*> 0 . DP=104;I16=55,47,0,0,3862,151566,0,0,6120,367200,0,0,2342,56784,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:102,0 000000F 571 . G <*> 0 . DP=104;I16=55,47,0,0,3733,145003,0,0,6120,367200,0,0,2325,56367,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:102,0 -000000F 572 . T A,G,<*> 0 . DP=103;I16=53,46,1,1,3664,142548,34,628,5940,356400,120,7200,2259,54733,50,1250;QS=0.990806,0.00594916,0.003245,0;VDB=0.22;SGB=-0.453602;RPBZ=0.219457;MQBZ=0;MQSBZ=0;BQBZ=-2.44659;SCBZ=0.216127;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:99,1,1,0 -000000F 573 . C G,<*> 0 . DP=103;I16=54,46,0,1,3749,146645,12,144,6000,360000,60,3600,2267,54957,25,625;QS=0.996809,0.00319064,0;SGB=-0.379885;RPBZ=-0.428856;MQBZ=0;MQSBZ=0;BQBZ=-1.85387;SCBZ=-1.03794;FS=0;MQ0F=0 PL:AD 0,255,255,255,255,255:100,1,0 +000000F 572 . T A,G,<*> 0 . DP=103;I16=53,46,1,1,3664,142548,34,628,5940,356400,120,7200,2259,54733,50,1250;QS=0.990806,0.00594916,0.003245,0;VDB=0.22;SGB=-0.453602;RPBZ=0.219457;MQBZ=0;MQSBZ=0;BQBZ=-2.44659;SCBZ=0.216127;MQ0F=0 PL:AD 0,255,255,255,255,255,255,255,255,255:99,1,1,0 +000000F 573 . C G,<*> 0 . DP=103;I16=54,46,0,1,3749,146645,12,144,6000,360000,60,3600,2267,54957,25,625;QS=0.996809,0.00319064,0;SGB=-0.379885;RPBZ=-0.428856;MQBZ=0;MQSBZ=0;BQBZ=-1.85387;SCBZ=-1.03794;MQ0F=0 PL:AD 0,255,255,255,255,255:100,1,0 000000F 574 . A <*> 0 . DP=102;I16=54,46,0,0,3671,141999,0,0,6000,360000,0,0,2275,55165,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:100,0 000000F 575 . A <*> 0 . DP=101;I16=53,46,0,0,3653,142115,0,0,5940,356400,0,0,2259,54781,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:99,0 000000F 576 . C <*> 0 . DP=99;I16=52,45,0,0,3665,144129,0,0,5820,349200,0,0,2229,54203,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:97,0 @@ -213,84 +212,84 @@ 000000F 580 . A <*> 0 . DP=98;I16=51,45,0,0,3569,139629,0,0,5760,345600,0,0,2141,51599,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:96,0 000000F 581 . C <*> 0 . DP=95;I16=49,44,0,0,3512,137782,0,0,5580,334800,0,0,2096,50392,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:93,0 000000F 582 . A <*> 0 . DP=94;I16=49,43,0,0,3411,135315,0,0,5520,331200,0,0,2073,49673,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:92,0 -000000F 583 . G C,<*> 0 . DP=90;I16=46,41,1,0,3292,129550,12,144,5220,313200,60,3600,1985,47479,25,625;QS=0.996368,0.00363196,0;SGB=-0.379885;RPBZ=0.334737;MQBZ=0;MQSBZ=0;BQBZ=-1.89321;SCBZ=-1.01118;FS=0;MQ0F=0 PL:AD 0,245,255,255,255,255:87,1,0 +000000F 583 . G C,<*> 0 . DP=90;I16=46,41,1,0,3292,129550,12,144,5220,313200,60,3600,1985,47479,25,625;QS=0.996368,0.00363196,0;SGB=-0.379885;RPBZ=0.334737;MQBZ=0;MQSBZ=0;BQBZ=-1.89321;SCBZ=-1.01118;MQ0F=0 PL:AD 0,245,255,255,255,255:87,1,0 000000F 584 . A <*> 0 . DP=87;I16=45,40,0,0,3152,123280,0,0,5100,306000,0,0,1940,46204,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:85,0 000000F 585 . A <*> 0 . DP=88;I16=44,40,0,0,3202,127432,0,0,5040,302400,0,0,1914,45520,0,0;QS=1,0;MQ0F=0 PL:AD 0,253,255:84,0 -000000F 586 . A G,<*> 0 . DP=88;I16=43,40,1,0,2964,114852,12,144,4980,298800,60,3600,1875,44509,16,256;QS=0.995968,0.00403226,0;SGB=-0.379885;RPBZ=0.866495;MQBZ=0;MQSBZ=0;BQBZ=-1.73561;SCBZ=1.14098;FS=0;MQ0F=0 PL:AD 0,234,255,250,255,255:83,1,0 -000000F 587 . A C,<*> 0 . DP=88;I16=45,40,0,1,2997,115249,12,144,5100,306000,60,3600,1891,44583,25,625;QS=0.996012,0.00398804,0;SGB=-0.379885;RPBZ=-0.584321;MQBZ=0;MQSBZ=0;BQBZ=-1.64438;SCBZ=0.548806;FS=0;MQ0F=0 PL:AD 0,240,255,255,255,255:85,1,0 +000000F 586 . A G,<*> 0 . DP=88;I16=43,40,1,0,2964,114852,12,144,4980,298800,60,3600,1875,44509,16,256;QS=0.995968,0.00403226,0;SGB=-0.379885;RPBZ=0.866495;MQBZ=0;MQSBZ=0;BQBZ=-1.73561;SCBZ=1.14098;MQ0F=0 PL:AD 0,234,255,250,255,255:83,1,0 +000000F 587 . A C,<*> 0 . DP=88;I16=45,40,0,1,2997,115249,12,144,5100,306000,60,3600,1891,44583,25,625;QS=0.996012,0.00398804,0;SGB=-0.379885;RPBZ=-0.584321;MQBZ=0;MQSBZ=0;BQBZ=-1.64438;SCBZ=0.548806;MQ0F=0 PL:AD 0,240,255,255,255,255:85,1,0 000000F 588 . A <*> 0 . DP=87;I16=45,40,0,0,2971,113817,0,0,5100,306000,0,0,1891,44401,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:85,0 -000000F 589 . G A,<*> 0 . DP=87;I16=44,40,1,0,3059,117323,12,144,5040,302400,60,3600,1840,42970,25,625;QS=0.996092,0.00390752,0;SGB=-0.379885;RPBZ=0.550542;MQBZ=0;MQSBZ=0;BQBZ=-1.79452;SCBZ=1.68471;FS=0;MQ0F=0 PL:AD 0,237,255,253,255,255:84,1,0 +000000F 589 . G A,<*> 0 . DP=87;I16=44,40,1,0,3059,117323,12,144,5040,302400,60,3600,1840,42970,25,625;QS=0.996092,0.00390752,0;SGB=-0.379885;RPBZ=0.550542;MQBZ=0;MQSBZ=0;BQBZ=-1.79452;SCBZ=1.68471;MQ0F=0 PL:AD 0,237,255,253,255,255:84,1,0 000000F 590 . T <*> 0 . DP=87;I16=45,40,0,0,3019,114421,0,0,5100,306000,0,0,1839,42841,0,0;QS=1,0;MQ0F=0 PL:AD 0,255,255:85,0 -000000F 591 . G C,<*> 0 . DP=86;I16=43,40,1,0,3033,117015,12,144,4980,298800,60,3600,1807,42121,3,9;QS=0.996059,0.00394089,0;SGB=-0.379885;RPBZ=1.67089;MQBZ=0;MQSBZ=0;BQBZ=-1.80181;SCBZ=-1.01597;FS=0;MQ0F=0 PL:AD 0,234,255,250,255,255:83,1,0 -000000F 592 . A C,<*> 0 . DP=85;I16=44,38,0,2,2821,106231,24,288,4920,295200,120,7200,1748,40690,36,746;QS=0.991564,0.00843585,0;VDB=0.5;SGB=-0.453602;RPBZ=0.484389;MQBZ=0;MQSBZ=0;BQBZ=-2.1998;SCBZ=-0.0922779;FS=0;MQ0F=0 PL:AD 0,217,255,247,255,255:82,2,0 -000000F 593 . C G,A,<*> 0 . DP=84;I16=42,39,1,1,2912,110366,24,288,4860,291600,120,7200,1709,39543,50,1250;QS=0.991826,0.00408719,0.00408719,0;VDB=0.36;SGB=-0.453602;RPBZ=-0.0891287;MQBZ=0;MQSBZ=0;BQBZ=-2.57106;SCBZ=-0.108692;FS=0;MQ0F=0 PL:AD 0,228,255,228,255,255,244,255,255,255:81,1,1,0 +000000F 591 . G C,<*> 0 . DP=86;I16=43,40,1,0,3033,117015,12,144,4980,298800,60,3600,1807,42121,3,9;QS=0.996059,0.00394089,0;SGB=-0.379885;RPBZ=1.67089;MQBZ=0;MQSBZ=0;BQBZ=-1.80181;SCBZ=-1.01597;MQ0F=0 PL:AD 0,234,255,250,255,255:83,1,0 +000000F 592 . A C,<*> 0 . DP=85;I16=44,38,0,2,2821,106231,24,288,4920,295200,120,7200,1748,40690,36,746;QS=0.991564,0.00843585,0;VDB=0.5;SGB=-0.453602;RPBZ=0.484389;MQBZ=0;MQSBZ=0;BQBZ=-2.1998;SCBZ=-0.0922779;MQ0F=0 PL:AD 0,217,255,247,255,255:82,2,0 +000000F 593 . C G,A,<*> 0 . DP=84;I16=42,39,1,1,2912,110366,24,288,4860,291600,120,7200,1709,39543,50,1250;QS=0.991826,0.00408719,0.00408719,0;VDB=0.36;SGB=-0.453602;RPBZ=-0.0891287;MQBZ=0;MQSBZ=0;BQBZ=-2.57106;SCBZ=-0.108692;MQ0F=0 PL:AD 0,228,255,228,255,255,244,255,255,255:81,1,1,0 000000F 594 . T <*> 0 . DP=84;I16=43,40,0,0,2911,110919,0,0,4980,298800,0,0,1733,40151,0,0;QS=1,0;MQ0F=0 PL:AD 0,250,255:83,0 000000F 595 . G <*> 0 . DP=82;I16=42,39,0,0,2849,108157,0,0,4860,291600,0,0,1681,38837,0,0;QS=1,0;MQ0F=0 PL:AD 0,244,255:81,0 -000000F 596 . A C,<*> 0 . DP=81;I16=42,37,0,1,2846,108902,12,144,4740,284400,60,3600,1613,37303,25,625;QS=0.995801,0.00419874,0;SGB=-0.379885;RPBZ=-0.9748;MQBZ=0;MQSBZ=0;BQBZ=-1.73819;SCBZ=0.250526;FS=0;MQ0F=0 PL:AD 0,222,255,238,255,255:79,1,0 -000000F 597 . T G,<*> 0 . DP=80;I16=42,36,0,1,2742,102116,12,144,4680,280800,60,3600,1574,36614,15,225;QS=0.995643,0.0043573,0;SGB=-0.379885;RPBZ=0.833621;MQBZ=0;MQSBZ=0;BQBZ=-1.70797;SCBZ=0.254296;FS=0;MQ0F=0 PL:AD 0,219,255,235,255,255:78,1,0 +000000F 596 . A C,<*> 0 . DP=81;I16=42,37,0,1,2846,108902,12,144,4740,284400,60,3600,1613,37303,25,625;QS=0.995801,0.00419874,0;SGB=-0.379885;RPBZ=-0.9748;MQBZ=0;MQSBZ=0;BQBZ=-1.73819;SCBZ=0.250526;MQ0F=0 PL:AD 0,222,255,238,255,255:79,1,0 +000000F 597 . T G,<*> 0 . DP=80;I16=42,36,0,1,2742,102116,12,144,4680,280800,60,3600,1574,36614,15,225;QS=0.995643,0.0043573,0;SGB=-0.379885;RPBZ=0.833621;MQBZ=0;MQSBZ=0;BQBZ=-1.70797;SCBZ=0.254296;MQ0F=0 PL:AD 0,219,255,235,255,255:78,1,0 000000F 598 . T <*> 0 . DP=79;I16=41,37,0,0,2839,109553,0,0,4680,280800,0,0,1562,36238,0,0;QS=1,0;MQ0F=0 PL:AD 0,235,255:78,0 000000F 599 . A <*> 0 . DP=77;I16=40,36,0,0,2770,106710,0,0,4560,273600,0,0,1528,35518,0,0;QS=1,0;MQ0F=0 PL:AD 0,229,255:76,0 000000F 600 . G <*> 0 . DP=77;I16=40,36,0,0,2714,103152,0,0,4560,273600,0,0,1498,34792,0,0;QS=1,0;MQ0F=0 PL:AD 0,229,255:76,0 -000000F 601 . T G,C,<*> 0 . DP=77;I16=39,35,1,1,2583,97801,24,288,4440,266400,120,7200,1417,32827,50,1250;QS=0.990798,0.00460123,0.00460123,0;VDB=0.1;SGB=-0.453602;RPBZ=-0.795612;MQBZ=0;MQSBZ=0;BQBZ=-2.28816;SCBZ=0.0680273;FS=0;MQ0F=0 PL:AD 0,207,255,207,255,255,223,255,255,255:74,1,1,0 -000000F 602 . T A,C,<*> 0 . DP=74;I16=37,33,1,2,2416,90472,61,1657,4200,252000,180,10800,1357,31631,60,1350;QS=0.975373,0.019782,0.00484457,0;VDB=0.568985;SGB=-0.511536;RPBZ=0.333732;MQBZ=0;MQSBZ=0;BQBZ=-2.13242;SCBZ=0.845379;FS=0;MQ0F=0 PL:AD 0,164,255,195,255,255,211,255,255,255:70,2,1,0 -000000F 603 . A C,<*> 0 . DP=68;I16=35,30,1,0,2312,88408,12,144,3900,234000,60,3600,1347,31297,25,625;QS=0.994837,0.00516351,0;SGB=-0.379885;RPBZ=-0.131301;MQBZ=0;MQSBZ=0;BQBZ=-1.66952;SCBZ=-1.04349;FS=0;MQ0F=0 PL:AD 0,180,255,196,255,255:65,1,0 +000000F 601 . T G,C,<*> 0 . DP=77;I16=39,35,1,1,2583,97801,24,288,4440,266400,120,7200,1417,32827,50,1250;QS=0.990798,0.00460123,0.00460123,0;VDB=0.1;SGB=-0.453602;RPBZ=-0.795612;MQBZ=0;MQSBZ=0;BQBZ=-2.28816;SCBZ=0.0680273;MQ0F=0 PL:AD 0,207,255,207,255,255,223,255,255,255:74,1,1,0 +000000F 602 . T A,C,<*> 0 . DP=74;I16=37,33,1,2,2416,90472,61,1657,4200,252000,180,10800,1357,31631,60,1350;QS=0.975373,0.019782,0.00484457,0;VDB=0.568985;SGB=-0.511536;RPBZ=0.333732;MQBZ=0;MQSBZ=0;BQBZ=-2.13242;SCBZ=0.845379;MQ0F=0 PL:AD 0,164,255,195,255,255,211,255,255,255:70,2,1,0 +000000F 603 . A C,<*> 0 . DP=68;I16=35,30,1,0,2312,88408,12,144,3900,234000,60,3600,1347,31297,25,625;QS=0.994837,0.00516351,0;SGB=-0.379885;RPBZ=-0.131301;MQBZ=0;MQSBZ=0;BQBZ=-1.66952;SCBZ=-1.04349;MQ0F=0 PL:AD 0,180,255,196,255,255:65,1,0 000000F 604 . G <*> 0 . DP=67;I16=36,30,0,0,2403,93039,0,0,3960,237600,0,0,1349,31351,0,0;QS=1,0;MQ0F=0 PL:AD 0,199,255:66,0 -000000F 605 . A G,<*> 0 . DP=66;I16=35,28,1,1,2254,85780,24,288,3780,226800,120,7200,1292,30038,33,689;QS=0.989464,0.0105356,0;VDB=0.36;SGB=-0.453602;RPBZ=0.589131;MQBZ=0;MQSBZ=0;BQBZ=-2.37279;SCBZ=1.62638;FS=0;MQ0F=0 PL:AD 0,162,255,190,255,255:63,2,0 -000000F 606 . T G,<*> 0 . DP=65;I16=34,29,1,0,2247,87073,22,484,3780,226800,60,3600,1287,29883,13,169;QS=0.990304,0.0096959,0;SGB=-0.379885;RPBZ=1.00206;MQBZ=0;MQSBZ=0;BQBZ=-1.38823;SCBZ=-1.04683;FS=0;MQ0F=0 PL:AD 0,170,255,190,255,255:63,1,0 +000000F 605 . A G,<*> 0 . DP=66;I16=35,28,1,1,2254,85780,24,288,3780,226800,120,7200,1292,30038,33,689;QS=0.989464,0.0105356,0;VDB=0.36;SGB=-0.453602;RPBZ=0.589131;MQBZ=0;MQSBZ=0;BQBZ=-2.37279;SCBZ=1.62638;MQ0F=0 PL:AD 0,162,255,190,255,255:63,2,0 +000000F 606 . T G,<*> 0 . DP=65;I16=34,29,1,0,2247,87073,22,484,3780,226800,60,3600,1287,29883,13,169;QS=0.990304,0.0096959,0;SGB=-0.379885;RPBZ=1.00206;MQBZ=0;MQSBZ=0;BQBZ=-1.38823;SCBZ=-1.04683;MQ0F=0 PL:AD 0,170,255,190,255,255:63,1,0 000000F 607 . G <*> 0 . DP=64;I16=35,28,0,0,2255,86451,0,0,3780,226800,0,0,1255,29027,0,0;QS=1,0;MQ0F=0 PL:AD 0,190,255:63,0 -000000F 608 . T G,<*> 0 . DP=62;I16=33,27,1,0,2177,84023,8,64,3600,216000,60,3600,1182,27240,25,625;QS=0.996339,0.00366133,0;SGB=-0.379885;RPBZ=0.0852552;MQBZ=0;MQSBZ=0;BQBZ=-1.89659;SCBZ=-1.04111;FS=0;MQ0F=0 PL:AD 0,166,255,181,255,255:60,1,0 -000000F 609 . A G,<*> 0 . DP=60;I16=33,25,0,1,2036,77468,12,144,3480,208800,60,3600,1139,26307,25,625;QS=0.994141,0.00585938,0;SGB=-0.379885;RPBZ=-0.0881423;MQBZ=0;MQSBZ=0;BQBZ=-1.68674;SCBZ=1.23654;FS=0;MQ0F=0 PL:AD 0,160,255,175,255,255:58,1,0 +000000F 608 . T G,<*> 0 . DP=62;I16=33,27,1,0,2177,84023,8,64,3600,216000,60,3600,1182,27240,25,625;QS=0.996339,0.00366133,0;SGB=-0.379885;RPBZ=0.0852552;MQBZ=0;MQSBZ=0;BQBZ=-1.89659;SCBZ=-1.04111;MQ0F=0 PL:AD 0,166,255,181,255,255:60,1,0 +000000F 609 . A G,<*> 0 . DP=60;I16=33,25,0,1,2036,77468,12,144,3480,208800,60,3600,1139,26307,25,625;QS=0.994141,0.00585938,0;SGB=-0.379885;RPBZ=-0.0881423;MQBZ=0;MQSBZ=0;BQBZ=-1.68674;SCBZ=1.23654;MQ0F=0 PL:AD 0,160,255,175,255,255:58,1,0 000000F 610 . A <*> 0 . DP=59;I16=33,25,0,0,2025,77505,0,0,3480,208800,0,0,1144,26524,0,0;QS=1,0;MQ0F=0 PL:AD 0,175,255:58,0 -000000F 611 . C T,<*> 0 . DP=55;I16=14,12,16,12,990,39320,1009,38281,1560,93600,1680,100800,576,13946,550,12206;QS=0.495248,0.504752,0;VDB=1.84196e-06;SGB=-0.693054;RPBZ=1.75927;MQBZ=0;MQSBZ=0;BQBZ=-0.270305;SCBZ=-0.614376;FS=0;MQ0F=0 PL:AD 255,0,255,255,255,255:26,28,0 +000000F 611 . C T,<*> 0 . DP=55;I16=14,12,16,12,990,39320,1009,38281,1560,93600,1680,100800,576,13946,550,12206;QS=0.495248,0.504752,0;VDB=1.84196e-06;SGB=-0.693054;RPBZ=1.75927;MQBZ=0;MQSBZ=0;BQBZ=-0.270305;SCBZ=-0.614376;MQ0F=0 PL:AD 255,0,255,255,255,255:26,28,0 000000F 612 . T <*> 0 . DP=54;I16=29,24,0,0,1898,72790,0,0,3180,190800,0,0,1111,25815,0,0;QS=1,0;MQ0F=0 PL:AD 0,160,255:53,0 -000000F 613 . A G,C,<*> 0 . DP=54;I16=27,24,2,0,1946,77058,24,288,3060,183600,120,7200,1046,24258,50,1250;QS=0.987817,0.00609137,0.00609137,0;VDB=0.06;SGB=-0.453602;RPBZ=0.537207;MQBZ=0;MQSBZ=0;BQBZ=-2.67554;SCBZ=0.495445;FS=0;MQ0F=0 PL:AD 0,139,255,139,255,255,154,255,255,255:51,1,1,0 -000000F 614 . A C,<*> 0 . DP=53;I16=28,23,0,1,1870,73000,12,144,3060,183600,60,3600,1054,24458,25,625;QS=0.993624,0.0063762,0;SGB=-0.379885;RPBZ=0.033359;MQBZ=0;MQSBZ=0;BQBZ=-1.88;SCBZ=1.24225;FS=0;MQ0F=0 PL:AD 0,139,255,154,255,255:51,1,0 +000000F 613 . A G,C,<*> 0 . DP=54;I16=27,24,2,0,1946,77058,24,288,3060,183600,120,7200,1046,24258,50,1250;QS=0.987817,0.00609137,0.00609137,0;VDB=0.06;SGB=-0.453602;RPBZ=0.537207;MQBZ=0;MQSBZ=0;BQBZ=-2.67554;SCBZ=0.495445;MQ0F=0 PL:AD 0,139,255,139,255,255,154,255,255,255:51,1,1,0 +000000F 614 . A C,<*> 0 . DP=53;I16=28,23,0,1,1870,73000,12,144,3060,183600,60,3600,1054,24458,25,625;QS=0.993624,0.0063762,0;SGB=-0.379885;RPBZ=0.033359;MQBZ=0;MQSBZ=0;BQBZ=-1.88;SCBZ=1.24225;MQ0F=0 PL:AD 0,139,255,154,255,255:51,1,0 000000F 615 . T <*> 0 . DP=53;I16=28,24,0,0,1924,74686,0,0,3120,187200,0,0,1061,24643,0,0;QS=1,0;MQ0F=0 PL:AD 0,157,255:52,0 -000000F 616 . T G,<*> 0 . DP=53;I16=28,23,0,1,1815,69225,12,144,3060,183600,60,3600,1017,23565,25,625;QS=0.993432,0.00656814,0;SGB=-0.379885;RPBZ=-0.833529;MQBZ=0;MQSBZ=0;BQBZ=-1.66586;SCBZ=0.352496;FS=0;MQ0F=0 PL:AD 0,139,255,154,255,255:51,1,0 +000000F 616 . T G,<*> 0 . DP=53;I16=28,23,0,1,1815,69225,12,144,3060,183600,60,3600,1017,23565,25,625;QS=0.993432,0.00656814,0;SGB=-0.379885;RPBZ=-0.833529;MQBZ=0;MQSBZ=0;BQBZ=-1.66586;SCBZ=0.352496;MQ0F=0 PL:AD 0,139,255,154,255,255:51,1,0 000000F 617 . T <*> 0 . DP=52;I16=27,24,0,0,1844,70962,0,0,3060,183600,0,0,1024,23774,0,0;QS=1,0;MQ0F=0 PL:AD 0,154,255:51,0 000000F 618 . C <*> 0 . DP=52;I16=27,24,0,0,1782,67390,0,0,3060,183600,0,0,1005,23345,0,0;QS=1,0;MQ0F=0 PL:AD 0,154,255:51,0 -000000F 619 . A C,<*> 0 . DP=52;I16=26,24,1,0,1756,66842,12,144,3000,180000,60,3600,961,22329,25,625;QS=0.993213,0.00678733,0;SGB=-0.379885;RPBZ=0.612053;MQBZ=0;MQSBZ=0;BQBZ=-1.58836;SCBZ=1.65684;FS=0;MQ0F=0 PL:AD 0,136,255,151,255,255:50,1,0 +000000F 619 . A C,<*> 0 . DP=52;I16=26,24,1,0,1756,66842,12,144,3000,180000,60,3600,961,22329,25,625;QS=0.993213,0.00678733,0;SGB=-0.379885;RPBZ=0.612053;MQBZ=0;MQSBZ=0;BQBZ=-1.58836;SCBZ=1.65684;MQ0F=0 PL:AD 0,136,255,151,255,255:50,1,0 000000F 620 . A <*> 0 . DP=50;I16=25,24,0,0,1670,63616,0,0,2940,176400,0,0,969,22599,0,0;QS=1,0;MQ0F=0 PL:AD 0,148,255:49,0 000000F 621 . C <*> 0 . DP=49;I16=24,24,0,0,1738,67580,0,0,2880,172800,0,0,953,22277,0,0;QS=1,0;MQ0F=0 PL:AD 0,144,255:48,0 000000F 622 . T <*> 0 . DP=47;I16=23,23,0,0,1642,63060,0,0,2760,165600,0,0,921,21681,0,0;QS=1,0;MQ0F=0 PL:AD 0,138,255:46,0 -000000F 623 . A G,C,<*> 0 . DP=46;I16=22,21,1,1,1593,61369,24,288,2580,154800,120,7200,862,20368,44,986;QS=0.985158,0.00742115,0.00742115,0;VDB=0.28;SGB=-0.453602;RPBZ=0.110272;MQBZ=0;MQSBZ=0;BQBZ=-2.46441;SCBZ=-0.699329;FS=0;MQ0F=0 PL:AD 0,116,255,116,255,255,129,255,255,255:43,1,1,0 +000000F 623 . A G,C,<*> 0 . DP=46;I16=22,21,1,1,1593,61369,24,288,2580,154800,120,7200,862,20368,44,986;QS=0.985158,0.00742115,0.00742115,0;VDB=0.28;SGB=-0.453602;RPBZ=0.110272;MQBZ=0;MQSBZ=0;BQBZ=-2.46441;SCBZ=-0.699329;MQ0F=0 PL:AD 0,116,255,116,255,255,129,255,255,255:43,1,1,0 000000F 624 . T <*> 0 . DP=45;I16=22,22,0,0,1522,57304,0,0,2640,158400,0,0,892,21056,0,0;QS=1,0;MQ0F=0 PL:AD 0,132,255:44,0 000000F 625 . C <*> 0 . DP=43;I16=20,23,0,0,1462,54230,0,0,2580,154800,0,0,905,21409,0,0;QS=1,0;MQ0F=0 PL:AD 0,129,255:43,0 -000000F 626 . T A,<*> 0 . DP=42;I16=19,22,0,1,1407,52739,12,144,2460,147600,60,3600,869,20535,25,625;QS=0.991543,0.00845666,0;SGB=-0.379885;RPBZ=0.0826192;MQBZ=0;MQSBZ=0;BQBZ=-1.63079;SCBZ=-0.998652;FS=0;MQ0F=0 PL:AD 0,110,255,123,255,255:41,1,0 +000000F 626 . T A,<*> 0 . DP=42;I16=19,22,0,1,1407,52739,12,144,2460,147600,60,3600,869,20535,25,625;QS=0.991543,0.00845666,0;SGB=-0.379885;RPBZ=0.0826192;MQBZ=0;MQSBZ=0;BQBZ=-1.63079;SCBZ=-0.998652;MQ0F=0 PL:AD 0,110,255,123,255,255:41,1,0 000000F 627 . A <*> 0 . DP=42;I16=19,23,0,0,1458,54660,0,0,2520,151200,0,0,880,20786,0,0;QS=1,0;MQ0F=0 PL:AD 0,126,255:42,0 -000000F 628 . G C,<*> 0 . DP=41;I16=17,23,1,0,1491,57863,12,144,2400,144000,60,3600,838,19618,24,576;QS=0.992016,0.00798403,0;SGB=-0.379885;RPBZ=0.296217;MQBZ=0;MQSBZ=0;BQBZ=-1.99912;SCBZ=-0.981384;FS=0;MQ0F=0 PL:AD 0,107,255,120,255,255:40,1,0 +000000F 628 . G C,<*> 0 . DP=41;I16=17,23,1,0,1491,57863,12,144,2400,144000,60,3600,838,19618,24,576;QS=0.992016,0.00798403,0;SGB=-0.379885;RPBZ=0.296217;MQBZ=0;MQSBZ=0;BQBZ=-1.99912;SCBZ=-0.981384;MQ0F=0 PL:AD 0,107,255,120,255,255:40,1,0 000000F 629 . T <*> 0 . DP=40;I16=18,22,0,0,1452,55272,0,0,2400,144000,0,0,827,19349,0,0;QS=1,0;MQ0F=0 PL:AD 0,120,255:40,0 000000F 630 . C <*> 0 . DP=38;I16=16,22,0,0,1338,50174,0,0,2280,136800,0,0,812,18860,0,0;QS=1,0;MQ0F=0 PL:AD 0,114,255:38,0 -000000F 631 . T G,<*> 0 . DP=37;I16=14,22,1,0,1280,48224,32,1024,2160,129600,60,3600,783,18083,11,121;QS=0.97561,0.0243902,0;SGB=-0.379885;RPBZ=1.36088;MQBZ=0;MQSBZ=0;BQBZ=-1.06419;SCBZ=-0.906765;FS=0;MQ0F=0 PL:AD 0,79,255,108,255,255:36,1,0 +000000F 631 . T G,<*> 0 . DP=37;I16=14,22,1,0,1280,48224,32,1024,2160,129600,60,3600,783,18083,11,121;QS=0.97561,0.0243902,0;SGB=-0.379885;RPBZ=1.36088;MQBZ=0;MQSBZ=0;BQBZ=-1.06419;SCBZ=-0.906765;MQ0F=0 PL:AD 0,79,255,108,255,255:36,1,0 000000F 632 . T <*> 0 . DP=36;I16=15,21,0,0,1320,50548,0,0,2160,129600,0,0,761,17359,0,0;QS=1,0;MQ0F=0 PL:AD 0,108,255:36,0 -000000F 633 . C A,<*> 0 . DP=35;I16=14,19,0,2,1183,44803,24,288,1980,118800,120,7200,678,15322,47,1109;QS=0.980116,0.019884,0;VDB=0.26;SGB=-0.453602;RPBZ=0.463397;MQBZ=0;MQSBZ=0;BQBZ=-2.3085;SCBZ=1.47371;FS=0;MQ0F=0 PL:AD 0,76,255,99,255,255:33,2,0 +000000F 633 . C A,<*> 0 . DP=35;I16=14,19,0,2,1183,44803,24,288,1980,118800,120,7200,678,15322,47,1109;QS=0.980116,0.019884,0;VDB=0.26;SGB=-0.453602;RPBZ=0.463397;MQBZ=0;MQSBZ=0;BQBZ=-2.3085;SCBZ=1.47371;MQ0F=0 PL:AD 0,76,255,99,255,255:33,2,0 000000F 634 . C <*> 0 . DP=35;I16=14,21,0,0,1290,49572,0,0,2100,126000,0,0,708,15898,0,0;QS=1,0;MQ0F=0 PL:AD 0,105,255:35,0 000000F 635 . T <*> 0 . DP=35;I16=14,21,0,0,1242,47888,0,0,2100,126000,0,0,691,15399,0,0;QS=1,0;MQ0F=0 PL:AD 0,105,255:35,0 -000000F 636 . C T,<*> 0 . DP=34;I16=13,20,1,0,1163,44105,12,144,1980,118800,60,3600,643,14453,16,256;QS=0.989787,0.0102128,0;SGB=-0.379885;RPBZ=0.66524;MQBZ=0;MQSBZ=0;BQBZ=-1.57615;SCBZ=-0.84147;FS=0;MQ0F=0 PL:AD 0,87,255,99,255,255:33,1,0 +000000F 636 . C T,<*> 0 . DP=34;I16=13,20,1,0,1163,44105,12,144,1980,118800,60,3600,643,14453,16,256;QS=0.989787,0.0102128,0;SGB=-0.379885;RPBZ=0.66524;MQBZ=0;MQSBZ=0;BQBZ=-1.57615;SCBZ=-0.84147;MQ0F=0 PL:AD 0,87,255,99,255,255:33,1,0 000000F 637 . T <*> 0 . DP=33;I16=14,19,0,0,1151,43717,0,0,1980,118800,0,0,627,14033,0,0;QS=1,0;MQ0F=0 PL:AD 0,99,255:33,0 000000F 638 . A <*> 0 . DP=32;I16=13,19,0,0,1113,41153,0,0,1920,115200,0,0,605,13531,0,0;QS=1,0;MQ0F=0 PL:AD 0,96,255:32,0 -000000F 639 . A T,<*> 0 . DP=30;I16=13,16,0,1,965,34529,12,144,1740,104400,60,3600,577,12917,13,169;QS=0.987718,0.0122825,0;SGB=-0.379885;RPBZ=0.988773;MQBZ=0;MQSBZ=0;BQBZ=-1.63451;SCBZ=-0.878553;FS=0;MQ0F=0 PL:AD 0,75,255,87,255,255:29,1,0 +000000F 639 . A T,<*> 0 . DP=30;I16=13,16,0,1,965,34529,12,144,1740,104400,60,3600,577,12917,13,169;QS=0.987718,0.0122825,0;SGB=-0.379885;RPBZ=0.988773;MQBZ=0;MQSBZ=0;BQBZ=-1.63451;SCBZ=-0.878553;MQ0F=0 PL:AD 0,75,255,87,255,255:29,1,0 000000F 640 . A <*> 0 . DP=29;I16=12,17,0,0,994,36924,0,0,1740,104400,0,0,575,12621,0,0;QS=1,0;MQ0F=0 PL:AD 0,87,255:29,0 -000000F 641 . G T,<*> 0 . DP=27;I16=11,15,0,1,869,31995,12,144,1560,93600,60,3600,529,11623,11,121;QS=0.986379,0.0136209,0;SGB=-0.379885;RPBZ=1.35554;MQBZ=0;MQSBZ=0;BQBZ=-1.5086;SCBZ=-0.793551;FS=0;MQ0F=0 PL:AD 0,66,255,78,255,255:26,1,0 -000000F 642 . A C,<*> 0 . DP=26;I16=11,14,0,1,850,31010,22,484,1500,90000,60,3600,504,11078,9,81;QS=0.974771,0.0252294,0;SGB=-0.379885;RPBZ=1.41458;MQBZ=0;MQSBZ=0;BQBZ=-1.18957;SCBZ=0.532911;FS=0;MQ0F=0 PL:AD 0,56,255,75,255,255:25,1,0 +000000F 641 . G T,<*> 0 . DP=27;I16=11,15,0,1,869,31995,12,144,1560,93600,60,3600,529,11623,11,121;QS=0.986379,0.0136209,0;SGB=-0.379885;RPBZ=1.35554;MQBZ=0;MQSBZ=0;BQBZ=-1.5086;SCBZ=-0.793551;MQ0F=0 PL:AD 0,66,255,78,255,255:26,1,0 +000000F 642 . A C,<*> 0 . DP=26;I16=11,14,0,1,850,31010,22,484,1500,90000,60,3600,504,11078,9,81;QS=0.974771,0.0252294,0;SGB=-0.379885;RPBZ=1.41458;MQBZ=0;MQSBZ=0;BQBZ=-1.18957;SCBZ=0.532911;MQ0F=0 PL:AD 0,56,255,75,255,255:25,1,0 000000F 643 . C <*> 0 . DP=26;I16=11,15,0,0,912,34334,0,0,1560,93600,0,0,499,10747,0,0;QS=1,0;MQ0F=0 PL:AD 0,78,255:26,0 -000000F 644 . C A,<*> 0 . DP=26;I16=11,14,0,1,869,31707,12,144,1500,90000,60,3600,464,9914,20,400;QS=0.986379,0.0136209,0;SGB=-0.379885;RPBZ=0.268045;MQBZ=0;MQSBZ=0;BQBZ=-1.6731;SCBZ=0.989693;FS=0;MQ0F=0 PL:AD 0,63,255,75,255,255:25,1,0 +000000F 644 . C A,<*> 0 . DP=26;I16=11,14,0,1,869,31707,12,144,1500,90000,60,3600,464,9914,20,400;QS=0.986379,0.0136209,0;SGB=-0.379885;RPBZ=0.268045;MQBZ=0;MQSBZ=0;BQBZ=-1.6731;SCBZ=0.989693;MQ0F=0 PL:AD 0,63,255,75,255,255:25,1,0 000000F 645 . C <*> 0 . DP=26;I16=11,15,0,0,911,33421,0,0,1560,93600,0,0,466,9764,0,0;QS=1,0;MQ0F=0 PL:AD 0,78,255:26,0 000000F 646 . C <*> 0 . DP=26;I16=11,15,0,0,850,29718,0,0,1560,93600,0,0,447,9201,0,0;QS=1,0;MQ0F=0 PL:AD 0,78,255:26,0 -000000F 647 . T C,<*> 0 . DP=26;I16=11,14,0,1,898,34076,12,144,1500,90000,60,3600,423,8651,5,25;QS=0.986813,0.0131868,0;SGB=-0.379885;RPBZ=1.14097;MQBZ=0;MQSBZ=0;BQBZ=-1.57982;SCBZ=-0.760963;FS=0;MQ0F=0 PL:AD 0,63,255,75,255,255:25,1,0 +000000F 647 . T C,<*> 0 . DP=26;I16=11,14,0,1,898,34076,12,144,1500,90000,60,3600,423,8651,5,25;QS=0.986813,0.0131868,0;SGB=-0.379885;RPBZ=1.14097;MQBZ=0;MQSBZ=0;BQBZ=-1.57982;SCBZ=-0.760963;MQ0F=0 PL:AD 0,63,255,75,255,255:25,1,0 000000F 648 . A <*> 0 . DP=26;I16=11,15,0,0,870,32110,0,0,1560,93600,0,0,407,8091,0,0;QS=1,0;MQ0F=0 PL:AD 0,78,255:26,0 000000F 649 . C <*> 0 . DP=26;I16=11,15,0,0,928,35102,0,0,1560,93600,0,0,386,7548,0,0;QS=1,0;MQ0F=0 PL:AD 0,78,255:26,0 -000000F 650 . T C,<*> 0 . DP=26;I16=11,14,0,1,897,33867,12,144,1500,90000,60,3600,359,6973,5,25;QS=0.986799,0.0132013,0;SGB=-0.379885;RPBZ=0.874779;MQBZ=0;MQSBZ=0;BQBZ=-1.67266;SCBZ=-0.760963;FS=0;MQ0F=0 PL:AD 0,63,255,75,255,255:25,1,0 +000000F 650 . T C,<*> 0 . DP=26;I16=11,14,0,1,897,33867,12,144,1500,90000,60,3600,359,6973,5,25;QS=0.986799,0.0132013,0;SGB=-0.379885;RPBZ=0.874779;MQBZ=0;MQSBZ=0;BQBZ=-1.67266;SCBZ=-0.760963;MQ0F=0 PL:AD 0,63,255,75,255,255:25,1,0 000000F 651 . T <*> 0 . DP=26;I16=11,15,0,0,905,33255,0,0,1560,93600,0,0,342,6492,0,0;QS=1,0;MQ0F=0 PL:AD 0,78,255:26,0 000000F 652 . T <*> 0 . DP=25;I16=11,14,0,0,891,32693,0,0,1500,90000,0,0,321,6029,0,0;QS=1,0;MQ0F=0 PL:AD 0,75,255:25,0 000000F 653 . A <*> 0 . DP=21;I16=9,12,0,0,804,31130,0,0,1260,75600,0,0,303,5555,0,0;QS=1,0;MQ0F=0 PL:AD 0,63,255:21,0 000000F 654 . A <*> 0 . DP=21;I16=9,12,0,0,659,22061,0,0,1260,75600,0,0,285,5117,0,0;QS=1,0;MQ0F=0 PL:AD 0,63,255:21,0 000000F 655 . C <*> 0 . DP=21;I16=9,12,0,0,664,22342,0,0,1260,75600,0,0,266,4666,0,0;QS=1,0;MQ0F=0 PL:AD 0,63,255:21,0 -000000F 655 . CACAATACAA CACAA 0 . INDEL;IDV=6;IMF=0.285714;DP=21;I16=4,11,5,1,1800,216000,720,86400,900,54000,360,21600,166,2878,100,1788;QS=0.371728,0.628272;VDB=0.00189453;SGB=-0.616816;RPBZ=-2.81289;MQBZ=0;MQSBZ=0;BQBZ=-1.67266;SCBZ=-2.52262;FS=0;MQ0F=0 PL:AD 129,0,28:15,6 +000000F 655 . CACAATACAA CACAA 0 . INDEL;IDV=6;IMF=0.285714;DP=21;I16=4,11,5,1,1800,216000,720,86400,900,54000,360,21600,166,2878,100,1788;QS=0.371728,0.628272;VDB=0.00189453;SGB=-0.616816;RPBZ=-2.81289;MQBZ=0;MQSBZ=0;BQBZ=-1.67266;SCBZ=-2.52262;MQ0F=0 PL:AD 129,0,28:15,6 000000F 656 . A <*> 0 . DP=11;I16=4,7,0,0,404,15690,0,0,660,39600,0,0,141,2411,0,0;QS=1,0;MQ0F=0 PL:AD 0,33,255:11,0 000000F 657 . C <*> 0 . DP=11;I16=4,7,0,0,413,15607,0,0,660,39600,0,0,131,2189,0,0;QS=1,0;MQ0F=0 PL:AD 0,33,255:11,0 000000F 658 . A <*> 0 . DP=10;I16=3,7,0,0,121,1651,0,0,600,36000,0,0,122,1986,0,0;QS=1,0;MQ0F=0 PL:AD 0,30,79:10,0 -000000F 658 . AA AAATTA 0 . INDEL;IDV=2;IMF=0.125;DP=16;I16=5,6,1,2,1100,110000,300,30000,660,39600,180,10800,141,2389,50,902;QS=0.418605,0.581395;VDB=0.045681;SGB=-0.511536;RPBZ=-1.70026;MQBZ=0;MQSBZ=0;BQBZ=-1.67266;SCBZ=-1.35678;FS=0;MQ0F=0 PL:AD 76,0,29:11,3 +000000F 658 . AA AAATTA 0 . INDEL;IDV=2;IMF=0.125;DP=16;I16=5,6,1,2,1100,110000,300,30000,660,39600,180,10800,141,2389,50,902;QS=0.418605,0.581395;VDB=0.045681;SGB=-0.511536;RPBZ=-1.70026;MQBZ=0;MQSBZ=0;BQBZ=-1.67266;SCBZ=-1.35678;MQ0F=0 PL:AD 76,0,29:11,3 000000F 659 . A <*> 0 . DP=10;I16=3,5,0,0,86,1088,0,0,480,28800,0,0,75,1077,0,0;QS=1,0;MQ0F=0 PL:AD 0,24,63:8,0 000000F 660 . T <*> 0 . DP=2;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;QS=0,0;MQ0F=0 PL:AD 0,0,0:0,0 000000F 661 . A <*> 0 . DP=8;I16=0,2,0,0,8,32,0,0,120,7200,0,0,26,340,0,0;QS=1,0;MQ0F=0 PL:AD 0,6,7:2,0 diff --git a/test/mpileup/indel-AD.2.out b/test/mpileup/indel-AD.2.out index 23b51dda6..67e5b5791 100644 --- a/test/mpileup/indel-AD.2.out +++ b/test/mpileup/indel-AD.2.out @@ -12,7 +12,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -21,4 +20,4 @@ ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample 11 75 . G <*> 0 . DP=68;I16=6,62,0,0,2437,87909,0,0,3770,217210,0,0,838,15940,0,0;QS=1,0;MQ0F=0 PL:AD 0,205,255:68,0 -11 75 . GTAAAATAAAATAAAATAAAATAAA GTAAAATAAAATAAAATAAAATAAAATAAA 0 . INDEL;IDV=6;IMF=0.0882353;DP=68;I16=5,57,1,5,7440,892800,720,86400,3596,212164,174,5046,691,12331,147,3609;QS=0.834915,0.165085;VDB=0.00452698;SGB=-0.616816;RPBZ=-3.24592;MQBZ=-6.13241;MQSBZ=0;BQBZ=0;SCBZ=-0.546919;FS=0;MQ0F=0 PL:AD 0,54,150:62,6 +11 75 . GTAAAATAAAATAAAATAAAATAAA GTAAAATAAAATAAAATAAAATAAAATAAA 0 . INDEL;IDV=6;IMF=0.0882353;DP=68;I16=5,57,1,5,7440,892800,720,86400,3596,212164,174,5046,691,12331,147,3609;QS=0.834915,0.165085;VDB=0.00452698;SGB=-0.616816;RPBZ=-3.24592;MQBZ=-6.13241;MQSBZ=0;BQBZ=0;SCBZ=-0.546919;MQ0F=0 PL:AD 0,54,150:62,6 diff --git a/test/mpileup/indel-AD.3.out b/test/mpileup/indel-AD.3.out index 23b51dda6..67e5b5791 100644 --- a/test/mpileup/indel-AD.3.out +++ b/test/mpileup/indel-AD.3.out @@ -12,7 +12,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -21,4 +20,4 @@ ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample 11 75 . G <*> 0 . DP=68;I16=6,62,0,0,2437,87909,0,0,3770,217210,0,0,838,15940,0,0;QS=1,0;MQ0F=0 PL:AD 0,205,255:68,0 -11 75 . GTAAAATAAAATAAAATAAAATAAA GTAAAATAAAATAAAATAAAATAAAATAAA 0 . INDEL;IDV=6;IMF=0.0882353;DP=68;I16=5,57,1,5,7440,892800,720,86400,3596,212164,174,5046,691,12331,147,3609;QS=0.834915,0.165085;VDB=0.00452698;SGB=-0.616816;RPBZ=-3.24592;MQBZ=-6.13241;MQSBZ=0;BQBZ=0;SCBZ=-0.546919;FS=0;MQ0F=0 PL:AD 0,54,150:62,6 +11 75 . GTAAAATAAAATAAAATAAAATAAA GTAAAATAAAATAAAATAAAATAAAATAAA 0 . INDEL;IDV=6;IMF=0.0882353;DP=68;I16=5,57,1,5,7440,892800,720,86400,3596,212164,174,5046,691,12331,147,3609;QS=0.834915,0.165085;VDB=0.00452698;SGB=-0.616816;RPBZ=-3.24592;MQBZ=-6.13241;MQSBZ=0;BQBZ=0;SCBZ=-0.546919;MQ0F=0 PL:AD 0,54,150:62,6 diff --git a/test/mpileup/indel-AD.4.out b/test/mpileup/indel-AD.4.out index 23b51dda6..67e5b5791 100644 --- a/test/mpileup/indel-AD.4.out +++ b/test/mpileup/indel-AD.4.out @@ -12,7 +12,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -21,4 +20,4 @@ ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample 11 75 . G <*> 0 . DP=68;I16=6,62,0,0,2437,87909,0,0,3770,217210,0,0,838,15940,0,0;QS=1,0;MQ0F=0 PL:AD 0,205,255:68,0 -11 75 . GTAAAATAAAATAAAATAAAATAAA GTAAAATAAAATAAAATAAAATAAAATAAA 0 . INDEL;IDV=6;IMF=0.0882353;DP=68;I16=5,57,1,5,7440,892800,720,86400,3596,212164,174,5046,691,12331,147,3609;QS=0.834915,0.165085;VDB=0.00452698;SGB=-0.616816;RPBZ=-3.24592;MQBZ=-6.13241;MQSBZ=0;BQBZ=0;SCBZ=-0.546919;FS=0;MQ0F=0 PL:AD 0,54,150:62,6 +11 75 . GTAAAATAAAATAAAATAAAATAAA GTAAAATAAAATAAAATAAAATAAAATAAA 0 . INDEL;IDV=6;IMF=0.0882353;DP=68;I16=5,57,1,5,7440,892800,720,86400,3596,212164,174,5046,691,12331,147,3609;QS=0.834915,0.165085;VDB=0.00452698;SGB=-0.616816;RPBZ=-3.24592;MQBZ=-6.13241;MQSBZ=0;BQBZ=0;SCBZ=-0.546919;MQ0F=0 PL:AD 0,54,150:62,6 diff --git a/test/mpileup/mpileup-SCR.out b/test/mpileup/mpileup-SCR.out index 1134b26a6..b4b3804c7 100644 --- a/test/mpileup/mpileup-SCR.out +++ b/test/mpileup/mpileup-SCR.out @@ -12,7 +12,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -32,7 +31,7 @@ 1 72 . C <*> 0 . DP=9;SCR=3;I16=6,3,0,0,318,11254,0,0,456,24672,0,0,82,1074,0,0;QS=1,0;MQ0F=0 PL:SCR 0,27,216:3 1 73 . C <*> 0 . DP=10;SCR=3;I16=7,3,0,0,348,12146,0,0,516,28272,0,0,91,1247,0,0;QS=1,0;MQ0F=0 PL:SCR 0,30,224:3 1 74 . C <*> 0 . DP=10;SCR=3;I16=7,3,0,0,350,12278,0,0,516,28272,0,0,100,1388,0,0;QS=1,0;MQ0F=0 PL:SCR 0,30,228:3 -1 75 . C G,<*> 0 . DP=12;SCR=4;I16=6,2,3,1,274,9444,132,4392,480,28800,119,3601,55,501,54,1046;QS=0.697201,0.302799,0;VDB=0.0533436;SGB=-0.556411;RPBZ=1.63069;MQBZ=-3.26599;MQSBZ=0.111111;BQBZ=-0.515877;SCBZ=3.23349;FS=0;MQ0F=0 PL:SCR 73,0,170,97,182,252:4 +1 75 . C G,<*> 0 . DP=12;SCR=4;I16=6,2,3,1,274,9444,132,4392,480,28800,119,3601,55,501,54,1046;QS=0.697201,0.302799,0;VDB=0.0533436;SGB=-0.556411;RPBZ=1.63069;MQBZ=-3.26599;MQSBZ=0.111111;BQBZ=-0.515877;SCBZ=3.23349;MQ0F=0 PL:SCR 73,0,170,97,182,252:4 1 76 . C <*> 0 . DP=12;SCR=4;I16=9,3,0,0,410,14076,0,0,599,32401,0,0,120,1726,0,0;QS=1,0;MQ0F=0 PL:SCR 0,36,233:4 1 77 . G <*> 0 . DP=12;SCR=4;I16=9,3,0,0,385,12495,0,0,599,32401,0,0,131,1927,0,0;QS=1,0;MQ0F=0 PL:SCR 0,36,225:4 1 78 . T <*> 0 . DP=12;SCR=4;I16=9,3,0,0,365,11201,0,0,599,32401,0,0,142,2150,0,0;QS=1,0;MQ0F=0 PL:SCR 0,36,213:4 diff --git a/test/mpileup/mpileup-filter.1.out b/test/mpileup/mpileup-filter.1.out index ecd87f1f8..445b33c01 100644 --- a/test/mpileup/mpileup-filter.1.out +++ b/test/mpileup/mpileup-filter.1.out @@ -12,7 +12,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= diff --git a/test/mpileup/mpileup-filter.2.out b/test/mpileup/mpileup-filter.2.out index dcd95f2fe..f852e9920 100644 --- a/test/mpileup/mpileup-filter.2.out +++ b/test/mpileup/mpileup-filter.2.out @@ -12,7 +12,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= diff --git a/test/mpileup/mpileup.1.out b/test/mpileup/mpileup.1.out index 93b366e20..5c0643a5a 100644 --- a/test/mpileup/mpileup.1.out +++ b/test/mpileup/mpileup.1.out @@ -12,7 +12,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -22,29 +21,29 @@ 17 100 . C <*> 0 . DP=18;I16=16,1,0,0,672,27586,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0 PL 0,27,189 0,9,118 0,15,134 17 101 . C <*> 0 . DP=18;I16=16,1,0,0,630,24730,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL 0,27,182 0,9,108 0,15,132 17 102 . C <*> 0 . DP=18;I16=16,1,0,0,676,27812,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL 0,27,188 0,9,121 0,15,139 -17 103 . T C,<*> 0 . DP=18;I16=15,1,1,0,668,28542,6,36,929,54841,29,841,323,7035,6,36;QS=2.98256,0.0174419,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64924;SCBZ=4;FS=0;MQ0F=0 PL 0,17,184,24,187,185 0,9,118,9,118,118 0,15,147,15,147,147 -17 104 . G C,<*> 0 . DP=18;I16=15,1,1,0,601,24163,3,9,929,54841,29,841,320,6884,7,49;QS=2.98726,0.0127389,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64309;SCBZ=4;FS=0;MQ0F=0 PL 0,18,173,24,176,173 0,9,101,9,101,101 0,15,133,15,133,133 +17 103 . T C,<*> 0 . DP=18;I16=15,1,1,0,668,28542,6,36,929,54841,29,841,323,7035,6,36;QS=2.98256,0.0174419,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64924;SCBZ=4;MQ0F=0 PL 0,17,184,24,187,185 0,9,118,9,118,118 0,15,147,15,147,147 +17 104 . G C,<*> 0 . DP=18;I16=15,1,1,0,601,24163,3,9,929,54841,29,841,320,6884,7,49;QS=2.98726,0.0127389,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64309;SCBZ=4;MQ0F=0 PL 0,18,173,24,176,173 0,9,101,9,101,101 0,15,133,15,133,133 17 105 . G <*> 0 . DP=19;I16=17,1,0,0,603,22351,0,0,1018,59282,0,0,325,6815,0,0;QS=3,0;MQ0F=0 PL 0,30,171 0,9,106 0,15,125 17 106 . G <*> 0 . DP=19;I16=17,1,0,0,636,25058,0,0,1018,59282,0,0,324,6718,0,0;QS=3,0;MQ0F=0 PL 0,30,190 0,9,92 0,15,124 17 107 . C <*> 0 . DP=19;I16=17,1,0,0,686,27952,0,0,1018,59282,0,0,323,6643,0,0;QS=3,0;MQ0F=0 PL 0,30,192 0,9,119 0,15,136 17 108 . C <*> 0 . DP=19;I16=17,1,0,0,681,27429,0,0,1018,59282,0,0,322,6590,0,0;QS=3,0;MQ0F=0 PL 0,30,190 0,9,119 0,15,135 -17 109 . T C,<*> 0 . DP=19;I16=16,1,1,0,716,30648,2,4,989,58441,29,841,309,6415,12,144;QS=2.98922,0.0107817,0;SGB=-0.556633;RPBZ=-0.674966;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.6661;SCBZ=3;FS=0;MQ0F=0 PL 0,20,191,27,194,191 0,9,120,9,120,120 0,15,150,15,150,150 +17 109 . T C,<*> 0 . DP=19;I16=16,1,1,0,716,30648,2,4,989,58441,29,841,309,6415,12,144;QS=2.98922,0.0107817,0;SGB=-0.556633;RPBZ=-0.674966;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.6661;SCBZ=3;MQ0F=0 PL 0,20,191,27,194,191 0,9,120,9,120,120 0,15,150,15,150,150 17 110 . G <*> 0 . DP=19;I16=17,1,0,0,688,28036,0,0,1018,59282,0,0,320,6550,0,0;QS=3,0;MQ0F=0 PL 0,30,194 0,9,113 0,15,136 17 111 . G <*> 0 . DP=19;I16=17,1,0,0,573,21453,0,0,1018,59282,0,0,318,6514,0,0;QS=3,0;MQ0F=0 PL 0,30,167 0,9,95 0,15,119 -17 112 . C G,<*> 0 . DP=19;I16=16,1,1,0,657,26565,2,4,989,58441,29,841,301,6277,15,225;QS=2.98907,0.010929,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65292;SCBZ=3;FS=0;MQ0F=0 PL 0,20,187,27,190,187 0,9,103,9,103,103 0,15,135,15,135,135 -17 113 . A G,<*> 0 . DP=19;I16=16,1,1,0,635,25055,4,16,989,58441,29,841,297,6207,16,256;QS=2.98817,0.0118343,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65205;SCBZ=3;FS=0;MQ0F=0 PL 0,20,172,27,175,172 0,9,102,9,102,102 0,15,139,15,139,139 +17 112 . C G,<*> 0 . DP=19;I16=16,1,1,0,657,26565,2,4,989,58441,29,841,301,6277,15,225;QS=2.98907,0.010929,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65292;SCBZ=3;MQ0F=0 PL 0,20,187,27,190,187 0,9,103,9,103,103 0,15,135,15,135,135 +17 113 . A G,<*> 0 . DP=19;I16=16,1,1,0,635,25055,4,16,989,58441,29,841,297,6207,16,256;QS=2.98817,0.0118343,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65205;SCBZ=3;MQ0F=0 PL 0,20,172,27,175,172 0,9,102,9,102,102 0,15,139,15,139,139 17 114 . C <*> 0 . DP=19;I16=17,1,0,0,660,25876,0,0,1018,59282,0,0,310,6446,0,0;QS=3,0;MQ0F=0 PL 0,30,181 0,9,113 0,15,133 -17 115 . C A,<*> 0 . DP=21;I16=17,2,1,0,688,27426,12,144,1078,62882,29,841,283,5827,25,625;QS=2.88785,0.11215,0;SGB=-0.556633;RPBZ=0.260329;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.47798;SCBZ=-0.418446;FS=0;MQ0F=0 PL 0,30,189,30,189,189 3,0,86,9,89,93 0,21,153,21,153,153 -17 116 . A C,<*> 0 . DP=21;I16=17,2,1,0,705,27791,2,4,1078,62882,29,841,287,6073,19,361;QS=2.98873,0.0112676,0;SGB=-0.556633;RPBZ=0.0867763;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.65814;SCBZ=2.65016;FS=0;MQ0F=0 PL 0,20,179,27,182,179 0,9,102,9,102,102 0,21,175,21,175,175 +17 115 . C A,<*> 0 . DP=21;I16=17,2,1,0,688,27426,12,144,1078,62882,29,841,283,5827,25,625;QS=2.88785,0.11215,0;SGB=-0.556633;RPBZ=0.260329;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.47798;SCBZ=-0.418446;MQ0F=0 PL 0,30,189,30,189,189 3,0,86,9,89,93 0,21,153,21,153,153 +17 116 . A C,<*> 0 . DP=21;I16=17,2,1,0,705,27791,2,4,1078,62882,29,841,287,6073,19,361;QS=2.98873,0.0112676,0;SGB=-0.556633;RPBZ=0.0867763;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.65814;SCBZ=2.65016;MQ0F=0 PL 0,20,179,27,182,179 0,9,102,9,102,102 0,21,175,21,175,175 17 117 . G <*> 0 . DP=21;I16=18,2,0,0,715,28045,0,0,1107,63723,0,0,304,6444,0,0;QS=3,0;MQ0F=0 PL 0,30,185 0,9,97 0,21,177 17 118 . G <*> 0 . DP=20;I16=17,2,0,0,620,23470,0,0,1047,60123,0,0,303,6481,0,0;QS=3,0;MQ0F=0 PL 0,27,175 0,9,65 0,21,162 17 119 . G <*> 0 . DP=19;I16=16,2,0,0,619,23459,0,0,987,56523,0,0,301,6493,0,0;QS=3,0;MQ0F=0 PL 0,27,176 0,6,76 0,21,160 -17 120 . A G,<*> 0 . DP=19;I16=15,2,1,0,646,25392,4,16,958,55682,29,841,277,5999,23,529;QS=2.9873,0.0126984,0;SGB=-0.556633;RPBZ=0.28942;MQBZ=-2.23607;MQSBZ=-1.30384;BQBZ=-1.6486;SCBZ=3;FS=0;MQ0F=0 PL 0,18,171,24,174,171 0,6,88,6,88,88 0,21,171,21,171,171 +17 120 . A G,<*> 0 . DP=19;I16=15,2,1,0,646,25392,4,16,958,55682,29,841,277,5999,23,529;QS=2.9873,0.0126984,0;SGB=-0.556633;RPBZ=0.28942;MQBZ=-2.23607;MQSBZ=-1.30384;BQBZ=-1.6486;SCBZ=3;MQ0F=0 PL 0,18,171,24,174,171 0,6,88,6,88,88 0,21,171,21,171,171 17 121 . G <*> 0 . DP=19;I16=16,2,0,0,650,25148,0,0,987,56523,0,0,298,6534,0,0;QS=3,0;MQ0F=0 PL 0,27,181 0,6,84 0,21,168 17 122 . C <*> 0 . DP=20;I16=17,2,0,0,696,27784,0,0,1047,60123,0,0,296,6560,0,0;QS=3,0;MQ0F=0 PL 0,27,180 0,9,107 0,21,178 17 123 . T <*> 0 . DP=18;I16=15,2,0,0,647,26145,0,0,927,52923,0,0,296,6554,0,0;QS=3,0;MQ0F=0 PL 0,24,170 0,9,123 0,18,166 17 124 . T <*> 0 . DP=19;I16=16,2,0,0,606,22002,0,0,987,56523,0,0,296,6564,0,0;QS=3,0;MQ0F=0 PL 0,27,154 0,9,114 0,18,154 -17 125 . A T,<*> 0 . DP=18;I16=14,2,1,0,589,22565,4,16,898,52082,29,841,272,5916,25,625;QS=2.98444,0.0155642,0;SGB=-0.556633;RPBZ=1.02125;MQBZ=-2.16025;MQSBZ=-1.23956;BQBZ=-1.64106;SCBZ=2.91548;FS=0;MQ0F=0 PL 0,15,149,21,152,149 0,9,114,9,114,114 0,18,162,18,162,162 +17 125 . A T,<*> 0 . DP=18;I16=14,2,1,0,589,22565,4,16,898,52082,29,841,272,5916,25,625;QS=2.98444,0.0155642,0;SGB=-0.556633;RPBZ=1.02125;MQBZ=-2.16025;MQSBZ=-1.23956;BQBZ=-1.64106;SCBZ=2.91548;MQ0F=0 PL 0,15,149,21,152,149 0,9,114,9,114,114 0,18,162,18,162,162 17 126 . A <*> 0 . DP=18;I16=15,2,0,0,629,24725,0,0,927,52923,0,0,298,6536,0,0;QS=3,0;MQ0F=0 PL 0,24,162 0,9,117 0,18,174 17 127 . C <*> 0 . DP=18;I16=15,2,0,0,627,24331,0,0,927,52923,0,0,299,6549,0,0;QS=3,0;MQ0F=0 PL 0,24,163 0,9,119 0,18,160 17 128 . A <*> 0 . DP=18;I16=15,2,0,0,660,26364,0,0,927,52923,0,0,300,6580,0,0;QS=3,0;MQ0F=0 PL 0,24,169 0,9,121 0,18,168 diff --git a/test/mpileup/mpileup.10.out b/test/mpileup/mpileup.10.out index 3328e27d8..c988d877a 100644 --- a/test/mpileup/mpileup.10.out +++ b/test/mpileup/mpileup.10.out @@ -12,7 +12,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -22,29 +21,29 @@ 17 100 . C <*> 0 . DP=16;I16=14,1,0,0,593,24461,0,0,838,48482,0,0,310,7132,0,0;QS=5,0;MQ0F=0 PL 0,3,19 0,6,78 0,12,128 0,9,118 0,15,134 17 101 . C <*> 0 . DP=16;I16=14,1,0,0,567,22633,0,0,838,48482,0,0,309,7011,0,0;QS=5,0;MQ0F=0 PL 0,3,22 0,6,79 0,12,123 0,9,108 0,15,132 17 102 . C <*> 0 . DP=16;I16=14,1,0,0,602,25074,0,0,838,48482,0,0,308,6904,0,0;QS=5,0;MQ0F=0 PL 0,3,20 0,6,78 0,12,129 0,9,121 0,15,139 -17 103 . T C,<*> 0 . DP=16;I16=13,1,1,0,588,25334,6,36,809,47641,29,841,301,6775,6,36;QS=4,1,0;SGB=-0.587685;RPBZ=-1.15831;MQBZ=-2.54951;MQSBZ=0.392232;BQBZ=-1.64233;SCBZ=3.74166;FS=0;MQ0F=0 PL 6,3,0,6,3,6 0,6,79,6,79,79 0,12,131,12,131,131 0,9,118,9,118,118 0,15,147,15,147,147 -17 104 . G C,<*> 0 . DP=16;I16=13,1,1,0,536,21966,3,9,809,47641,29,841,298,6634,7,49;QS=4,1,0;SGB=-0.587685;RPBZ=-1.15831;MQBZ=-2.54951;MQSBZ=0.392232;BQBZ=-1.63041;SCBZ=3.74166;FS=0;MQ0F=0 PL 4,3,0,4,3,4 0,6,78,6,78,78 0,12,123,12,123,123 0,9,101,9,101,101 0,15,133,15,133,133 +17 103 . T C,<*> 0 . DP=16;I16=13,1,1,0,588,25334,6,36,809,47641,29,841,301,6775,6,36;QS=4,1,0;SGB=-0.587685;RPBZ=-1.15831;MQBZ=-2.54951;MQSBZ=0.392232;BQBZ=-1.64233;SCBZ=3.74166;MQ0F=0 PL 6,3,0,6,3,6 0,6,79,6,79,79 0,12,131,12,131,131 0,9,118,9,118,118 0,15,147,15,147,147 +17 104 . G C,<*> 0 . DP=16;I16=13,1,1,0,536,21966,3,9,809,47641,29,841,298,6634,7,49;QS=4,1,0;SGB=-0.587685;RPBZ=-1.15831;MQBZ=-2.54951;MQSBZ=0.392232;BQBZ=-1.63041;SCBZ=3.74166;MQ0F=0 PL 4,3,0,4,3,4 0,6,78,6,78,78 0,12,123,12,123,123 0,9,101,9,101,101 0,15,133,15,133,133 17 105 . G <*> 0 . DP=17;I16=15,1,0,0,541,20301,0,0,898,52082,0,0,303,6571,0,0;QS=5,0;MQ0F=0 PL 0,6,35 0,6,77 0,12,106 0,9,106 0,15,125 17 106 . G <*> 0 . DP=17;I16=15,1,0,0,562,22318,0,0,898,52082,0,0,302,6476,0,0;QS=5,0;MQ0F=0 PL 0,6,44 0,6,75 0,12,130 0,9,92 0,15,124 17 107 . C <*> 0 . DP=17;I16=15,1,0,0,606,24752,0,0,898,52082,0,0,301,6399,0,0;QS=5,0;MQ0F=0 PL 0,6,36 0,6,77 0,12,130 0,9,119 0,15,136 17 108 . C <*> 0 . DP=17;I16=15,1,0,0,604,24464,0,0,898,52082,0,0,300,6340,0,0;QS=5,0;MQ0F=0 PL 0,6,37 0,6,78 0,12,128 0,9,119 0,15,135 -17 109 . T C,<*> 0 . DP=17;I16=14,1,1,0,639,27679,2,4,869,51241,29,841,287,6155,12,144;QS=4.89189,0.108108,0;SGB=-0.587685;RPBZ=-0.759816;MQBZ=-2.64575;MQSBZ=0.377964;BQBZ=-1.6641;SCBZ=2.82843;FS=0;MQ0F=0 PL 0,1,28,3,31,30 0,6,77,6,77,77 0,12,133,12,133,133 0,9,120,9,120,120 0,15,150,15,150,150 +17 109 . T C,<*> 0 . DP=17;I16=14,1,1,0,639,27679,2,4,869,51241,29,841,287,6155,12,144;QS=4.89189,0.108108,0;SGB=-0.587685;RPBZ=-0.759816;MQBZ=-2.64575;MQSBZ=0.377964;BQBZ=-1.6641;SCBZ=2.82843;MQ0F=0 PL 0,1,28,3,31,30 0,6,77,6,77,77 0,12,133,12,133,133 0,9,120,9,120,120 0,15,150,15,150,150 17 110 . G <*> 0 . DP=17;I16=15,1,0,0,608,24834,0,0,898,52082,0,0,298,6276,0,0;QS=5,0;MQ0F=0 PL 0,6,40 0,6,78 0,12,130 0,9,113 0,15,136 17 111 . G <*> 0 . DP=17;I16=15,1,0,0,503,18985,0,0,898,52082,0,0,296,6222,0,0;QS=5,0;MQ0F=0 PL 0,6,45 0,6,75 0,12,92 0,9,95 0,15,119 -17 112 . C G,<*> 0 . DP=17;I16=14,1,1,0,577,23365,2,4,869,51241,29,841,279,5963,15,225;QS=4.88235,0.117647,0;SGB=-0.587685;RPBZ=-0.542725;MQBZ=-2.64575;MQSBZ=0.377964;BQBZ=-1.63663;SCBZ=2.82843;FS=0;MQ0F=0 PL 0,1,25,3,28,27 0,6,77,6,77,77 0,12,129,12,129,129 0,9,103,9,103,103 0,15,135,15,135,135 -17 113 . A G,<*> 0 . DP=17;I16=14,1,1,0,565,22603,4,16,869,51241,29,841,275,5867,16,256;QS=4.88235,0.117647,0;SGB=-0.587685;RPBZ=-0.542725;MQBZ=-2.64575;MQSBZ=0.377964;BQBZ=-1.64646;SCBZ=2.82843;FS=0;MQ0F=0 PL 0,1,25,3,28,27 0,6,71,6,71,71 0,12,120,12,120,120 0,9,102,9,102,102 0,15,139,15,139,139 +17 112 . C G,<*> 0 . DP=17;I16=14,1,1,0,577,23365,2,4,869,51241,29,841,279,5963,15,225;QS=4.88235,0.117647,0;SGB=-0.587685;RPBZ=-0.542725;MQBZ=-2.64575;MQSBZ=0.377964;BQBZ=-1.63663;SCBZ=2.82843;MQ0F=0 PL 0,1,25,3,28,27 0,6,77,6,77,77 0,12,129,12,129,129 0,9,103,9,103,103 0,15,135,15,135,135 +17 113 . A G,<*> 0 . DP=17;I16=14,1,1,0,565,22603,4,16,869,51241,29,841,275,5867,16,256;QS=4.88235,0.117647,0;SGB=-0.587685;RPBZ=-0.542725;MQBZ=-2.64575;MQSBZ=0.377964;BQBZ=-1.64646;SCBZ=2.82843;MQ0F=0 PL 0,1,25,3,28,27 0,6,71,6,71,71 0,12,120,12,120,120 0,9,102,9,102,102 0,15,139,15,139,139 17 114 . C <*> 0 . DP=17;I16=15,1,0,0,581,22755,0,0,898,52082,0,0,288,6076,0,0;QS=5,0;MQ0F=0 PL 0,6,38 0,6,75 0,12,118 0,9,113 0,15,133 -17 115 . C A,<*> 0 . DP=19;I16=15,2,1,0,615,24761,12,144,958,55682,29,841,261,5423,25,625;QS=4.88785,0.11215,0;SGB=-0.587685;RPBZ=0.28942;MQBZ=-2.23607;MQSBZ=-1.30384;BQBZ=-1.4501;SCBZ=-0.445021;FS=0;MQ0F=0 PL 0,6,43,6,43,43 0,6,80,6,80,80 0,12,123,12,123,123 3,0,86,9,89,93 0,21,153,21,153,153 -17 116 . A C,<*> 0 . DP=19;I16=15,2,1,0,631,25045,2,4,958,55682,29,841,265,5631,19,361;QS=4.90244,0.097561,0;SGB=-0.587685;RPBZ=0.0964735;MQBZ=-2.23607;MQSBZ=-1.30384;BQBZ=-1.65205;SCBZ=2.52179;FS=0;MQ0F=0 PL 0,1,32,3,35,34 0,6,75,6,75,75 0,12,121,12,121,121 0,9,102,9,102,102 0,21,175,21,175,175 +17 115 . C A,<*> 0 . DP=19;I16=15,2,1,0,615,24761,12,144,958,55682,29,841,261,5423,25,625;QS=4.88785,0.11215,0;SGB=-0.587685;RPBZ=0.28942;MQBZ=-2.23607;MQSBZ=-1.30384;BQBZ=-1.4501;SCBZ=-0.445021;MQ0F=0 PL 0,6,43,6,43,43 0,6,80,6,80,80 0,12,123,12,123,123 3,0,86,9,89,93 0,21,153,21,153,153 +17 116 . A C,<*> 0 . DP=19;I16=15,2,1,0,631,25045,2,4,958,55682,29,841,265,5631,19,361;QS=4.90244,0.097561,0;SGB=-0.587685;RPBZ=0.0964735;MQBZ=-2.23607;MQSBZ=-1.30384;BQBZ=-1.65205;SCBZ=2.52179;MQ0F=0 PL 0,1,32,3,35,34 0,6,75,6,75,75 0,12,121,12,121,121 0,9,102,9,102,102 0,21,175,21,175,175 17 117 . G <*> 0 . DP=19;I16=16,2,0,0,635,24843,0,0,987,56523,0,0,282,5960,0,0;QS=5,0;MQ0F=0 PL 0,6,42 0,6,77 0,12,117 0,9,97 0,21,177 17 118 . G <*> 0 . DP=19;I16=16,2,0,0,583,22101,0,0,987,56523,0,0,280,5952,0,0;QS=5,0;MQ0F=0 PL 0,6,43 0,6,77 0,12,116 0,9,65 0,21,162 17 119 . G <*> 0 . DP=18;I16=15,2,0,0,581,22015,0,0,927,52923,0,0,277,5917,0,0;QS=5,0;MQ0F=0 PL 0,6,47 0,6,78 0,12,114 0,6,76 0,21,160 -17 120 . A G,<*> 0 . DP=18;I16=14,2,1,0,608,23948,4,16,898,52082,29,841,252,5374,23,529;QS=4.91111,0.0888889,0;SGB=-0.587685;RPBZ=0.204375;MQBZ=-2.16025;MQSBZ=-1.23956;BQBZ=-1.64411;SCBZ=2.91548;FS=0;MQ0F=0 PL 0,1,36,3,39,38 0,6,75,6,75,75 0,12,116,12,116,116 0,6,88,6,88,88 0,21,171,21,171,171 +17 120 . A G,<*> 0 . DP=18;I16=14,2,1,0,608,23948,4,16,898,52082,29,841,252,5374,23,529;QS=4.91111,0.0888889,0;SGB=-0.587685;RPBZ=0.204375;MQBZ=-2.16025;MQSBZ=-1.23956;BQBZ=-1.64411;SCBZ=2.91548;MQ0F=0 PL 0,1,36,3,39,38 0,6,75,6,75,75 0,12,116,12,116,116 0,6,88,6,88,88 0,21,171,21,171,171 17 121 . G <*> 0 . DP=18;I16=15,2,0,0,619,24187,0,0,927,52923,0,0,273,5909,0,0;QS=5,0;MQ0F=0 PL 0,6,48 0,6,80 0,12,121 0,6,84 0,21,168 17 122 . C <*> 0 . DP=19;I16=16,2,0,0,655,26103,0,0,987,56523,0,0,271,5935,0,0;QS=5,0;MQ0F=0 PL 0,6,42 0,6,78 0,12,119 0,9,107 0,21,178 17 123 . T <*> 0 . DP=17;I16=14,2,0,0,610,24776,0,0,867,49323,0,0,271,5929,0,0;QS=5,0;MQ0F=0 PL 0,6,48 0,6,75 0,9,99 0,9,123 0,18,166 17 124 . T <*> 0 . DP=17;I16=14,2,0,0,547,20261,0,0,867,49323,0,0,271,5939,0,0;QS=5,0;MQ0F=0 PL 0,6,33 0,6,70 0,9,89 0,9,114 0,18,154 -17 125 . A T,<*> 0 . DP=16;I16=12,2,1,0,522,20316,4,16,778,44882,29,841,246,5290,25,625;QS=4.90476,0.0952381,0;SGB=-0.587685;RPBZ=0.926648;MQBZ=-2;MQSBZ=-1.1007;BQBZ=-1.62747;SCBZ=2.73861;FS=0;MQ0F=0 PL 0,1,33,3,36,35 0,6,72,6,72,72 0,6,63,6,63,63 0,9,114,9,114,114 0,18,162,18,162,162 +17 125 . A T,<*> 0 . DP=16;I16=12,2,1,0,522,20316,4,16,778,44882,29,841,246,5290,25,625;QS=4.90476,0.0952381,0;SGB=-0.587685;RPBZ=0.926648;MQBZ=-2;MQSBZ=-1.1007;BQBZ=-1.62747;SCBZ=2.73861;MQ0F=0 PL 0,1,33,3,36,35 0,6,72,6,72,72 0,6,63,6,63,63 0,9,114,9,114,114 0,18,162,18,162,162 17 126 . A <*> 0 . DP=16;I16=13,2,0,0,558,22192,0,0,807,45723,0,0,271,5907,0,0;QS=5,0;MQ0F=0 PL 0,6,50 0,6,72 0,6,67 0,9,117 0,18,174 17 127 . C <*> 0 . DP=16;I16=13,2,0,0,554,21662,0,0,807,45723,0,0,271,5915,0,0;QS=5,0;MQ0F=0 PL 0,6,46 0,6,69 0,6,75 0,9,119 0,18,160 17 128 . A <*> 0 . DP=16;I16=13,2,0,0,588,23772,0,0,807,45723,0,0,271,5939,0,0;QS=5,0;MQ0F=0 PL 0,6,59 0,6,74 0,6,72 0,9,121 0,18,168 diff --git a/test/mpileup/mpileup.11.out b/test/mpileup/mpileup.11.out index adee2884f..93d61a644 100644 --- a/test/mpileup/mpileup.11.out +++ b/test/mpileup/mpileup.11.out @@ -12,7 +12,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -177,7 +176,7 @@ 17 156 . C <*> 0 . DP=5;I16=4,1,0,0,190,7238,0,0,269,15241,0,0,101,2311,0,0;QS=1,0;MQ0F=0 PL 0,15,150 17 157 . C <*> 0 . DP=5;I16=4,1,0,0,192,7384,0,0,269,15241,0,0,101,2341,0,0;QS=1,0;MQ0F=0 PL 0,15,149 17 158 . T <*> 0 . DP=5;I16=4,1,0,0,205,8455,0,0,269,15241,0,0,101,2375,0,0;QS=1,0;MQ0F=0 PL 0,15,159 -17 159 . A G,<*> 0 . DP=6;I16=4,1,1,0,179,6513,5,25,269,15241,60,3600,101,2413,0,0;QS=0.97076,0.0292398,0;SGB=-0.379885;RPBZ=-1.46385;MQBZ=0.447214;MQSBZ=-2.23607;BQBZ=-1.46385;SCBZ=0;FS=0;MQ0F=0 PL 0,10,129,15,132,129 +17 159 . A G,<*> 0 . DP=6;I16=4,1,1,0,179,6513,5,25,269,15241,60,3600,101,2413,0,0;QS=0.97076,0.0292398,0;SGB=-0.379885;RPBZ=-1.46385;MQBZ=0.447214;MQSBZ=-2.23607;BQBZ=-1.46385;SCBZ=0;MQ0F=0 PL 0,10,129,15,132,129 17 160 . G <*> 0 . DP=6;I16=5,1,0,0,187,6199,0,0,329,18841,0,0,102,2456,0,0;QS=1,0;MQ0F=0 PL 0,18,139 17 161 . A <*> 0 . DP=6;I16=5,1,0,0,225,8479,0,0,329,18841,0,0,103,2505,0,0;QS=1,0;MQ0F=0 PL 0,18,162 17 162 . A <*> 0 . DP=6;I16=5,1,0,0,233,9149,0,0,329,18841,0,0,103,2509,0,0;QS=1,0;MQ0F=0 PL 0,18,167 @@ -208,7 +207,7 @@ 17 187 . C <*> 0 . DP=7;I16=6,1,0,0,252,9238,0,0,389,22441,0,0,142,3234,0,0;QS=1,0;MQ0F=0 PL 0,21,172 17 188 . C <*> 0 . DP=7;I16=6,1,0,0,239,8387,0,0,389,22441,0,0,143,3297,0,0;QS=1,0;MQ0F=0 PL 0,21,162 17 189 . C <*> 0 . DP=7;I16=6,1,0,0,247,8819,0,0,389,22441,0,0,144,3366,0,0;QS=1,0;MQ0F=0 PL 0,21,167 -17 190 . A C,<*> 0 . DP=7;I16=5,1,1,0,219,8109,5,25,329,18841,60,3600,118,2716,25,625;QS=0.976636,0.0233645,0;SGB=-0.379885;RPBZ=0;MQBZ=0.408248;MQSBZ=-2.44949;BQBZ=-1.51357;SCBZ=0;FS=0;MQ0F=0 PL 0,12,153,18,156,153 +17 190 . A C,<*> 0 . DP=7;I16=5,1,1,0,219,8109,5,25,329,18841,60,3600,118,2716,25,625;QS=0.976636,0.0233645,0;SGB=-0.379885;RPBZ=0;MQBZ=0.408248;MQSBZ=-2.44949;BQBZ=-1.51357;SCBZ=0;MQ0F=0 PL 0,12,153,18,156,153 17 191 . T <*> 0 . DP=7;I16=6,1,0,0,247,8853,0,0,389,22441,0,0,141,3273,0,0;QS=1,0;MQ0F=0 PL 0,21,169 17 192 . G <*> 0 . DP=7;I16=6,1,0,0,221,7309,0,0,389,22441,0,0,139,3213,0,0;QS=1,0;MQ0F=0 PL 0,21,151 17 193 . T <*> 0 . DP=7;I16=6,1,0,0,229,8027,0,0,389,22441,0,0,137,3161,0,0;QS=1,0;MQ0F=0 PL 0,21,157 @@ -244,7 +243,7 @@ 17 223 . G <*> 0 . DP=4;I16=4,0,0,0,104,2810,0,0,240,14400,0,0,88,2044,0,0;QS=1,0;MQ0F=0 PL 0,12,81 17 224 . G <*> 0 . DP=4;I16=4,0,0,0,89,2077,0,0,240,14400,0,0,87,2019,0,0;QS=1,0;MQ0F=0 PL 0,12,70 17 225 . C <*> 0 . DP=4;I16=4,0,0,0,107,3369,0,0,240,14400,0,0,86,1996,0,0;QS=1,0;MQ0F=0 PL 0,12,86 -17 226 . A G,<*> 0 . DP=4;I16=3,0,1,0,98,3430,3,9,180,10800,60,3600,60,1350,25,625;QS=0.960784,0.0392157,0;SGB=-0.379885;RPBZ=-0.447214;MQBZ=0;BQBZ=-1.34164;SCBZ=0;FS=0;MQ0F=0 PL 0,5,79,9,82,80 +17 226 . A G,<*> 0 . DP=4;I16=3,0,1,0,98,3430,3,9,180,10800,60,3600,60,1350,25,625;QS=0.960784,0.0392157,0;SGB=-0.379885;RPBZ=-0.447214;MQBZ=0;BQBZ=-1.34164;SCBZ=0;MQ0F=0 PL 0,5,79,9,82,80 17 227 . C <*> 0 . DP=4;I16=4,0,0,0,91,2685,0,0,240,14400,0,0,84,1956,0,0;QS=1,0;MQ0F=0 PL 0,12,75 17 228 . C <*> 0 . DP=4;I16=4,0,0,0,121,3947,0,0,240,14400,0,0,83,1939,0,0;QS=1,0;MQ0F=0 PL 0,12,96 17 229 . G <*> 0 . DP=4;I16=4,0,0,0,91,2097,0,0,240,14400,0,0,82,1924,0,0;QS=1,0;MQ0F=0 PL 0,12,70 @@ -255,7 +254,7 @@ 17 234 . A <*> 0 . DP=5;I16=5,0,0,0,170,5930,0,0,300,18000,0,0,79,1883,0,0;QS=1,0;MQ0F=0 PL 0,15,123 17 235 . A <*> 0 . DP=5;I16=5,0,0,0,155,5325,0,0,300,18000,0,0,78,1836,0,0;QS=1,0;MQ0F=0 PL 0,15,115 17 236 . G <*> 0 . DP=5;I16=5,0,0,0,141,4187,0,0,300,18000,0,0,77,1795,0,0;QS=1,0;MQ0F=0 PL 0,15,103 -17 237 . A C,<*> 0 . DP=4;I16=3,0,1,0,109,4005,8,64,180,10800,60,3600,52,1134,25,625;QS=0.931624,0.0683761,0;SGB=-0.379885;RPBZ=0.447214;MQBZ=0;BQBZ=-1.34164;SCBZ=0;FS=0;MQ0F=0 PL 0,3,84,9,87,87 +17 237 . A C,<*> 0 . DP=4;I16=3,0,1,0,109,4005,8,64,180,10800,60,3600,52,1134,25,625;QS=0.931624,0.0683761,0;SGB=-0.379885;RPBZ=0.447214;MQBZ=0;BQBZ=-1.34164;SCBZ=0;MQ0F=0 PL 0,3,84,9,87,87 17 238 . C <*> 0 . DP=4;I16=4,0,0,0,104,2856,0,0,240,14400,0,0,77,1727,0,0;QS=1,0;MQ0F=0 PL 0,12,82 17 239 . A <*> 0 . DP=4;I16=4,0,0,0,138,4886,0,0,240,14400,0,0,77,1699,0,0;QS=1,0;MQ0F=0 PL 0,12,108 17 240 . C <*> 0 . DP=4;I16=4,0,0,0,136,4700,0,0,240,14400,0,0,76,1626,0,0;QS=1,0;MQ0F=0 PL 0,12,106 @@ -321,7 +320,7 @@ 17 300 . A <*> 0 . DP=7;I16=2,5,0,0,296,12578,0,0,358,19682,0,0,133,3069,0,0;QS=1,0;MQ0F=0 PL 0,21,210 17 301 . G <*> 0 . DP=7;I16=2,5,0,0,274,10742,0,0,358,19682,0,0,136,3138,0,0;QS=1,0;MQ0F=0 PL 0,21,196 17 302 . T <*> 0 . DP=7;I16=2,5,0,0,283,11451,0,0,358,19682,0,0,139,3213,0,0;QS=1,0;MQ0F=0 PL 0,21,202 -17 302 . T TA 0 . INDEL;IDV=7;IMF=1;DP=7;I16=0,0,2,5,0,0,280,11200,0,0,358,19682,0,0,139,3213;QS=0,1;VDB=0.355905;SGB=-0.636426;BQBZ=-1.34164;FS=0;MQ0F=0 PL 201,21,0 +17 302 . T TA 0 . INDEL;IDV=7;IMF=1;DP=7;I16=0,0,2,5,0,0,280,11200,0,0,358,19682,0,0,139,3213;QS=0,1;VDB=0.355905;SGB=-0.636426;BQBZ=-1.34164;MQ0F=0 PL 201,21,0 17 303 . G <*> 0 . DP=7;I16=2,5,0,0,280,11264,0,0,358,19682,0,0,144,3330,0,0;QS=1,0;MQ0F=0 PL 0,21,195 17 304 . C <*> 0 . DP=8;I16=2,6,0,0,304,11716,0,0,418,23282,0,0,146,3370,0,0;QS=1,0;MQ0F=0 PL 0,24,200 17 305 . C <*> 0 . DP=8;I16=2,6,0,0,318,12738,0,0,418,23282,0,0,149,3415,0,0;QS=1,0;MQ0F=0 PL 0,24,211 @@ -354,7 +353,7 @@ 17 332 . A <*> 0 . DP=11;I16=4,7,0,0,411,15645,0,0,598,34082,0,0,189,4043,0,0;QS=1,0;MQ0F=0 PL 0,33,255 17 333 . A <*> 0 . DP=11;I16=4,7,0,0,405,15523,0,0,598,34082,0,0,191,4029,0,0;QS=1,0;MQ0F=0 PL 0,33,255 17 334 . A <*> 0 . DP=11;I16=4,7,0,0,404,15090,0,0,598,34082,0,0,193,4027,0,0;QS=1,0;MQ0F=0 PL 0,33,255 -17 335 . A G,<*> 0 . DP=12;I16=4,7,1,0,382,13732,4,16,598,34082,60,3600,195,4037,0,0;QS=0.989189,0.0108108,0;SGB=-0.379885;RPBZ=-1.59605;MQBZ=0.447214;MQSBZ=-1.25357;BQBZ=-1.59886;SCBZ=-0.301511;FS=0;MQ0F=0 PL 0,25,245,33,248,245 +17 335 . A G,<*> 0 . DP=12;I16=4,7,1,0,382,13732,4,16,598,34082,60,3600,195,4037,0,0;QS=0.989189,0.0108108,0;SGB=-0.379885;RPBZ=-1.59605;MQBZ=0.447214;MQSBZ=-1.25357;BQBZ=-1.59886;SCBZ=-0.301511;MQ0F=0 PL 0,25,245,33,248,245 17 336 . A <*> 0 . DP=12;I16=5,7,0,0,382,12810,0,0,658,37682,0,0,198,4060,0,0;QS=1,0;MQ0F=0 PL 0,36,255 17 337 . C <*> 0 . DP=12;I16=5,7,0,0,443,16735,0,0,658,37682,0,0,200,4048,0,0;QS=1,0;MQ0F=0 PL 0,36,255 17 338 . T <*> 0 . DP=12;I16=5,7,0,0,482,19532,0,0,658,37682,0,0,202,4052,0,0;QS=1,0;MQ0F=0 PL 0,36,255 @@ -394,7 +393,7 @@ 17 372 . C <*> 0 . DP=11;I16=5,6,0,0,422,16450,0,0,660,39600,0,0,212,4894,0,0;QS=1,0;MQ0F=0 PL 0,33,255 17 373 . A <*> 0 . DP=11;I16=5,6,0,0,416,16096,0,0,660,39600,0,0,211,4831,0,0;QS=1,0;MQ0F=0 PL 0,33,255 17 374 . T <*> 0 . DP=11;I16=5,6,0,0,395,14795,0,0,660,39600,0,0,210,4778,0,0;QS=1,0;MQ0F=0 PL 0,33,255 -17 375 . A T,<*> 0 . DP=11;I16=5,5,0,1,399,15985,14,196,600,36000,60,3600,205,4719,4,16;QS=0.966102,0.0338983,0;SGB=-0.379885;RPBZ=-1.58474;MQBZ=0;MQSBZ=0;BQBZ=-1.59942;SCBZ=0;FS=0;MQ0F=0 PL 0,18,255,30,255,255 +17 375 . A T,<*> 0 . DP=11;I16=5,5,0,1,399,15985,14,196,600,36000,60,3600,205,4719,4,16;QS=0.966102,0.0338983,0;SGB=-0.379885;RPBZ=-1.58474;MQBZ=0;MQSBZ=0;BQBZ=-1.59942;SCBZ=0;MQ0F=0 PL 0,18,255,30,255,255 17 376 . G <*> 0 . DP=11;I16=5,6,0,0,419,16089,0,0,660,39600,0,0,208,4702,0,0;QS=1,0;MQ0F=0 PL 0,33,255 17 377 . T <*> 0 . DP=11;I16=5,6,0,0,414,16104,0,0,660,39600,0,0,207,4679,0,0;QS=1,0;MQ0F=0 PL 0,33,255 17 378 . T <*> 0 . DP=10;I16=5,5,0,0,399,16003,0,0,600,36000,0,0,207,4665,0,0;QS=1,0;MQ0F=0 PL 0,30,255 @@ -420,7 +419,7 @@ 17 398 . A <*> 0 . DP=10;I16=6,4,0,0,397,15817,0,0,569,33241,0,0,193,4447,0,0;QS=1,0;MQ0F=0 PL 0,30,255 17 399 . A <*> 0 . DP=10;I16=6,4,0,0,400,16172,0,0,569,33241,0,0,193,4417,0,0;QS=1,0;MQ0F=0 PL 0,30,255 17 400 . A <*> 0 . DP=11;I16=6,5,0,0,425,16735,0,0,629,36841,0,0,191,4297,0,0;QS=1,0;MQ0F=0 PL 0,33,255 -17 401 . A C,<*> 0 . DP=11;I16=6,4,0,1,396,15798,8,64,569,33241,60,3600,165,3565,25,625;QS=0.979849,0.0201511,0;SGB=-0.379885;RPBZ=-0.633898;MQBZ=0.316228;MQSBZ=0.912871;BQBZ=-1.58838;SCBZ=0;FS=0;MQ0F=0 PL 0,22,255,30,255,255 +17 401 . A C,<*> 0 . DP=11;I16=6,4,0,1,396,15798,8,64,569,33241,60,3600,165,3565,25,625;QS=0.979849,0.0201511,0;SGB=-0.379885;RPBZ=-0.633898;MQBZ=0.316228;MQSBZ=0.912871;BQBZ=-1.58838;SCBZ=0;MQ0F=0 PL 0,22,255,30,255,255 17 402 . T <*> 0 . DP=11;I16=6,5,0,0,415,15961,0,0,629,36841,0,0,189,4097,0,0;QS=1,0;MQ0F=0 PL 0,33,255 17 403 . T <*> 0 . DP=11;I16=6,5,0,0,426,16580,0,0,629,36841,0,0,188,4018,0,0;QS=1,0;MQ0F=0 PL 0,33,255 17 404 . G <*> 0 . DP=11;I16=6,5,0,0,421,16197,0,0,629,36841,0,0,187,3953,0,0;QS=1,0;MQ0F=0 PL 0,33,255 @@ -456,7 +455,7 @@ 17 434 . T <*> 0 . DP=10;I16=5,5,0,0,339,11787,0,0,538,30482,0,0,191,4285,0,0;QS=1,0;MQ0F=0 PL 0,30,243 17 435 . A <*> 0 . DP=10;I16=5,5,0,0,346,12322,0,0,538,30482,0,0,192,4318,0,0;QS=1,0;MQ0F=0 PL 0,30,237 17 436 . T <*> 0 . DP=9;I16=4,5,0,0,305,10551,0,0,478,26882,0,0,194,4360,0,0;QS=1,0;MQ0F=0 PL 0,27,223 -17 437 . T G,<*> 0 . DP=9;I16=3,5,1,0,271,9505,6,36,449,26041,29,841,180,4154,16,256;QS=0.978102,0.0218978,0;SGB=-0.379885;RPBZ=-1.36123;MQBZ=-1.87083;MQSBZ=1.69031;BQBZ=-1.55569;SCBZ=0;FS=0;MQ0F=0 PL 0,17,200,24,203,201 +17 437 . T G,<*> 0 . DP=9;I16=3,5,1,0,271,9505,6,36,449,26041,29,841,180,4154,16,256;QS=0.978102,0.0218978,0;SGB=-0.379885;RPBZ=-1.36123;MQBZ=-1.87083;MQSBZ=1.69031;BQBZ=-1.55569;SCBZ=0;MQ0F=0 PL 0,17,200,24,203,201 17 438 . A <*> 0 . DP=9;I16=4,5,0,0,298,10570,0,0,478,26882,0,0,198,4468,0,0;QS=1,0;MQ0F=0 PL 0,27,220 17 439 . C <*> 0 . DP=9;I16=4,5,0,0,311,10989,0,0,478,26882,0,0,200,4534,0,0;QS=1,0;MQ0F=0 PL 0,27,224 17 440 . A <*> 0 . DP=9;I16=4,5,0,0,346,13482,0,0,478,26882,0,0,202,4608,0,0;QS=1,0;MQ0F=0 PL 0,27,247 @@ -484,13 +483,13 @@ 17 462 . G <*> 0 . DP=10;I16=5,5,0,0,350,12490,0,0,515,28251,0,0,199,4569,0,0;QS=1,0;MQ0F=0 PL 0,30,241 17 463 . G <*> 0 . DP=10;I16=5,5,0,0,310,10258,0,0,515,28251,0,0,200,4584,0,0;QS=1,0;MQ0F=0 PL 0,30,221 17 464 . A <*> 0 . DP=10;I16=5,5,0,0,304,10594,0,0,515,28251,0,0,201,4605,0,0;QS=1,0;MQ0F=0 PL 0,30,217 -17 465 . C T,<*> 0 . DP=10;I16=5,4,0,1,326,11950,4,16,455,24651,60,3600,196,4596,6,36;QS=0.987342,0.0126582,0;SGB=-0.379885;RPBZ=1.57147;MQBZ=0.645497;MQSBZ=0.903696;BQBZ=-1.61645;SCBZ=0;FS=0;MQ0F=0 PL 0,20,224,27,227,224 +17 465 . C T,<*> 0 . DP=10;I16=5,4,0,1,326,11950,4,16,455,24651,60,3600,196,4596,6,36;QS=0.987342,0.0126582,0;SGB=-0.379885;RPBZ=1.57147;MQBZ=0.645497;MQSBZ=0.903696;BQBZ=-1.61645;SCBZ=0;MQ0F=0 PL 0,20,224,27,227,224 17 466 . A <*> 0 . DP=10;I16=5,5,0,0,379,14569,0,0,515,28251,0,0,203,4665,0,0;QS=1,0;MQ0F=0 PL 0,30,255 17 467 . A <*> 0 . DP=10;I16=5,5,0,0,367,14303,0,0,515,28251,0,0,203,4655,0,0;QS=1,0;MQ0F=0 PL 0,30,251 17 468 . A <*> 0 . DP=10;I16=5,5,0,0,357,13375,0,0,515,28251,0,0,202,4604,0,0;QS=1,0;MQ0F=0 PL 0,30,251 17 469 . A <*> 0 . DP=10;I16=5,5,0,0,387,15581,0,0,515,28251,0,0,201,4563,0,0;QS=1,0;MQ0F=0 PL 0,30,255 17 470 . G <*> 0 . DP=10;I16=5,5,0,0,328,11334,0,0,515,28251,0,0,200,4532,0,0;QS=1,0;MQ0F=0 PL 0,30,238 -17 471 . T G,C,<*> 0 . DP=11;I16=5,4,0,2,319,11637,18,162,478,26882,97,4969,183,4255,16,256;QS=0.945289,0.0273556,0.0273556,0;VDB=0.96;SGB=-0.453602;RPBZ=0.23624;MQBZ=-0.451335;MQSBZ=1.04881;BQBZ=-2.14585;SCBZ=0;FS=0;MQ0F=0 PL 0,19,219,19,221,219,27,222,222,221 +17 471 . T G,C,<*> 0 . DP=11;I16=5,4,0,2,319,11637,18,162,478,26882,97,4969,183,4255,16,256;QS=0.945289,0.0273556,0.0273556,0;VDB=0.96;SGB=-0.453602;RPBZ=0.23624;MQBZ=-0.451335;MQSBZ=1.04881;BQBZ=-2.14585;SCBZ=0;MQ0F=0 PL 0,19,219,19,221,219,27,222,222,221 17 472 . T <*> 0 . DP=10;I16=5,5,0,0,340,12388,0,0,515,28251,0,0,200,4500,0,0;QS=1,0;MQ0F=0 PL 0,30,241 17 473 . G <*> 0 . DP=10;I16=5,5,0,0,363,14103,0,0,515,28251,0,0,201,4499,0,0;QS=1,0;MQ0F=0 PL 0,30,250 17 474 . G <*> 0 . DP=11;I16=6,5,0,0,378,13788,0,0,575,31851,0,0,202,4508,0,0;QS=1,0;MQ0F=0 PL 0,33,255 @@ -507,7 +506,7 @@ 17 485 . G <*> 0 . DP=11;I16=6,5,0,0,419,16073,0,0,575,31851,0,0,202,4328,0,0;QS=1,0;MQ0F=0 PL 0,33,255 17 486 . A <*> 0 . DP=11;I16=6,5,0,0,452,18618,0,0,575,31851,0,0,200,4280,0,0;QS=1,0;MQ0F=0 PL 0,33,255 17 487 . G <*> 0 . DP=11;I16=6,5,0,0,403,14875,0,0,575,31851,0,0,198,4244,0,0;QS=1,0;MQ0F=0 PL 0,33,255 -17 488 . A G,<*> 0 . DP=11;I16=5,5,1,0,388,15102,4,16,546,31010,29,841,171,3595,25,625;QS=0.989474,0.0105263,0;SGB=-0.379885;RPBZ=0;MQBZ=-1.81659;MQSBZ=0.699206;BQBZ=-1.60315;SCBZ=0;FS=0;MQ0F=0 PL 0,23,255,30,255,255 +17 488 . A G,<*> 0 . DP=11;I16=5,5,1,0,388,15102,4,16,546,31010,29,841,171,3595,25,625;QS=0.989474,0.0105263,0;SGB=-0.379885;RPBZ=0;MQBZ=-1.81659;MQSBZ=0.699206;BQBZ=-1.60315;SCBZ=0;MQ0F=0 PL 0,23,255,30,255,255 17 489 . A <*> 0 . DP=11;I16=6,5,0,0,393,14565,0,0,575,31851,0,0,194,4208,0,0;QS=1,0;MQ0F=0 PL 0,33,255 17 490 . A <*> 0 . DP=11;I16=6,5,0,0,401,14927,0,0,575,31851,0,0,192,4208,0,0;QS=1,0;MQ0F=0 PL 0,33,255 17 491 . T <*> 0 . DP=11;I16=6,5,0,0,385,13773,0,0,575,31851,0,0,190,4220,0,0;QS=1,0;MQ0F=0 PL 0,33,255 @@ -623,7 +622,7 @@ 17 601 . T <*> 0 . DP=8;I16=4,4,0,0,305,11697,0,0,480,28800,0,0,132,2768,0,0;QS=1,0;MQ0F=0 PL 0,24,235 17 602 . G <*> 0 . DP=8;I16=4,4,0,0,298,11176,0,0,480,28800,0,0,136,2836,0,0;QS=1,0;MQ0F=0 PL 0,24,229 17 603 . G <*> 0 . DP=8;I16=4,4,0,0,277,9947,0,0,480,28800,0,0,139,2863,0,0;QS=1,0;MQ0F=0 PL 0,24,216 -17 604 . T G,<*> 0 . DP=8;I16=3,4,1,0,265,10121,4,16,420,25200,60,3600,117,2275,25,625;QS=0.98513,0.0148699,0;SGB=-0.379885;RPBZ=0.219529;MQBZ=0;MQSBZ=0;BQBZ=-1.52753;SCBZ=-0.377964;FS=0;MQ0F=0 PL 0,15,205,21,208,205 +17 604 . T G,<*> 0 . DP=8;I16=3,4,1,0,265,10121,4,16,420,25200,60,3600,117,2275,25,625;QS=0.98513,0.0148699,0;SGB=-0.379885;RPBZ=0.219529;MQBZ=0;MQSBZ=0;BQBZ=-1.52753;SCBZ=-0.377964;MQ0F=0 PL 0,15,205,21,208,205 17 605 . T <*> 0 . DP=8;I16=4,4,0,0,273,10339,0,0,480,28800,0,0,145,2947,0,0;QS=1,0;MQ0F=0 PL 0,24,215 17 606 . T <*> 0 . DP=8;I16=4,4,0,0,278,9966,0,0,480,28800,0,0,148,3004,0,0;QS=1,0;MQ0F=0 PL 0,24,217 17 607 . A <*> 0 . DP=8;I16=4,4,0,0,288,10428,0,0,480,28800,0,0,151,3071,0,0;QS=1,0;MQ0F=0 PL 0,24,222 @@ -734,7 +733,7 @@ 17 712 . C <*> 0 . DP=6;I16=0,6,0,0,228,8740,0,0,298,16082,0,0,127,2781,0,0;QS=1,0;MQ0F=0 PL 0,18,146 17 713 . T <*> 0 . DP=6;I16=0,6,0,0,225,8639,0,0,298,16082,0,0,130,2888,0,0;QS=1,0;MQ0F=0 PL 0,18,149 17 714 . C <*> 0 . DP=6;I16=0,6,0,0,183,6221,0,0,298,16082,0,0,133,3001,0,0;QS=1,0;MQ0F=0 PL 0,18,127 -17 715 . A C,<*> 0 . DP=6;I16=0,5,0,1,162,5642,6,36,269,15241,29,841,117,2759,19,361;QS=0.964286,0.0357143,0;SGB=-0.379885;RPBZ=-0.87831;MQBZ=-1.41421;BQBZ=-1.48522;SCBZ=1.03923;FS=0;MQ0F=0 PL 0,9,114,15,117,115 +17 715 . A C,<*> 0 . DP=6;I16=0,5,0,1,162,5642,6,36,269,15241,29,841,117,2759,19,361;QS=0.964286,0.0357143,0;SGB=-0.379885;RPBZ=-0.87831;MQBZ=-1.41421;BQBZ=-1.48522;SCBZ=1.03923;MQ0F=0 PL 0,9,114,15,117,115 17 716 . C <*> 0 . DP=6;I16=0,6,0,0,215,7981,0,0,298,16082,0,0,139,3245,0,0;QS=1,0;MQ0F=0 PL 0,18,145 17 717 . A <*> 0 . DP=6;I16=0,6,0,0,229,9051,0,0,298,16082,0,0,142,3376,0,0;QS=1,0;MQ0F=0 PL 0,18,153 17 718 . G <*> 0 . DP=6;I16=0,6,0,0,209,7521,0,0,298,16082,0,0,145,3513,0,0;QS=1,0;MQ0F=0 PL 0,18,139 @@ -742,17 +741,17 @@ 17 720 . G <*> 0 . DP=6;I16=0,6,0,0,235,9247,0,0,298,16082,0,0,149,3701,0,0;QS=1,0;MQ0F=0 PL 0,18,147 17 721 . C <*> 0 . DP=6;I16=0,6,0,0,227,8683,0,0,298,16082,0,0,150,3750,0,0;QS=1,0;MQ0F=0 PL 0,18,147 17 722 . A <*> 0 . DP=6;I16=0,6,0,0,218,8102,0,0,298,16082,0,0,149,3701,0,0;QS=1,0;MQ0F=0 PL 0,18,143 -17 723 . A G,<*> 0 . DP=6;I16=0,5,0,1,196,7704,7,49,269,15241,29,841,122,2980,25,625;QS=0.964103,0.0358974,0;SGB=-0.379885;RPBZ=-1.46385;MQBZ=-1.41421;BQBZ=-1.48522;SCBZ=1.73205;FS=0;MQ0F=0 PL 0,9,129,15,132,130 +17 723 . A G,<*> 0 . DP=6;I16=0,5,0,1,196,7704,7,49,269,15241,29,841,122,2980,25,625;QS=0.964103,0.0358974,0;SGB=-0.379885;RPBZ=-1.46385;MQBZ=-1.41421;BQBZ=-1.48522;SCBZ=1.73205;MQ0F=0 PL 0,9,129,15,132,130 17 724 . C <*> 0 . DP=6;I16=0,6,0,0,216,8000,0,0,298,16082,0,0,145,3513,0,0;QS=1,0;MQ0F=0 PL 0,18,140 17 725 . A <*> 0 . DP=6;I16=0,6,0,0,211,7579,0,0,298,16082,0,0,143,3425,0,0;QS=1,0;MQ0F=0 PL 0,18,137 17 726 . C <*> 0 . DP=6;I16=0,6,0,0,199,6927,0,0,298,16082,0,0,141,3341,0,0;QS=1,0;MQ0F=0 PL 0,18,136 -17 727 . A C,<*> 0 . DP=6;I16=0,5,0,1,173,6285,17,289,269,15241,29,841,114,2636,25,625;QS=0.908108,0.0918919,0;SGB=-0.379885;RPBZ=-1.46385;MQBZ=-1.41421;BQBZ=-1.46385;SCBZ=1.03923;FS=0;MQ0F=0 PL 0,1,109,15,112,119 +17 727 . A C,<*> 0 . DP=6;I16=0,5,0,1,173,6285,17,289,269,15241,29,841,114,2636,25,625;QS=0.908108,0.0918919,0;SGB=-0.379885;RPBZ=-1.46385;MQBZ=-1.41421;BQBZ=-1.46385;SCBZ=1.03923;MQ0F=0 PL 0,1,109,15,112,119 17 728 . C <*> 0 . DP=6;I16=0,6,0,0,214,7890,0,0,298,16082,0,0,137,3185,0,0;QS=1,0;MQ0F=0 PL 0,18,142 17 729 . T <*> 0 . DP=6;I16=0,6,0,0,215,7867,0,0,298,16082,0,0,135,3113,0,0;QS=1,0;MQ0F=0 PL 0,18,142 17 730 . A <*> 0 . DP=6;I16=0,6,0,0,198,7286,0,0,298,16082,0,0,133,3045,0,0;QS=1,0;MQ0F=0 PL 0,18,137 17 731 . T <*> 0 . DP=6;I16=0,6,0,0,219,8327,0,0,298,16082,0,0,131,2981,0,0;QS=1,0;MQ0F=0 PL 0,18,148 17 732 . C <*> 0 . DP=6;I16=0,6,0,0,190,6622,0,0,298,16082,0,0,129,2921,0,0;QS=1,0;MQ0F=0 PL 0,18,132 -17 733 . T C,<*> 0 . DP=6;I16=0,5,0,1,186,7036,4,16,269,15241,29,841,102,2240,25,625;QS=0.978947,0.0210526,0;SGB=-0.379885;RPBZ=-1.46385;MQBZ=-1.41421;BQBZ=-1.48522;SCBZ=1.03923;FS=0;MQ0F=0 PL 0,10,128,15,131,129 +17 733 . T C,<*> 0 . DP=6;I16=0,5,0,1,186,7036,4,16,269,15241,29,841,102,2240,25,625;QS=0.978947,0.0210526,0;SGB=-0.379885;RPBZ=-1.46385;MQBZ=-1.41421;BQBZ=-1.48522;SCBZ=1.03923;MQ0F=0 PL 0,10,128,15,131,129 17 734 . G <*> 0 . DP=6;I16=0,6,0,0,212,7610,0,0,298,16082,0,0,125,2813,0,0;QS=1,0;MQ0F=0 PL 0,18,139 17 735 . A <*> 0 . DP=7;I16=0,7,0,0,235,8595,0,0,358,19682,0,0,123,2765,0,0;QS=1,0;MQ0F=0 PL 0,21,150 17 736 . C <*> 0 . DP=7;I16=0,7,0,0,239,9173,0,0,358,19682,0,0,122,2722,0,0;QS=1,0;MQ0F=0 PL 0,21,152 @@ -762,7 +761,7 @@ 17 740 . T <*> 0 . DP=7;I16=0,7,0,0,248,9042,0,0,358,19682,0,0,118,2610,0,0;QS=1,0;MQ0F=0 PL 0,21,155 17 741 . T <*> 0 . DP=7;I16=0,7,0,0,244,8970,0,0,358,19682,0,0,116,2548,0,0;QS=1,0;MQ0F=0 PL 0,21,151 17 742 . C <*> 0 . DP=7;I16=0,7,0,0,212,7112,0,0,358,19682,0,0,114,2494,0,0;QS=1,0;MQ0F=0 PL 0,21,138 -17 743 . A C,<*> 0 . DP=7;I16=0,6,0,1,189,6467,10,100,329,18841,29,841,87,1823,25,625;QS=0.949749,0.0502513,0;SGB=-0.379885;RPBZ=-1;MQBZ=-1.58114;BQBZ=-1.5;SCBZ=-0.408248;FS=0;MQ0F=0 PL 0,10,123,18,126,126 +17 743 . A C,<*> 0 . DP=7;I16=0,6,0,1,189,6467,10,100,329,18841,29,841,87,1823,25,625;QS=0.949749,0.0502513,0;SGB=-0.379885;RPBZ=-1;MQBZ=-1.58114;BQBZ=-1.5;SCBZ=-0.408248;MQ0F=0 PL 0,10,123,18,126,126 17 744 . T <*> 0 . DP=7;I16=0,7,0,0,259,9751,0,0,358,19682,0,0,110,2410,0,0;QS=1,0;MQ0F=0 PL 0,21,154 17 745 . G <*> 0 . DP=8;I16=1,7,0,0,280,10088,0,0,418,23282,0,0,108,2380,0,0;QS=1,0;MQ0F=0 PL 0,24,182 17 746 . G <*> 0 . DP=8;I16=1,7,0,0,274,9756,0,0,418,23282,0,0,107,2359,0,0;QS=1,0;MQ0F=0 PL 0,24,178 @@ -776,14 +775,14 @@ 17 754 . T <*> 0 . DP=6;I16=1,5,0,0,234,9250,0,0,298,16082,0,0,114,2438,0,0;QS=1,0;MQ0F=0 PL 0,18,172 17 755 . G <*> 0 . DP=6;I16=1,5,0,0,220,8164,0,0,298,16082,0,0,115,2475,0,0;QS=1,0;MQ0F=0 PL 0,18,162 17 756 . G <*> 0 . DP=6;I16=1,5,0,0,200,7040,0,0,298,16082,0,0,116,2518,0,0;QS=1,0;MQ0F=0 PL 0,18,157 -17 757 . A C,<*> 0 . DP=6;I16=1,4,0,1,187,7063,9,81,269,15241,29,841,92,1942,25,625;QS=0.953608,0.0463918,0;SGB=-0.379885;RPBZ=-0.29277;MQBZ=-1.41421;MQSBZ=-0.707107;BQBZ=-1.48522;SCBZ=-0.447214;FS=0;MQ0F=0 PL 0,8,144,15,147,146 +17 757 . A C,<*> 0 . DP=6;I16=1,4,0,1,187,7063,9,81,269,15241,29,841,92,1942,25,625;QS=0.953608,0.0463918,0;SGB=-0.379885;RPBZ=-0.29277;MQBZ=-1.41421;MQSBZ=-0.707107;BQBZ=-1.48522;SCBZ=-0.447214;MQ0F=0 PL 0,8,144,15,147,146 17 758 . A <*> 0 . DP=6;I16=1,5,0,0,205,7219,0,0,298,16082,0,0,118,2622,0,0;QS=1,0;MQ0F=0 PL 0,18,156 -17 759 . A G,<*> 0 . DP=6;I16=1,4,0,1,181,6927,4,16,269,15241,29,841,113,2647,6,36;QS=0.978378,0.0216216,0;SGB=-0.379885;RPBZ=1.46385;MQBZ=-1.41421;MQSBZ=-0.707107;BQBZ=-1.46385;SCBZ=2.23607;FS=0;MQ0F=0 PL 0,10,145,15,148,145 +17 759 . A G,<*> 0 . DP=6;I16=1,4,0,1,181,6927,4,16,269,15241,29,841,113,2647,6,36;QS=0.978378,0.0216216,0;SGB=-0.379885;RPBZ=1.46385;MQBZ=-1.41421;MQSBZ=-0.707107;BQBZ=-1.46385;SCBZ=2.23607;MQ0F=0 PL 0,10,145,15,148,145 17 760 . C <*> 0 . DP=7;I16=1,6,0,0,171,4987,0,0,358,19682,0,0,120,2750,0,0;QS=1,0;MQ0F=0 PL 0,21,130 17 761 . G <*> 0 . DP=7;I16=1,6,0,0,203,7135,0,0,358,19682,0,0,121,2773,0,0;QS=1,0;MQ0F=0 PL 0,21,155 17 762 . G <*> 0 . DP=7;I16=1,6,0,0,249,9197,0,0,358,19682,0,0,122,2802,0,0;QS=1,0;MQ0F=0 PL 0,21,173 -17 763 . C A,<*> 0 . DP=7;I16=1,5,0,1,223,8479,15,225,329,18841,29,841,121,2833,2,4;QS=0.936975,0.0630252,0;SGB=-0.379885;RPBZ=1.5;MQBZ=-1.58114;MQSBZ=-0.632456;BQBZ=-1.51357;SCBZ=2.44949;FS=0;MQ0F=0 PL 0,6,158,18,161,165 -17 764 . A C,<*> 0 . DP=7;I16=1,5,0,1,211,7679,8,64,329,18841,29,841,99,2253,25,625;QS=0.96347,0.0365297,0;SGB=-0.379885;RPBZ=0;MQBZ=-1.58114;MQSBZ=-0.632456;BQBZ=-1.52753;SCBZ=-0.408248;FS=0;MQ0F=0 PL 0,11,156,18,159,158 +17 763 . C A,<*> 0 . DP=7;I16=1,5,0,1,223,8479,15,225,329,18841,29,841,121,2833,2,4;QS=0.936975,0.0630252,0;SGB=-0.379885;RPBZ=1.5;MQBZ=-1.58114;MQSBZ=-0.632456;BQBZ=-1.51357;SCBZ=2.44949;MQ0F=0 PL 0,6,158,18,161,165 +17 764 . A C,<*> 0 . DP=7;I16=1,5,0,1,211,7679,8,64,329,18841,29,841,99,2253,25,625;QS=0.96347,0.0365297,0;SGB=-0.379885;RPBZ=0;MQBZ=-1.58114;MQSBZ=-0.632456;BQBZ=-1.52753;SCBZ=-0.408248;MQ0F=0 PL 0,11,156,18,159,158 17 765 . A <*> 0 . DP=7;I16=1,6,0,0,237,8863,0,0,358,19682,0,0,125,2925,0,0;QS=1,0;MQ0F=0 PL 0,21,170 17 766 . C <*> 0 . DP=6;I16=1,5,0,0,219,8097,0,0,329,18841,0,0,127,2977,0,0;QS=1,0;MQ0F=0 PL 0,18,164 17 767 . A <*> 0 . DP=6;I16=1,5,0,0,187,6311,0,0,329,18841,0,0,129,3033,0,0;QS=1,0;MQ0F=0 PL 0,18,148 @@ -800,7 +799,7 @@ 17 778 . A <*> 0 . DP=6;I16=1,5,0,0,246,10108,0,0,329,18841,0,0,118,2412,0,0;QS=1,0;MQ0F=0 PL 0,18,181 17 779 . G <*> 0 . DP=6;I16=1,5,0,0,219,8227,0,0,329,18841,0,0,116,2352,0,0;QS=1,0;MQ0F=0 PL 0,18,170 17 780 . A <*> 0 . DP=6;I16=1,5,0,0,217,7995,0,0,329,18841,0,0,114,2300,0,0;QS=1,0;MQ0F=0 PL 0,18,166 -17 781 . A C,<*> 0 . DP=6;I16=1,4,0,1,196,7720,10,100,300,18000,29,841,97,2031,15,225;QS=0.951456,0.0485437,0;SGB=-0.379885;RPBZ=0.29277;MQBZ=-2.23607;MQSBZ=-0.447214;BQBZ=-1.48522;SCBZ=0;FS=0;MQ0F=0 PL 0,7,150,15,153,154 +17 781 . A C,<*> 0 . DP=6;I16=1,4,0,1,196,7720,10,100,300,18000,29,841,97,2031,15,225;QS=0.951456,0.0485437,0;SGB=-0.379885;RPBZ=0.29277;MQBZ=-2.23607;MQSBZ=-0.447214;BQBZ=-1.48522;SCBZ=0;MQ0F=0 PL 0,7,150,15,153,154 17 782 . A <*> 0 . DP=6;I16=1,5,0,0,223,8435,0,0,329,18841,0,0,110,2220,0,0;QS=1,0;MQ0F=0 PL 0,18,171 17 783 . A <*> 0 . DP=7;I16=1,6,0,0,248,9014,0,0,389,22441,0,0,108,2192,0,0;QS=1,0;MQ0F=0 PL 0,21,178 17 784 . C <*> 0 . DP=7;I16=1,6,0,0,259,9613,0,0,389,22441,0,0,107,2173,0,0;QS=1,0;MQ0F=0 PL 0,21,178 @@ -847,13 +846,13 @@ 17 825 . A <*> 0 . DP=4;I16=1,3,0,0,132,4446,0,0,240,14400,0,0,80,1750,0,0;QS=1,0;MQ0F=0 PL 0,12,116 17 826 . T <*> 0 . DP=4;I16=1,3,0,0,133,4477,0,0,240,14400,0,0,78,1692,0,0;QS=1,0;MQ0F=0 PL 0,12,117 17 827 . A <*> 0 . DP=4;I16=1,3,0,0,139,4901,0,0,240,14400,0,0,76,1638,0,0;QS=1,0;MQ0F=0 PL 0,12,123 -17 828 . T C,<*> 0 . DP=4;I16=0,0,1,3,0,0,135,4719,0,0,240,14400,0,0,74,1588;QS=0,1,0;VDB=0.292086;SGB=-0.556411;MQSBZ=0;FS=0;MQ0F=0 PL 120,12,0,120,12,120 +17 828 . T C,<*> 0 . DP=4;I16=0,0,1,3,0,0,135,4719,0,0,240,14400,0,0,74,1588;QS=0,1,0;VDB=0.292086;SGB=-0.556411;MQSBZ=0;MQ0F=0 PL 120,12,0,120,12,120 17 829 . T <*> 0 . DP=4;I16=1,3,0,0,149,5635,0,0,240,14400,0,0,72,1542,0,0;QS=1,0;MQ0F=0 PL 0,12,132 17 830 . C <*> 0 . DP=4;I16=1,3,0,0,153,5865,0,0,240,14400,0,0,70,1500,0,0;QS=1,0;MQ0F=0 PL 0,12,134 17 831 . T <*> 0 . DP=4;I16=1,3,0,0,151,5761,0,0,240,14400,0,0,68,1462,0,0;QS=1,0;MQ0F=0 PL 0,12,133 17 832 . C <*> 0 . DP=4;I16=1,3,0,0,139,4905,0,0,240,14400,0,0,66,1428,0,0;QS=1,0;MQ0F=0 PL 0,12,123 17 833 . T <*> 0 . DP=5;I16=1,4,0,0,185,6853,0,0,300,18000,0,0,64,1398,0,0;QS=1,0;MQ0F=0 PL 0,15,149 -17 834 . G A,<*> 0 . DP=5;I16=0,0,1,4,0,0,163,5375,0,0,300,18000,0,0,63,1373;QS=0,1,0;VDB=0.877481;SGB=-0.590765;MQSBZ=0;FS=0;MQ0F=0 PL 133,15,0,133,15,133 +17 834 . G A,<*> 0 . DP=5;I16=0,0,1,4,0,0,163,5375,0,0,300,18000,0,0,63,1373;QS=0,1,0;VDB=0.877481;SGB=-0.590765;MQSBZ=0;MQ0F=0 PL 133,15,0,133,15,133 17 835 . T <*> 0 . DP=5;I16=1,4,0,0,164,5828,0,0,300,18000,0,0,62,1354,0,0;QS=1,0;MQ0F=0 PL 0,15,138 17 836 . G <*> 0 . DP=4;I16=1,3,0,0,149,5551,0,0,240,14400,0,0,61,1291,0,0;QS=1,0;MQ0F=0 PL 0,12,131 17 837 . T <*> 0 . DP=4;I16=1,3,0,0,161,6499,0,0,240,14400,0,0,60,1234,0,0;QS=1,0;MQ0F=0 PL 0,12,143 @@ -1113,7 +1112,7 @@ 17 1091 . C <*> 0 . DP=9;I16=9,0,0,0,333,12443,0,0,540,32400,0,0,153,3305,0,0;QS=1,0;MQ0F=0 PL 0,27,177 17 1092 . T <*> 0 . DP=9;I16=9,0,0,0,378,15912,0,0,540,32400,0,0,156,3404,0,0;QS=1,0;MQ0F=0 PL 0,27,198 17 1093 . G <*> 0 . DP=9;I16=9,0,0,0,348,13536,0,0,540,32400,0,0,159,3513,0,0;QS=1,0;MQ0F=0 PL 0,27,184 -17 1094 . G T,<*> 0 . DP=9;I16=8,0,1,0,326,13362,12,144,480,28800,60,3600,155,3583,7,49;QS=0.964497,0.035503,0;SGB=-0.379885;RPBZ=-1.55569;MQBZ=0;BQBZ=-1.56227;SCBZ=0;FS=0;MQ0F=0 PL 0,14,177,24,180,181 +17 1094 . G T,<*> 0 . DP=9;I16=8,0,1,0,326,13362,12,144,480,28800,60,3600,155,3583,7,49;QS=0.964497,0.035503,0;SGB=-0.379885;RPBZ=-1.55569;MQBZ=0;BQBZ=-1.56227;SCBZ=0;MQ0F=0 PL 0,14,177,24,180,181 17 1095 . A <*> 0 . DP=8;I16=8,0,0,0,310,12292,0,0,480,28800,0,0,165,3709,0,0;QS=1,0;MQ0F=0 PL 0,24,178 17 1096 . T <*> 0 . DP=9;I16=9,0,0,0,331,12443,0,0,540,32400,0,0,168,3792,0,0;QS=1,0;MQ0F=0 PL 0,27,178 17 1097 . A <*> 0 . DP=9;I16=9,0,0,0,330,12450,0,0,540,32400,0,0,172,3882,0,0;QS=1,0;MQ0F=0 PL 0,27,177 @@ -1148,7 +1147,7 @@ 17 1126 . C <*> 0 . DP=13;I16=10,2,0,0,507,21851,0,0,720,43200,0,0,225,4893,0,0;QS=1,0;MQ0F=0 PL 0,36,255 17 1127 . T <*> 0 . DP=13;I16=10,2,0,0,513,22447,0,0,720,43200,0,0,227,4945,0,0;QS=1,0;MQ0F=0 PL 0,36,255 17 1128 . G <*> 0 . DP=13;I16=10,2,0,0,501,21369,0,0,720,43200,0,0,229,5009,0,0;QS=1,0;MQ0F=0 PL 0,36,255 -17 1129 . A G,<*> 0 . DP=13;I16=10,1,0,1,463,19969,32,1024,660,39600,60,3600,205,4409,25,625;QS=0.935354,0.0646465,0;SGB=-0.379885;RPBZ=-0.724207;MQBZ=0;MQSBZ=0;BQBZ=-1.31512;SCBZ=0;FS=0;MQ0F=0 PL 0,4,230,33,233,251 +17 1129 . A G,<*> 0 . DP=13;I16=10,1,0,1,463,19969,32,1024,660,39600,60,3600,205,4409,25,625;QS=0.935354,0.0646465,0;SGB=-0.379885;RPBZ=-0.724207;MQBZ=0;MQSBZ=0;BQBZ=-1.31512;SCBZ=0;MQ0F=0 PL 0,4,230,33,233,251 17 1130 . A <*> 0 . DP=13;I16=10,2,0,0,506,21796,0,0,720,43200,0,0,231,5069,0,0;QS=1,0;MQ0F=0 PL 0,36,255 17 1131 . A <*> 0 . DP=13;I16=10,2,0,0,502,21496,0,0,720,43200,0,0,232,5114,0,0;QS=1,0;MQ0F=0 PL 0,36,255 17 1132 . T <*> 0 . DP=13;I16=10,2,0,0,499,21159,0,0,720,43200,0,0,233,5169,0,0;QS=1,0;MQ0F=0 PL 0,36,255 @@ -1243,7 +1242,7 @@ 17 1221 . A <*> 0 . DP=5;I16=2,3,0,0,186,7098,0,0,300,18000,0,0,100,2500,0,0;QS=1,0;MQ0F=0 PL 0,15,163 17 1222 . T <*> 0 . DP=4;I16=1,3,0,0,161,6531,0,0,240,14400,0,0,100,2500,0,0;QS=1,0;MQ0F=0 PL 0,12,142 17 1223 . T <*> 0 . DP=4;I16=1,3,0,0,136,5460,0,0,240,14400,0,0,100,2500,0,0;QS=1,0;MQ0F=0 PL 0,12,124 -17 1224 . C A,<*> 0 . DP=4;I16=1,2,0,1,119,4723,8,64,180,10800,60,3600,75,1875,25,625;QS=0.937008,0.0629921,0;SGB=-0.379885;RPBZ=1.41421;MQBZ=0;MQSBZ=0;BQBZ=-1.41421;SCBZ=0;FS=0;MQ0F=0 PL 0,3,103,9,106,106 +17 1224 . C A,<*> 0 . DP=4;I16=1,2,0,1,119,4723,8,64,180,10800,60,3600,75,1875,25,625;QS=0.937008,0.0629921,0;SGB=-0.379885;RPBZ=1.41421;MQBZ=0;MQSBZ=0;BQBZ=-1.41421;SCBZ=0;MQ0F=0 PL 0,3,103,9,106,106 17 1225 . A <*> 0 . DP=4;I16=1,3,0,0,162,6572,0,0,240,14400,0,0,100,2500,0,0;QS=1,0;MQ0F=0 PL 0,12,142 17 1226 . A <*> 0 . DP=4;I16=1,3,0,0,168,7058,0,0,240,14400,0,0,100,2500,0,0;QS=1,0;MQ0F=0 PL 0,12,147 17 1227 . A <*> 0 . DP=4;I16=1,3,0,0,167,6977,0,0,240,14400,0,0,100,2500,0,0;QS=1,0;MQ0F=0 PL 0,12,146 @@ -1386,10 +1385,10 @@ 17 1364 . G <*> 0 . DP=9;I16=1,8,0,0,331,12219,0,0,540,32400,0,0,196,4708,0,0;QS=1,0;MQ0F=0 PL 0,27,200 17 1365 . G <*> 0 . DP=9;I16=1,8,0,0,336,12570,0,0,540,32400,0,0,196,4680,0,0;QS=1,0;MQ0F=0 PL 0,27,202 17 1366 . G <*> 0 . DP=9;I16=1,8,0,0,332,12268,0,0,540,32400,0,0,196,4656,0,0;QS=1,0;MQ0F=0 PL 0,27,199 -17 1367 . G C,<*> 0 . DP=9;I16=1,7,0,1,296,10982,27,729,480,28800,60,3600,181,4411,15,225;QS=0.916409,0.0835913,0;SGB=-0.379885;RPBZ=1.55569;MQBZ=0;MQSBZ=0;BQBZ=-1.58251;SCBZ=0;FS=0;MQ0F=0 PL 0,0,171,24,174,189 +17 1367 . G C,<*> 0 . DP=9;I16=1,7,0,1,296,10982,27,729,480,28800,60,3600,181,4411,15,225;QS=0.916409,0.0835913,0;SGB=-0.379885;RPBZ=1.55569;MQBZ=0;MQSBZ=0;BQBZ=-1.58251;SCBZ=0;MQ0F=0 PL 0,0,171,24,174,189 17 1368 . A <*> 0 . DP=9;I16=1,8,0,0,320,11562,0,0,540,32400,0,0,196,4620,0,0;QS=1,0;MQ0F=0 PL 0,27,197 17 1369 . T <*> 0 . DP=9;I16=1,8,0,0,309,10987,0,0,540,32400,0,0,196,4608,0,0;QS=1,0;MQ0F=0 PL 0,27,194 -17 1370 . T C,<*> 0 . DP=10;I16=1,8,0,1,347,13421,2,4,540,32400,60,3600,171,3975,25,625;QS=0.988604,0.011396,0;SGB=-0.379885;RPBZ=-0.873038;MQBZ=0;MQSBZ=0;BQBZ=-1.59599;SCBZ=0;FS=0;MQ0F=0 PL 0,20,208,27,211,208 +17 1370 . T C,<*> 0 . DP=10;I16=1,8,0,1,347,13421,2,4,540,32400,60,3600,171,3975,25,625;QS=0.988604,0.011396,0;SGB=-0.379885;RPBZ=-0.873038;MQBZ=0;MQSBZ=0;BQBZ=-1.59599;SCBZ=0;MQ0F=0 PL 0,20,208,27,211,208 17 1371 . C <*> 0 . DP=10;I16=1,9,0,0,338,11742,0,0,600,36000,0,0,197,4597,0,0;QS=1,0;MQ0F=0 PL 0,30,196 17 1372 . C <*> 0 . DP=10;I16=1,9,0,0,343,12099,0,0,600,36000,0,0,198,4600,0,0;QS=1,0;MQ0F=0 PL 0,30,200 17 1373 . C <*> 0 . DP=10;I16=1,9,0,0,332,11388,0,0,600,36000,0,0,198,4560,0,0;QS=1,0;MQ0F=0 PL 0,30,195 @@ -1404,7 +1403,7 @@ 17 1382 . G <*> 0 . DP=12;I16=2,10,0,0,425,15501,0,0,720,43200,0,0,197,4421,0,0;QS=1,0;MQ0F=0 PL 0,36,243 17 1383 . C <*> 0 . DP=11;I16=2,9,0,0,398,14630,0,0,660,39600,0,0,199,4423,0,0;QS=1,0;MQ0F=0 PL 0,33,241 17 1384 . C <*> 0 . DP=11;I16=2,9,0,0,392,14362,0,0,660,39600,0,0,201,4437,0,0;QS=1,0;MQ0F=0 PL 0,33,239 -17 1385 . A C,<*> 0 . DP=11;I16=2,8,0,1,369,13727,2,4,600,36000,60,3600,179,3887,24,576;QS=0.989276,0.0107239,0;SGB=-0.379885;RPBZ=-0.633898;MQBZ=0;MQSBZ=0;BQBZ=-1.59571;SCBZ=0;FS=0;MQ0F=0 PL 0,23,229,30,232,229 +17 1385 . A C,<*> 0 . DP=11;I16=2,8,0,1,369,13727,2,4,600,36000,60,3600,179,3887,24,576;QS=0.989276,0.0107239,0;SGB=-0.379885;RPBZ=-0.633898;MQBZ=0;MQSBZ=0;BQBZ=-1.59571;SCBZ=0;MQ0F=0 PL 0,23,229,30,232,229 17 1386 . C <*> 0 . DP=11;I16=2,9,0,0,421,16205,0,0,660,39600,0,0,205,4501,0,0;QS=1,0;MQ0F=0 PL 0,33,254 17 1387 . C <*> 0 . DP=11;I16=2,9,0,0,424,16430,0,0,660,39600,0,0,206,4500,0,0;QS=1,0;MQ0F=0 PL 0,33,252 17 1388 . C <*> 0 . DP=11;I16=2,9,0,0,355,11631,0,0,660,39600,0,0,207,4509,0,0;QS=1,0;MQ0F=0 PL 0,33,211 @@ -1478,10 +1477,10 @@ 17 1456 . T <*> 0 . DP=5;I16=2,3,0,0,197,7771,0,0,300,18000,0,0,80,1592,0,0;QS=1,0;MQ0F=0 PL 0,15,170 17 1457 . G <*> 0 . DP=5;I16=2,3,0,0,189,7193,0,0,300,18000,0,0,77,1481,0,0;QS=1,0;MQ0F=0 PL 0,15,164 17 1458 . T <*> 0 . DP=5;I16=2,3,0,0,190,7292,0,0,300,18000,0,0,74,1380,0,0;QS=1,0;MQ0F=0 PL 0,15,165 -17 1459 . C A,<*> 0 . DP=5;I16=2,2,0,1,164,6734,24,576,240,14400,60,3600,69,1285,2,4;QS=0.87234,0.12766,0;SGB=-0.379885;RPBZ=1.41421;MQBZ=0;MQSBZ=0;BQBZ=-1.41421;SCBZ=-0.5;FS=0;MQ0F=0 PL 9,0,135,21,138,152 +17 1459 . C A,<*> 0 . DP=5;I16=2,2,0,1,164,6734,24,576,240,14400,60,3600,69,1285,2,4;QS=0.87234,0.12766,0;SGB=-0.379885;RPBZ=1.41421;MQBZ=0;MQSBZ=0;BQBZ=-1.41421;SCBZ=-0.5;MQ0F=0 PL 9,0,135,21,138,152 17 1460 . T <*> 0 . DP=5;I16=2,3,0,0,195,7679,0,0,300,18000,0,0,68,1208,0,0;QS=1,0;MQ0F=0 PL 0,15,170 17 1461 . G <*> 0 . DP=5;I16=2,3,0,0,173,6171,0,0,300,18000,0,0,65,1137,0,0;QS=1,0;MQ0F=0 PL 0,15,152 -17 1462 . C G,<*> 0 . DP=4;I16=1,2,1,0,119,4745,5,25,180,10800,60,3600,46,786,17,289;QS=0.959677,0.0403226,0;SGB=-0.379885;RPBZ=-1.34164;MQBZ=0;MQSBZ=0;BQBZ=-1.34164;SCBZ=-0.57735;FS=0;MQ0F=0 PL 0,5,106,9,109,107 +17 1462 . C G,<*> 0 . DP=4;I16=1,2,1,0,119,4745,5,25,180,10800,60,3600,46,786,17,289;QS=0.959677,0.0403226,0;SGB=-0.379885;RPBZ=-1.34164;MQBZ=0;MQSBZ=0;BQBZ=-1.34164;SCBZ=-0.57735;MQ0F=0 PL 0,5,106,9,109,107 17 1463 . T <*> 0 . DP=4;I16=2,2,0,0,151,5805,0,0,240,14400,0,0,61,1021,0,0;QS=1,0;MQ0F=0 PL 0,12,139 17 1464 . G <*> 0 . DP=5;I16=2,3,0,0,165,5535,0,0,300,18000,0,0,59,975,0,0;QS=1,0;MQ0F=0 PL 0,15,144 17 1465 . T <*> 0 . DP=5;I16=2,3,0,0,191,7315,0,0,300,18000,0,0,58,938,0,0;QS=1,0;MQ0F=0 PL 0,15,166 @@ -1635,7 +1634,7 @@ 17 1613 . C <*> 0 . DP=2;I16=1,1,0,0,63,2129,0,0,120,7200,0,0,48,1154,0,0;QS=1,0;MQ0F=0 PL 0,6,63 17 1614 . A <*> 0 . DP=2;I16=1,1,0,0,69,2465,0,0,120,7200,0,0,49,1201,0,0;QS=1,0;MQ0F=0 PL 0,6,69 17 1615 . C <*> 0 . DP=2;I16=1,1,0,0,51,1445,0,0,120,7200,0,0,50,1250,0,0;QS=1,0;MQ0F=0 PL 0,6,51 -17 1616 . T C,<*> 0 . DP=2;I16=1,0,0,1,42,1764,1,1,60,3600,60,3600,25,625,25,625;QS=0.913043,0.0869565,0;SGB=-0.379885;RPBZ=-1;MQBZ=0;MQSBZ=0;BQBZ=-1;SCBZ=0;FS=0;MQ0F=0 PL 0,1,37,3,40,39 +17 1616 . T C,<*> 0 . DP=2;I16=1,0,0,1,42,1764,1,1,60,3600,60,3600,25,625,25,625;QS=0.913043,0.0869565,0;SGB=-0.379885;RPBZ=-1;MQBZ=0;MQSBZ=0;BQBZ=-1;SCBZ=0;MQ0F=0 PL 0,1,37,3,40,39 17 1617 . C <*> 0 . DP=2;I16=1,1,0,0,53,1885,0,0,120,7200,0,0,50,1250,0,0;QS=1,0;MQ0F=0 PL 0,6,53 17 1618 . A <*> 0 . DP=2;I16=1,1,0,0,81,3281,0,0,120,7200,0,0,49,1201,0,0;QS=1,0;MQ0F=0 PL 0,6,81 17 1619 . G <*> 0 . DP=2;I16=1,1,0,0,67,2269,0,0,120,7200,0,0,48,1154,0,0;QS=1,0;MQ0F=0 PL 0,6,67 @@ -1684,7 +1683,7 @@ 17 1662 . C <*> 0 . DP=4;I16=1,3,0,0,123,3901,0,0,209,11641,0,0,86,1996,0,0;QS=1,0;MQ0F=0 PL 0,12,100 17 1663 . C <*> 0 . DP=4;I16=1,3,0,0,124,3894,0,0,209,11641,0,0,87,2019,0,0;QS=1,0;MQ0F=0 PL 0,12,101 17 1664 . A <*> 0 . DP=4;I16=1,3,0,0,130,4468,0,0,209,11641,0,0,88,2044,0,0;QS=1,0;MQ0F=0 PL 0,12,109 -17 1665 . T C,<*> 0 . DP=4;I16=0,2,1,1,68,2330,58,1924,120,7200,89,4441,50,1250,39,821;QS=0.591304,0.408696,0;VDB=0.1;SGB=-0.453602;RPBZ=-1.54919;MQBZ=-1;MQSBZ=1.73205;BQBZ=0;SCBZ=0.408248;FS=0;MQ0F=0 PL 35,0,51,41,57,90 +17 1665 . T C,<*> 0 . DP=4;I16=0,2,1,1,68,2330,58,1924,120,7200,89,4441,50,1250,39,821;QS=0.591304,0.408696,0;VDB=0.1;SGB=-0.453602;RPBZ=-1.54919;MQBZ=-1;MQSBZ=1.73205;BQBZ=0;SCBZ=0.408248;MQ0F=0 PL 35,0,51,41,57,90 17 1666 . G <*> 0 . DP=4;I16=1,3,0,0,129,4165,0,0,209,11641,0,0,88,2002,0,0;QS=1,0;MQ0F=0 PL 0,12,111 17 1667 . G <*> 0 . DP=4;I16=1,3,0,0,144,5304,0,0,209,11641,0,0,87,1939,0,0;QS=1,0;MQ0F=0 PL 0,12,115 17 1668 . A <*> 0 . DP=4;I16=1,3,0,0,153,5865,0,0,209,11641,0,0,86,1882,0,0;QS=1,0;MQ0F=0 PL 0,12,124 @@ -1698,7 +1697,7 @@ 17 1676 . G <*> 0 . DP=4;I16=1,3,0,0,107,3465,0,0,209,11641,0,0,78,1642,0,0;QS=1,0;MQ0F=0 PL 0,12,95 17 1677 . C <*> 0 . DP=4;I16=1,3,0,0,93,3133,0,0,209,11641,0,0,76,1588,0,0;QS=1,0;MQ0F=0 PL 0,12,74 17 1678 . C <*> 0 . DP=4;I16=1,3,0,0,110,3654,0,0,209,11641,0,0,74,1538,0,0;QS=1,0;MQ0F=0 PL 0,12,87 -17 1679 . A G,<*> 0 . DP=4;I16=1,2,0,1,125,5211,6,36,149,8041,60,3600,47,867,25,625;QS=0.94958,0.0504202,0;SGB=-0.379885;RPBZ=-0.447214;MQBZ=0.57735;MQSBZ=1.73205;BQBZ=-1.41421;SCBZ=1.41421;FS=0;MQ0F=0 PL 0,4,99,9,102,101 +17 1679 . A G,<*> 0 . DP=4;I16=1,2,0,1,125,5211,6,36,149,8041,60,3600,47,867,25,625;QS=0.94958,0.0504202,0;SGB=-0.379885;RPBZ=-0.447214;MQBZ=0.57735;MQSBZ=1.73205;BQBZ=-1.41421;SCBZ=1.41421;MQ0F=0 PL 0,4,99,9,102,101 17 1680 . G <*> 0 . DP=4;I16=1,3,0,0,130,4382,0,0,209,11641,0,0,70,1450,0,0;QS=1,0;MQ0F=0 PL 0,12,104 17 1681 . C <*> 0 . DP=4;I16=1,3,0,0,95,2849,0,0,209,11641,0,0,68,1412,0,0;QS=1,0;MQ0F=0 PL 0,12,74 17 1682 . G <*> 0 . DP=4;I16=1,3,0,0,111,3081,0,0,209,11641,0,0,66,1378,0,0;QS=1,0;MQ0F=0 PL 0,12,98 @@ -1708,7 +1707,7 @@ 17 1686 . C <*> 0 . DP=4;I16=1,3,0,0,127,4127,0,0,209,11641,0,0,58,1282,0,0;QS=1,0;MQ0F=0 PL 0,12,103 17 1687 . C <*> 0 . DP=4;I16=1,3,0,0,129,4325,0,0,209,11641,0,0,56,1268,0,0;QS=1,0;MQ0F=0 PL 0,12,106 17 1688 . C <*> 0 . DP=4;I16=1,3,0,0,147,5445,0,0,209,11641,0,0,54,1258,0,0;QS=1,0;MQ0F=0 PL 0,12,120 -17 1689 . T A,<*> 0 . DP=4;I16=1,2,0,1,111,4185,33,1089,149,8041,60,3600,27,627,25,625;QS=0.744186,0.255814,0;SGB=-0.379885;RPBZ=-0.447214;MQBZ=0.57735;MQSBZ=1.73205;BQBZ=-0.447214;SCBZ=1;FS=0;MQ0F=0 PL 21,0,79,30,82,106 +17 1689 . T A,<*> 0 . DP=4;I16=1,2,0,1,111,4185,33,1089,149,8041,60,3600,27,627,25,625;QS=0.744186,0.255814,0;SGB=-0.379885;RPBZ=-0.447214;MQBZ=0.57735;MQSBZ=1.73205;BQBZ=-0.447214;SCBZ=1;MQ0F=0 PL 21,0,79,30,82,106 17 1690 . C <*> 0 . DP=4;I16=1,3,0,0,120,3996,0,0,209,11641,0,0,50,1250,0,0;QS=1,0;MQ0F=0 PL 0,12,95 17 1691 . T <*> 0 . DP=2;I16=1,1,0,0,71,2633,0,0,89,4441,0,0,50,1250,0,0;QS=1,0;MQ0F=0 PL 0,6,57 17 1692 . G <*> 0 . DP=2;I16=1,1,0,0,73,2705,0,0,89,4441,0,0,50,1250,0,0;QS=1,0;MQ0F=0 PL 0,6,61 @@ -1755,7 +1754,7 @@ 17 1733 . C <*> 0 . DP=5;I16=4,1,0,0,170,5934,0,0,269,15241,0,0,99,2235,0,0;QS=1,0;MQ0F=0 PL 0,15,136 17 1734 . C <*> 0 . DP=5;I16=4,1,0,0,176,6536,0,0,269,15241,0,0,99,2213,0,0;QS=1,0;MQ0F=0 PL 0,15,141 17 1735 . T <*> 0 . DP=5;I16=4,1,0,0,193,7605,0,0,269,15241,0,0,99,2195,0,0;QS=1,0;MQ0F=0 PL 0,15,148 -17 1736 . G T,<*> 0 . DP=5;I16=3,1,1,0,142,5070,6,36,209,11641,60,3600,74,1556,25,625;QS=0.957143,0.0428571,0;SGB=-0.379885;RPBZ=-0.725476;MQBZ=0.5;MQSBZ=0.5;BQBZ=-1.41421;SCBZ=2;FS=0;MQ0F=0 PL 0,7,111,12,114,112 +17 1736 . G T,<*> 0 . DP=5;I16=3,1,1,0,142,5070,6,36,209,11641,60,3600,74,1556,25,625;QS=0.957143,0.0428571,0;SGB=-0.379885;RPBZ=-0.725476;MQBZ=0.5;MQSBZ=0.5;BQBZ=-1.41421;SCBZ=2;MQ0F=0 PL 0,7,111,12,114,112 17 1737 . A <*> 0 . DP=5;I16=4,1,0,0,168,6138,0,0,269,15241,0,0,99,2171,0,0;QS=1,0;MQ0F=0 PL 0,15,131 17 1738 . C <*> 0 . DP=5;I16=4,1,0,0,164,5714,0,0,269,15241,0,0,99,2165,0,0;QS=1,0;MQ0F=0 PL 0,15,130 17 1739 . C <*> 0 . DP=5;I16=4,1,0,0,172,6730,0,0,269,15241,0,0,99,2163,0,0;QS=1,0;MQ0F=0 PL 0,15,138 @@ -1888,7 +1887,7 @@ 17 1866 . G <*> 0 . DP=1;I16=0,1,0,0,36,1296,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0 PL 0,3,36 17 1867 . C <*> 0 . DP=1;I16=0,1,0,0,38,1444,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0 PL 0,3,38 17 1868 . C <*> 0 . DP=1;I16=0,1,0,0,41,1681,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0 PL 0,3,41 -17 1869 . A T,<*> 0 . DP=1;I16=0,0,0,1,0,0,42,1764,0,0,60,3600,0,0,25,625;QS=0,1,0;SGB=-0.379885;FS=0;MQ0F=0 PL 42,3,0,42,3,42 +17 1869 . A T,<*> 0 . DP=1;I16=0,0,0,1,0,0,42,1764,0,0,60,3600,0,0,25,625;QS=0,1,0;SGB=-0.379885;MQ0F=0 PL 42,3,0,42,3,42 17 1870 . C <*> 0 . DP=1;I16=0,1,0,0,36,1296,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0 PL 0,3,36 17 1871 . C <*> 0 . DP=1;I16=0,1,0,0,29,841,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0 PL 0,3,29 17 1872 . G <*> 0 . DP=1;I16=0,1,0,0,43,1849,0,0,60,3600,0,0,25,625,0,0;QS=1,0;MQ0F=0 PL 0,3,43 @@ -1916,7 +1915,7 @@ 17 1894 . G <*> 0 . DP=2;I16=1,1,0,0,75,2817,0,0,120,7200,0,0,6,26,0,0;QS=1,0;MQ0F=0 PL 0,6,75 17 1895 . C <*> 0 . DP=2;I16=1,1,0,0,73,2665,0,0,120,7200,0,0,6,20,0,0;QS=1,0;MQ0F=0 PL 0,6,73 17 1896 . C <*> 0 . DP=2;I16=1,1,0,0,72,2600,0,0,120,7200,0,0,6,18,0,0;QS=1,0;MQ0F=0 PL 0,6,72 -17 1897 . G A,<*> 0 . DP=2;I16=1,0,0,1,27,729,37,1369,60,3600,60,3600,4,16,2,4;QS=0.421875,0.578125,0;SGB=-0.379885;RPBZ=1;MQBZ=0;MQSBZ=0;BQBZ=1;SCBZ=0;FS=0;MQ0F=0 PL 31,0,21,34,24,55 +17 1897 . G A,<*> 0 . DP=2;I16=1,0,0,1,27,729,37,1369,60,3600,60,3600,4,16,2,4;QS=0.421875,0.578125,0;SGB=-0.379885;RPBZ=1;MQBZ=0;MQSBZ=0;BQBZ=1;SCBZ=0;MQ0F=0 PL 31,0,21,34,24,55 17 1898 . T <*> 0 . DP=3;I16=2,1,0,0,106,3790,0,0,180,10800,0,0,6,26,0,0;QS=1,0;MQ0F=0 PL 0,9,100 17 1899 . G <*> 0 . DP=3;I16=2,1,0,0,100,3334,0,0,180,10800,0,0,7,37,0,0;QS=1,0;MQ0F=0 PL 0,9,94 17 1900 . T <*> 0 . DP=2;I16=2,0,0,0,76,2890,0,0,120,7200,0,0,9,53,0,0;QS=1,0;MQ0F=0 PL 0,6,69 @@ -1958,7 +1957,7 @@ 17 1936 . C <*> 0 . DP=5;I16=2,3,0,0,181,6735,0,0,269,15241,0,0,93,2051,0,0;QS=1,0;MQ0F=0 PL 0,15,159 17 1937 . T <*> 0 . DP=5;I16=2,3,0,0,195,7741,0,0,269,15241,0,0,96,2140,0,0;QS=1,0;MQ0F=0 PL 0,15,170 17 1938 . G <*> 0 . DP=5;I16=2,3,0,0,176,6536,0,0,269,15241,0,0,99,2235,0,0;QS=1,0;MQ0F=0 PL 0,15,155 -17 1939 . T C,<*> 0 . DP=5;I16=2,2,0,1,158,6250,3,9,240,14400,29,841,82,1924,19,361;QS=0.975309,0.0246914,0;SGB=-0.379885;RPBZ=-0.707107;MQBZ=-2;MQSBZ=-0.816497;BQBZ=-1.49071;SCBZ=-0.5;FS=0;MQ0F=0 PL 0,8,138,12,141,138 +17 1939 . T C,<*> 0 . DP=5;I16=2,2,0,1,158,6250,3,9,240,14400,29,841,82,1924,19,361;QS=0.975309,0.0246914,0;SGB=-0.379885;RPBZ=-0.707107;MQBZ=-2;MQSBZ=-0.816497;BQBZ=-1.49071;SCBZ=-0.5;MQ0F=0 PL 0,8,138,12,141,138 17 1940 . G <*> 0 . DP=5;I16=2,3,0,0,177,6449,0,0,269,15241,0,0,103,2339,0,0;QS=1,0;MQ0F=0 PL 0,15,155 17 1941 . G <*> 0 . DP=5;I16=2,3,0,0,180,6620,0,0,269,15241,0,0,105,2397,0,0;QS=1,0;MQ0F=0 PL 0,15,156 17 1942 . C <*> 0 . DP=5;I16=2,3,0,0,161,5973,0,0,269,15241,0,0,107,2459,0,0;QS=1,0;MQ0F=0 PL 0,15,144 @@ -1967,16 +1966,16 @@ 17 1945 . T <*> 0 . DP=5;I16=2,3,0,0,200,8062,0,0,269,15241,0,0,113,2669,0,0;QS=1,0;MQ0F=0 PL 0,15,171 17 1946 . G <*> 0 . DP=5;I16=2,3,0,0,188,7132,0,0,269,15241,0,0,114,2696,0,0;QS=1,0;MQ0F=0 PL 0,15,162 17 1947 . A <*> 0 . DP=5;I16=2,3,0,0,181,6939,0,0,269,15241,0,0,115,2725,0,0;QS=1,0;MQ0F=0 PL 0,15,160 -17 1948 . G C,<*> 0 . DP=5;I16=2,2,0,1,150,5708,16,256,240,14400,29,841,91,2131,25,625;QS=0.903614,0.0963855,0;SGB=-0.379885;RPBZ=-0.707107;MQBZ=-2;MQSBZ=-0.816497;BQBZ=-1.41421;SCBZ=-0.5;FS=0;MQ0F=0 PL 1,0,123,13,126,132 +17 1948 . G C,<*> 0 . DP=5;I16=2,2,0,1,150,5708,16,256,240,14400,29,841,91,2131,25,625;QS=0.903614,0.0963855,0;SGB=-0.379885;RPBZ=-0.707107;MQBZ=-2;MQSBZ=-0.816497;BQBZ=-1.41421;SCBZ=-0.5;MQ0F=0 PL 1,0,123,13,126,132 17 1949 . A <*> 0 . DP=5;I16=2,3,0,0,181,6599,0,0,269,15241,0,0,117,2789,0,0;QS=1,0;MQ0F=0 PL 0,15,155 17 1950 . A <*> 0 . DP=6;I16=2,4,0,0,222,8392,0,0,329,18841,0,0,118,2824,0,0;QS=1,0;MQ0F=0 PL 0,18,178 17 1951 . G <*> 0 . DP=6;I16=2,4,0,0,225,8533,0,0,329,18841,0,0,120,2862,0,0;QS=1,0;MQ0F=0 PL 0,18,181 17 1952 . A <*> 0 . DP=6;I16=2,4,0,0,219,8221,0,0,329,18841,0,0,122,2904,0,0;QS=1,0;MQ0F=0 PL 0,18,182 17 1953 . A <*> 0 . DP=6;I16=2,4,0,0,201,7161,0,0,329,18841,0,0,124,2950,0,0;QS=1,0;MQ0F=0 PL 0,18,168 -17 1954 . A C,<*> 0 . DP=6;I16=2,3,0,1,166,5942,18,324,300,18000,29,841,101,2375,25,625;QS=0.902174,0.0978261,0;SGB=-0.379885;RPBZ=-0.29277;MQBZ=-2.23607;MQSBZ=-0.707107;BQBZ=-0.87831;SCBZ=-0.447214;FS=0;MQ0F=0 PL 0,0,130,15,133,141 +17 1954 . A C,<*> 0 . DP=6;I16=2,3,0,1,166,5942,18,324,300,18000,29,841,101,2375,25,625;QS=0.902174,0.0978261,0;SGB=-0.379885;RPBZ=-0.29277;MQBZ=-2.23607;MQSBZ=-0.707107;BQBZ=-0.87831;SCBZ=-0.447214;MQ0F=0 PL 0,0,130,15,133,141 17 1955 . C <*> 0 . DP=6;I16=2,4,0,0,200,7332,0,0,329,18841,0,0,128,3054,0,0;QS=1,0;MQ0F=0 PL 0,18,168 17 1956 . C <*> 0 . DP=6;I16=2,4,0,0,191,7215,0,0,329,18841,0,0,130,3112,0,0;QS=1,0;MQ0F=0 PL 0,18,164 -17 1957 . C G,<*> 0 . DP=6;I16=2,3,0,1,192,7426,7,49,300,18000,29,841,107,2549,25,625;QS=0.964824,0.0351759,0;SGB=-0.379885;RPBZ=-0.29277;MQBZ=-2.23607;MQSBZ=-0.707107;BQBZ=-1.48522;SCBZ=-0.447214;FS=0;MQ0F=0 PL 0,9,159,15,162,161 +17 1957 . C G,<*> 0 . DP=6;I16=2,3,0,1,192,7426,7,49,300,18000,29,841,107,2549,25,625;QS=0.964824,0.0351759,0;SGB=-0.379885;RPBZ=-0.29277;MQBZ=-2.23607;MQSBZ=-0.707107;BQBZ=-1.48522;SCBZ=-0.447214;MQ0F=0 PL 0,9,159,15,162,161 17 1958 . C <*> 0 . DP=6;I16=2,4,0,0,234,9220,0,0,329,18841,0,0,133,3189,0,0;QS=1,0;MQ0F=0 PL 0,18,190 17 1959 . T <*> 0 . DP=6;I16=2,4,0,0,233,9255,0,0,329,18841,0,0,134,3206,0,0;QS=1,0;MQ0F=0 PL 0,18,193 17 1960 . T <*> 0 . DP=6;I16=2,4,0,0,227,8703,0,0,329,18841,0,0,135,3225,0,0;QS=1,0;MQ0F=0 PL 0,18,186 @@ -2005,11 +2004,11 @@ 17 1983 . G <*> 0 . DP=9;I16=4,5,0,0,337,12781,0,0,509,29641,0,0,140,2974,0,0;QS=1,0;MQ0F=0 PL 0,27,249 17 1984 . A <*> 0 . DP=9;I16=4,5,0,0,355,14231,0,0,509,29641,0,0,141,2959,0,0;QS=1,0;MQ0F=0 PL 0,27,255 17 1985 . G <*> 0 . DP=9;I16=4,5,0,0,307,10921,0,0,509,29641,0,0,142,2954,0,0;QS=1,0;MQ0F=0 PL 0,27,231 -17 1986 . A T,<*> 0 . DP=9;I16=4,4,0,1,287,10695,12,144,480,28800,29,841,118,2334,25,625;QS=0.959866,0.0401338,0;SGB=-0.379885;RPBZ=0.387298;MQBZ=-2.82843;MQSBZ=-0.894427;BQBZ=-1.55569;SCBZ=-0.53033;FS=0;MQ0F=0 PL 0,14,213,24,216,217 +17 1986 . A T,<*> 0 . DP=9;I16=4,4,0,1,287,10695,12,144,480,28800,29,841,118,2334,25,625;QS=0.959866,0.0401338,0;SGB=-0.379885;RPBZ=0.387298;MQBZ=-2.82843;MQSBZ=-0.894427;BQBZ=-1.55569;SCBZ=-0.53033;MQ0F=0 PL 0,14,213,24,216,217 17 1987 . A <*> 0 . DP=9;I16=4,5,0,0,333,12731,0,0,509,29641,0,0,144,2974,0,0;QS=1,0;MQ0F=0 PL 0,27,247 17 1988 . G <*> 0 . DP=9;I16=4,5,0,0,324,12106,0,0,509,29641,0,0,145,2999,0,0;QS=1,0;MQ0F=0 PL 0,27,239 17 1989 . G <*> 0 . DP=9;I16=4,5,0,0,322,12030,0,0,509,29641,0,0,145,2985,0,0;QS=1,0;MQ0F=0 PL 0,27,237 -17 1990 . G T,<*> 0 . DP=9;I16=4,4,0,1,282,10212,33,1089,480,28800,29,841,120,2358,25,625;QS=0.906752,0.0932476,0;SGB=-0.379885;RPBZ=0.387298;MQBZ=-2.82843;MQSBZ=-0.894427;BQBZ=-0.58585;SCBZ=-0.53033;FS=0;MQ0F=0 PL 2,0,195,26,198,215 +17 1990 . G T,<*> 0 . DP=9;I16=4,4,0,1,282,10212,33,1089,480,28800,29,841,120,2358,25,625;QS=0.906752,0.0932476,0;SGB=-0.379885;RPBZ=0.387298;MQBZ=-2.82843;MQSBZ=-0.894427;BQBZ=-0.58585;SCBZ=-0.53033;MQ0F=0 PL 2,0,195,26,198,215 17 1991 . A <*> 0 . DP=9;I16=4,5,0,0,335,13049,0,0,509,29641,0,0,145,2993,0,0;QS=1,0;MQ0F=0 PL 0,27,250 17 1992 . G <*> 0 . DP=9;I16=4,5,0,0,307,11009,0,0,509,29641,0,0,145,3015,0,0;QS=1,0;MQ0F=0 PL 0,27,231 17 1993 . T <*> 0 . DP=9;I16=4,5,0,0,344,13332,0,0,509,29641,0,0,145,3049,0,0;QS=1,0;MQ0F=0 PL 0,27,248 @@ -2029,8 +2028,8 @@ 17 2007 . A <*> 0 . DP=7;I16=2,5,0,0,249,9041,0,0,389,22441,0,0,144,3330,0,0;QS=1,0;MQ0F=0 PL 0,21,193 17 2008 . C <*> 0 . DP=7;I16=2,5,0,0,232,8210,0,0,389,22441,0,0,141,3245,0,0;QS=1,0;MQ0F=0 PL 0,21,183 17 2009 . A <*> 0 . DP=7;I16=2,5,0,0,266,10628,0,0,389,22441,0,0,138,3166,0,0;QS=1,0;MQ0F=0 PL 0,21,210 -17 2010 . G C,<*> 0 . DP=7;I16=2,4,0,1,204,7382,10,100,360,21600,29,841,125,2993,10,100;QS=0.953271,0.046729,0;SGB=-0.379885;RPBZ=1;MQBZ=-2.44949;MQSBZ=-0.632456;BQBZ=-1.51357;SCBZ=-0.62361;FS=0;MQ0F=0 PL 0,10,160,18,163,163 -17 2011 . C T,<*> 0 . DP=7;I16=2,4,0,1,211,7627,6,36,360,21600,29,841,123,2945,9,81;QS=0.97235,0.0276498,0;SGB=-0.379885;RPBZ=1;MQBZ=-2.44949;MQSBZ=-0.632456;BQBZ=-1.51357;SCBZ=-0.62361;FS=0;MQ0F=0 PL 0,12,168,18,171,168 +17 2010 . G C,<*> 0 . DP=7;I16=2,4,0,1,204,7382,10,100,360,21600,29,841,125,2993,10,100;QS=0.953271,0.046729,0;SGB=-0.379885;RPBZ=1;MQBZ=-2.44949;MQSBZ=-0.632456;BQBZ=-1.51357;SCBZ=-0.62361;MQ0F=0 PL 0,10,160,18,163,163 +17 2011 . C T,<*> 0 . DP=7;I16=2,4,0,1,211,7627,6,36,360,21600,29,841,123,2945,9,81;QS=0.97235,0.0276498,0;SGB=-0.379885;RPBZ=1;MQBZ=-2.44949;MQSBZ=-0.632456;BQBZ=-1.51357;SCBZ=-0.62361;MQ0F=0 PL 0,12,168,18,171,168 17 2012 . A <*> 0 . DP=7;I16=2,5,0,0,239,8743,0,0,389,22441,0,0,129,2965,0,0;QS=1,0;MQ0F=0 PL 0,21,189 17 2013 . C <*> 0 . DP=7;I16=2,5,0,0,198,6510,0,0,389,22441,0,0,126,2910,0,0;QS=1,0;MQ0F=0 PL 0,21,159 17 2014 . G <*> 0 . DP=6;I16=2,4,0,0,195,6881,0,0,329,18841,0,0,124,2860,0,0;QS=1,0;MQ0F=0 PL 0,18,160 @@ -2060,7 +2059,7 @@ 17 2038 . C <*> 0 . DP=7;I16=4,3,0,0,262,9910,0,0,420,25200,0,0,131,2667,0,0;QS=1,0;MQ0F=0 PL 0,21,211 17 2039 . A <*> 0 . DP=7;I16=4,3,0,0,265,10071,0,0,420,25200,0,0,133,2735,0,0;QS=1,0;MQ0F=0 PL 0,21,212 17 2040 . C <*> 0 . DP=7;I16=4,3,0,0,243,8635,0,0,420,25200,0,0,135,2811,0,0;QS=1,0;MQ0F=0 PL 0,21,196 -17 2041 . G A,<*> 0 . DP=7;I16=0,0,4,3,0,0,276,11066,0,0,420,25200,0,0,137,2895;QS=0,1,0;VDB=0.792147;SGB=-0.636426;MQSBZ=0;FS=0;MQ0F=0 PL 223,21,0,223,21,223 +17 2041 . G A,<*> 0 . DP=7;I16=0,0,4,3,0,0,276,11066,0,0,420,25200,0,0,137,2895;QS=0,1,0;VDB=0.792147;SGB=-0.636426;MQSBZ=0;MQ0F=0 PL 223,21,0,223,21,223 17 2042 . G <*> 0 . DP=7;I16=4,3,0,0,256,9542,0,0,420,25200,0,0,139,2987,0,0;QS=1,0;MQ0F=0 PL 0,21,206 17 2043 . G <*> 0 . DP=7;I16=4,3,0,0,240,8782,0,0,420,25200,0,0,141,3087,0,0;QS=1,0;MQ0F=0 PL 0,21,197 17 2044 . C <*> 0 . DP=7;I16=4,3,0,0,258,9636,0,0,420,25200,0,0,143,3195,0,0;QS=1,0;MQ0F=0 PL 0,21,207 @@ -2079,7 +2078,7 @@ 17 2057 . T <*> 0 . DP=6;I16=4,2,0,0,219,8015,0,0,360,21600,0,0,138,3272,0,0;QS=1,0;MQ0F=0 PL 0,18,178 17 2058 . A <*> 0 . DP=6;I16=4,2,0,0,217,7929,0,0,360,21600,0,0,135,3149,0,0;QS=1,0;MQ0F=0 PL 0,18,179 17 2059 . A <*> 0 . DP=6;I16=4,2,0,0,224,8446,0,0,360,21600,0,0,132,3032,0,0;QS=1,0;MQ0F=0 PL 0,18,184 -17 2060 . C G,<*> 0 . DP=6;I16=3,2,1,0,162,5622,2,4,300,18000,60,3600,107,2437,22,484;QS=0.975904,0.0240964,0;SGB=-0.379885;RPBZ=1.48522;MQBZ=0;MQSBZ=0;BQBZ=-1.46385;SCBZ=1.73205;FS=0;MQ0F=0 PL 0,10,137,15,140,137 +17 2060 . C G,<*> 0 . DP=6;I16=3,2,1,0,162,5622,2,4,300,18000,60,3600,107,2437,22,484;QS=0.975904,0.0240964,0;SGB=-0.379885;RPBZ=1.48522;MQBZ=0;MQSBZ=0;BQBZ=-1.46385;SCBZ=1.73205;MQ0F=0 PL 0,10,137,15,140,137 17 2061 . A <*> 0 . DP=5;I16=3,2,0,0,187,7029,0,0,300,18000,0,0,105,2375,0,0;QS=1,0;MQ0F=0 PL 0,15,163 17 2062 . A <*> 0 . DP=5;I16=3,2,0,0,187,7195,0,0,300,18000,0,0,103,2317,0,0;QS=1,0;MQ0F=0 PL 0,15,164 17 2063 . C <*> 0 . DP=5;I16=3,2,0,0,182,6678,0,0,300,18000,0,0,101,2263,0,0;QS=1,0;MQ0F=0 PL 0,15,158 @@ -2095,7 +2094,7 @@ 17 2073 . C <*> 0 . DP=5;I16=4,1,0,0,161,5287,0,0,300,18000,0,0,91,2003,0,0;QS=1,0;MQ0F=0 PL 0,15,133 17 2074 . G <*> 0 . DP=5;I16=4,1,0,0,104,2430,0,0,300,18000,0,0,91,2005,0,0;QS=1,0;MQ0F=0 PL 0,15,87 17 2075 . C <*> 0 . DP=5;I16=4,1,0,0,138,3910,0,0,300,18000,0,0,91,2011,0,0;QS=1,0;MQ0F=0 PL 0,15,113 -17 2076 . A G,<*> 0 . DP=5;I16=3,1,1,0,130,4242,1,1,240,14400,60,3600,80,1900,11,121;QS=0.970149,0.0298507,0;SGB=-0.379885;RPBZ=-1.45095;MQBZ=0;MQSBZ=0;BQBZ=-1.45095;SCBZ=-0.5;FS=0;MQ0F=0 PL 0,8,108,12,111,108 +17 2076 . A G,<*> 0 . DP=5;I16=3,1,1,0,130,4242,1,1,240,14400,60,3600,80,1900,11,121;QS=0.970149,0.0298507,0;SGB=-0.379885;RPBZ=-1.45095;MQBZ=0;MQSBZ=0;BQBZ=-1.45095;SCBZ=-0.5;MQ0F=0 PL 0,8,108,12,111,108 17 2077 . C <*> 0 . DP=5;I16=4,1,0,0,150,4766,0,0,300,18000,0,0,91,2035,0,0;QS=1,0;MQ0F=0 PL 0,15,125 17 2078 . A <*> 0 . DP=5;I16=4,1,0,0,180,6606,0,0,300,18000,0,0,91,2053,0,0;QS=1,0;MQ0F=0 PL 0,15,148 17 2079 . G <*> 0 . DP=5;I16=4,1,0,0,160,5324,0,0,300,18000,0,0,91,2075,0,0;QS=1,0;MQ0F=0 PL 0,15,133 @@ -2186,7 +2185,7 @@ 17 2164 . G <*> 0 . DP=5;I16=3,2,0,0,179,6519,0,0,300,18000,0,0,95,2237,0,0;QS=1,0;MQ0F=0 PL 0,15,156 17 2165 . C <*> 0 . DP=5;I16=3,2,0,0,173,6199,0,0,300,18000,0,0,94,2226,0,0;QS=1,0;MQ0F=0 PL 0,15,151 17 2166 . T <*> 0 . DP=4;I16=2,2,0,0,152,5976,0,0,240,14400,0,0,94,2220,0,0;QS=1,0;MQ0F=0 PL 0,12,140 -17 2167 . A G,<*> 0 . DP=4;I16=2,1,0,1,117,4565,7,49,180,10800,60,3600,72,1734,22,484;QS=0.943548,0.0564516,0;SGB=-0.379885;RPBZ=-1.34164;MQBZ=0;MQSBZ=0;BQBZ=-1.34164;SCBZ=1.73205;FS=0;MQ0F=0 PL 0,4,103,9,106,105 +17 2167 . A G,<*> 0 . DP=4;I16=2,1,0,1,117,4565,7,49,180,10800,60,3600,72,1734,22,484;QS=0.943548,0.0564516,0;SGB=-0.379885;RPBZ=-1.34164;MQBZ=0;MQSBZ=0;BQBZ=-1.34164;SCBZ=1.73205;MQ0F=0 PL 0,4,103,9,106,105 17 2168 . C <*> 0 . DP=4;I16=2,2,0,0,135,4671,0,0,240,14400,0,0,93,2171,0,0;QS=1,0;MQ0F=0 PL 0,12,124 17 2169 . T <*> 0 . DP=4;I16=2,2,0,0,154,6034,0,0,240,14400,0,0,92,2130,0,0;QS=1,0;MQ0F=0 PL 0,12,142 17 2170 . C <*> 0 . DP=4;I16=2,2,0,0,147,5435,0,0,240,14400,0,0,91,2095,0,0;QS=1,0;MQ0F=0 PL 0,12,135 @@ -2239,7 +2238,7 @@ 17 2217 . T <*> 0 . DP=4;I16=0,4,0,0,150,5810,0,0,240,14400,0,0,89,2015,0,0;QS=1,0;MQ0F=0 PL 0,12,118 17 2218 . C <*> 0 . DP=4;I16=0,4,0,0,154,5950,0,0,240,14400,0,0,89,2023,0,0;QS=1,0;MQ0F=0 PL 0,12,119 17 2219 . C <*> 0 . DP=4;I16=0,4,0,0,159,6331,0,0,240,14400,0,0,89,2035,0,0;QS=1,0;MQ0F=0 PL 0,12,122 -17 2220 . G A,<*> 0 . DP=4;I16=0,0,0,4,0,0,170,7254,0,0,240,14400,0,0,89,2051;QS=0,1,0;VDB=0.756056;SGB=-0.556411;FS=0;MQ0F=0 PL 131,12,0,131,12,131 +17 2220 . G A,<*> 0 . DP=4;I16=0,0,0,4,0,0,170,7254,0,0,240,14400,0,0,89,2051;QS=0,1,0;VDB=0.756056;SGB=-0.556411;MQ0F=0 PL 131,12,0,131,12,131 17 2221 . G <*> 0 . DP=4;I16=0,4,0,0,154,6054,0,0,240,14400,0,0,88,2022,0,0;QS=1,0;MQ0F=0 PL 0,12,120 17 2222 . C <*> 0 . DP=4;I16=0,4,0,0,133,4857,0,0,240,14400,0,0,86,1948,0,0;QS=1,0;MQ0F=0 PL 0,12,107 17 2223 . C <*> 0 . DP=4;I16=0,4,0,0,158,6262,0,0,240,14400,0,0,84,1878,0,0;QS=1,0;MQ0F=0 PL 0,12,122 @@ -2333,7 +2332,7 @@ 17 2311 . A <*> 0 . DP=4;I16=2,2,0,0,149,5751,0,0,240,14400,0,0,75,1563,0,0;QS=1,0;MQ0F=0 PL 0,12,137 17 2312 . G <*> 0 . DP=4;I16=2,2,0,0,138,5634,0,0,240,14400,0,0,77,1615,0,0;QS=1,0;MQ0F=0 PL 0,12,128 17 2313 . C <*> 0 . DP=4;I16=2,2,0,0,141,5299,0,0,240,14400,0,0,79,1671,0,0;QS=1,0;MQ0F=0 PL 0,12,130 -17 2314 . A C,<*> 0 . DP=4;I16=2,1,0,1,122,4964,6,36,180,10800,60,3600,66,1506,15,225;QS=0.953125,0.046875,0;SGB=-0.379885;RPBZ=-1.34164;MQBZ=0;MQSBZ=0;BQBZ=-1.41421;SCBZ=1.73205;FS=0;MQ0F=0 PL 0,4,107,9,110,109 +17 2314 . A C,<*> 0 . DP=4;I16=2,1,0,1,122,4964,6,36,180,10800,60,3600,66,1506,15,225;QS=0.953125,0.046875,0;SGB=-0.379885;RPBZ=-1.34164;MQBZ=0;MQSBZ=0;BQBZ=-1.41421;SCBZ=1.73205;MQ0F=0 PL 0,4,107,9,110,109 17 2315 . C <*> 0 . DP=5;I16=2,3,0,0,149,5511,0,0,300,18000,0,0,91,1859,0,0;QS=1,0;MQ0F=0 PL 0,15,135 17 2316 . T <*> 0 . DP=5;I16=2,3,0,0,193,7565,0,0,300,18000,0,0,94,1944,0,0;QS=1,0;MQ0F=0 PL 0,15,168 17 2317 . T <*> 0 . DP=5;I16=2,3,0,0,196,7722,0,0,300,18000,0,0,97,2035,0,0;QS=1,0;MQ0F=0 PL 0,15,170 @@ -2381,7 +2380,7 @@ 17 2359 . G <*> 0 . DP=7;I16=2,5,0,0,275,10815,0,0,420,25200,0,0,150,3478,0,0;QS=1,0;MQ0F=0 PL 0,21,209 17 2360 . A <*> 0 . DP=7;I16=2,5,0,0,286,11734,0,0,420,25200,0,0,148,3430,0,0;QS=1,0;MQ0F=0 PL 0,21,220 17 2361 . G <*> 0 . DP=7;I16=2,5,0,0,211,7113,0,0,420,25200,0,0,146,3386,0,0;QS=1,0;MQ0F=0 PL 0,21,168 -17 2362 . A C,<*> 0 . DP=7;I16=2,4,0,1,189,6417,4,16,360,21600,60,3600,119,2721,25,625;QS=0.979275,0.0207254,0;SGB=-0.379885;RPBZ=0;MQBZ=0;MQSBZ=0;BQBZ=-1.5;SCBZ=-0.408248;FS=0;MQ0F=0 PL 0,12,152,18,155,152 +17 2362 . A C,<*> 0 . DP=7;I16=2,4,0,1,189,6417,4,16,360,21600,60,3600,119,2721,25,625;QS=0.979275,0.0207254,0;SGB=-0.379885;RPBZ=0;MQBZ=0;MQSBZ=0;BQBZ=-1.5;SCBZ=-0.408248;MQ0F=0 PL 0,12,152,18,155,152 17 2363 . C <*> 0 . DP=7;I16=2,5,0,0,236,8478,0,0,420,25200,0,0,142,3310,0,0;QS=1,0;MQ0F=0 PL 0,21,187 17 2364 . C <*> 0 . DP=7;I16=2,5,0,0,263,9923,0,0,420,25200,0,0,140,3278,0,0;QS=1,0;MQ0F=0 PL 0,21,201 17 2365 . A <*> 0 . DP=7;I16=2,5,0,0,286,11700,0,0,420,25200,0,0,138,3250,0,0;QS=1,0;MQ0F=0 PL 0,21,221 @@ -2561,7 +2560,7 @@ 17 2539 . C <*> 0 . DP=4;I16=2,2,0,0,125,3961,0,0,240,14400,0,0,76,1876,0,0;QS=1,0;MQ0F=0 PL 0,12,115 17 2540 . G <*> 0 . DP=4;I16=2,2,0,0,119,4027,0,0,240,14400,0,0,77,1879,0,0;QS=1,0;MQ0F=0 PL 0,12,110 17 2541 . G <*> 0 . DP=4;I16=2,2,0,0,153,5891,0,0,240,14400,0,0,78,1884,0,0;QS=1,0;MQ0F=0 PL 0,12,140 -17 2542 . T A,<*> 0 . DP=4;I16=1,2,1,0,116,4534,7,49,180,10800,60,3600,75,1875,4,16;QS=0.943089,0.0569106,0;SGB=-0.379885;RPBZ=-1.34164;MQBZ=0;MQSBZ=0;BQBZ=-1.34164;SCBZ=0;FS=0;MQ0F=0 PL 0,4,101,9,104,104 +17 2542 . T A,<*> 0 . DP=4;I16=1,2,1,0,116,4534,7,49,180,10800,60,3600,75,1875,4,16;QS=0.943089,0.0569106,0;SGB=-0.379885;RPBZ=-1.34164;MQBZ=0;MQSBZ=0;BQBZ=-1.34164;SCBZ=0;MQ0F=0 PL 0,4,101,9,104,104 17 2543 . G <*> 0 . DP=4;I16=2,2,0,0,127,4511,0,0,240,14400,0,0,80,1900,0,0;QS=1,0;MQ0F=0 PL 0,12,117 17 2544 . A <*> 0 . DP=4;I16=2,2,0,0,143,5367,0,0,240,14400,0,0,81,1911,0,0;QS=1,0;MQ0F=0 PL 0,12,132 17 2545 . C <*> 0 . DP=4;I16=2,2,0,0,142,5122,0,0,240,14400,0,0,82,1924,0,0;QS=1,0;MQ0F=0 PL 0,12,130 @@ -2583,7 +2582,7 @@ 17 2561 . C <*> 0 . DP=5;I16=3,2,0,0,175,6231,0,0,300,18000,0,0,100,2144,0,0;QS=1,0;MQ0F=0 PL 0,15,153 17 2562 . T <*> 0 . DP=5;I16=3,2,0,0,190,7478,0,0,300,18000,0,0,101,2195,0,0;QS=1,0;MQ0F=0 PL 0,15,167 17 2563 . C <*> 0 . DP=5;I16=3,2,0,0,163,5483,0,0,300,18000,0,0,102,2252,0,0;QS=1,0;MQ0F=0 PL 0,15,142 -17 2564 . A G,<*> 0 . DP=5;I16=0,0,3,2,0,0,137,4729,0,0,300,18000,0,0,102,2264;QS=0,1,0;VDB=0.709369;SGB=-0.590765;MQSBZ=0;FS=0;MQ0F=0 PL 124,15,0,124,15,124 +17 2564 . A G,<*> 0 . DP=5;I16=0,0,3,2,0,0,137,4729,0,0,300,18000,0,0,102,2264;QS=0,1,0;VDB=0.709369;SGB=-0.590765;MQSBZ=0;MQ0F=0 PL 124,15,0,124,15,124 17 2565 . A <*> 0 . DP=5;I16=3,2,0,0,191,7347,0,0,300,18000,0,0,102,2280,0,0;QS=1,0;MQ0F=0 PL 0,15,166 17 2566 . A <*> 0 . DP=5;I16=3,2,0,0,186,6998,0,0,300,18000,0,0,101,2251,0,0;QS=1,0;MQ0F=0 PL 0,15,162 17 2567 . A <*> 0 . DP=5;I16=3,2,0,0,191,7375,0,0,300,18000,0,0,100,2228,0,0;QS=1,0;MQ0F=0 PL 0,15,166 @@ -2606,7 +2605,7 @@ 17 2584 . A <*> 0 . DP=6;I16=4,2,0,0,227,8731,0,0,360,21600,0,0,99,2015,0,0;QS=1,0;MQ0F=0 PL 0,18,187 17 2585 . A <*> 0 . DP=6;I16=4,2,0,0,232,9042,0,0,360,21600,0,0,99,2005,0,0;QS=1,0;MQ0F=0 PL 0,18,190 17 2586 . G <*> 0 . DP=6;I16=4,2,0,0,213,7767,0,0,360,21600,0,0,99,2003,0,0;QS=1,0;MQ0F=0 PL 0,18,176 -17 2587 . A C,<*> 0 . DP=6;I16=3,2,1,0,157,5641,6,36,300,18000,60,3600,74,1384,25,625;QS=0.96319,0.0368098,0;SGB=-0.379885;RPBZ=0.29277;MQBZ=0;MQSBZ=0;BQBZ=-1.46385;SCBZ=-0.447214;FS=0;MQ0F=0 PL 0,9,133,15,136,134 +17 2587 . A C,<*> 0 . DP=6;I16=3,2,1,0,157,5641,6,36,300,18000,60,3600,74,1384,25,625;QS=0.96319,0.0368098,0;SGB=-0.379885;RPBZ=0.29277;MQBZ=0;MQSBZ=0;BQBZ=-1.46385;SCBZ=-0.447214;MQ0F=0 PL 0,9,133,15,136,134 17 2588 . A <*> 0 . DP=6;I16=4,2,0,0,197,6815,0,0,360,21600,0,0,99,2023,0,0;QS=1,0;MQ0F=0 PL 0,18,165 17 2589 . A <*> 0 . DP=6;I16=4,2,0,0,209,7591,0,0,360,21600,0,0,99,2045,0,0;QS=1,0;MQ0F=0 PL 0,18,174 17 2590 . A <*> 0 . DP=6;I16=4,2,0,0,193,6705,0,0,360,21600,0,0,99,2075,0,0;QS=1,0;MQ0F=0 PL 0,18,163 @@ -2732,11 +2731,11 @@ 17 2710 . C <*> 0 . DP=2;I16=1,1,0,0,47,1525,0,0,89,4441,0,0,43,949,0,0;QS=1,0;MQ0F=0 PL 0,6,47 17 2711 . T <*> 0 . DP=2;I16=1,1,0,0,78,3074,0,0,89,4441,0,0,42,914,0,0;QS=1,0;MQ0F=0 PL 0,6,72 17 2712 . A <*> 0 . DP=2;I16=1,1,0,0,66,2196,0,0,89,4441,0,0,41,881,0,0;QS=1,0;MQ0F=0 PL 0,6,65 -17 2713 . G T,<*> 0 . DP=2;I16=1,0,0,1,37,1369,14,196,60,3600,29,841,15,225,25,625;QS=0.72549,0.27451,0;SGB=-0.379885;RPBZ=-1;MQBZ=-1;MQSBZ=-1;BQBZ=-1;SCBZ=1;FS=0;MQ0F=0 PL 8,0,31,11,34,42 +17 2713 . G T,<*> 0 . DP=2;I16=1,0,0,1,37,1369,14,196,60,3600,29,841,15,225,25,625;QS=0.72549,0.27451,0;SGB=-0.379885;RPBZ=-1;MQBZ=-1;MQSBZ=-1;BQBZ=-1;SCBZ=1;MQ0F=0 PL 8,0,31,11,34,42 17 2714 . G <*> 0 . DP=2;I16=1,1,0,0,65,2125,0,0,89,4441,0,0,39,821,0,0;QS=1,0;MQ0F=0 PL 0,6,64 17 2715 . A <*> 0 . DP=2;I16=1,1,0,0,63,2069,0,0,89,4441,0,0,38,794,0,0;QS=1,0;MQ0F=0 PL 0,6,63 17 2716 . T <*> 0 . DP=3;I16=1,2,0,0,95,3097,0,0,149,8041,0,0,37,769,0,0;QS=1,0;MQ0F=0 PL 0,9,90 -17 2717 . G T,<*> 0 . DP=3;I16=1,1,0,1,72,2592,9,81,120,7200,29,841,12,122,25,625;QS=0.888889,0.111111,0;SGB=-0.379885;RPBZ=0;MQBZ=-1.41421;MQSBZ=-0.707107;BQBZ=-1.41421;SCBZ=1.22474;FS=0;MQ0F=0 PL 1,0,63,7,66,68 +17 2717 . G T,<*> 0 . DP=3;I16=1,1,0,1,72,2592,9,81,120,7200,29,841,12,122,25,625;QS=0.888889,0.111111,0;SGB=-0.379885;RPBZ=0;MQBZ=-1.41421;MQSBZ=-0.707107;BQBZ=-1.41421;SCBZ=1.22474;MQ0F=0 PL 1,0,63,7,66,68 17 2718 . C <*> 0 . DP=3;I16=1,2,0,0,74,2234,0,0,149,8041,0,0,37,729,0,0;QS=1,0;MQ0F=0 PL 0,9,71 17 2719 . A <*> 0 . DP=3;I16=1,2,0,0,115,4427,0,0,149,8041,0,0,37,715,0,0;QS=1,0;MQ0F=0 PL 0,9,99 17 2720 . G <*> 0 . DP=3;I16=1,2,0,0,108,3902,0,0,149,8041,0,0,37,705,0,0;QS=1,0;MQ0F=0 PL 0,9,97 @@ -2752,7 +2751,7 @@ 17 2730 . G <*> 0 . DP=2;I16=0,2,0,0,52,1640,0,0,89,4441,0,0,39,821,0,0;QS=1,0;MQ0F=0 PL 0,6,49 17 2731 . C <*> 0 . DP=2;I16=0,2,0,0,57,1637,0,0,89,4441,0,0,40,850,0,0;QS=1,0;MQ0F=0 PL 0,6,52 17 2732 . C <*> 0 . DP=2;I16=0,2,0,0,41,881,0,0,89,4441,0,0,41,881,0,0;QS=1,0;MQ0F=0 PL 0,6,38 -17 2733 . C A,<*> 0 . DP=2;I16=0,1,0,1,24,576,13,169,60,3600,29,841,17,289,25,625;QS=0.648649,0.351351,0;SGB=-0.379885;RPBZ=1;MQBZ=-1;BQBZ=-1;SCBZ=1;FS=0;MQ0F=0 PL 7,0,18,10,21,28 +17 2733 . C A,<*> 0 . DP=2;I16=0,1,0,1,24,576,13,169,60,3600,29,841,17,289,25,625;QS=0.648649,0.351351,0;SGB=-0.379885;RPBZ=1;MQBZ=-1;BQBZ=-1;SCBZ=1;MQ0F=0 PL 7,0,18,10,21,28 17 2734 . C <*> 0 . DP=2;I16=0,2,0,0,46,1570,0,0,89,4441,0,0,43,949,0,0;QS=1,0;MQ0F=0 PL 0,6,44 17 2735 . T <*> 0 . DP=2;I16=0,2,0,0,48,1730,0,0,89,4441,0,0,44,986,0,0;QS=1,0;MQ0F=0 PL 0,6,46 17 2736 . C <*> 0 . DP=2;I16=0,2,0,0,40,1138,0,0,89,4441,0,0,45,1025,0,0;QS=1,0;MQ0F=0 PL 0,6,38 @@ -2774,7 +2773,7 @@ 17 2752 . T <*> 0 . DP=4;I16=2,2,0,0,130,4356,0,0,209,11641,0,0,63,1327,0,0;QS=1,0;MQ0F=0 PL 0,12,119 17 2753 . G <*> 0 . DP=4;I16=2,2,0,0,126,4374,0,0,209,11641,0,0,64,1314,0,0;QS=1,0;MQ0F=0 PL 0,12,116 17 2754 . C <*> 0 . DP=4;I16=2,2,0,0,120,4208,0,0,209,11641,0,0,65,1307,0,0;QS=1,0;MQ0F=0 PL 0,12,111 -17 2755 . C G,<*> 0 . DP=4;I16=2,1,0,1,103,3709,7,49,180,10800,29,841,46,906,20,400;QS=0.936364,0.0636364,0;SGB=-0.379885;RPBZ=1.34164;MQBZ=-1.73205;MQSBZ=-1;BQBZ=-1.34164;SCBZ=1.73205;FS=0;MQ0F=0 PL 0,4,89,9,92,91 +17 2755 . C G,<*> 0 . DP=4;I16=2,1,0,1,103,3709,7,49,180,10800,29,841,46,906,20,400;QS=0.936364,0.0636364,0;SGB=-0.379885;RPBZ=1.34164;MQBZ=-1.73205;MQSBZ=-1;BQBZ=-1.34164;SCBZ=1.73205;MQ0F=0 PL 0,4,89,9,92,91 17 2756 . C <*> 0 . DP=4;I16=2,2,0,0,109,3745,0,0,209,11641,0,0,67,1311,0,0;QS=1,0;MQ0F=0 PL 0,12,100 17 2757 . T <*> 0 . DP=5;I16=3,2,0,0,168,6208,0,0,269,15241,0,0,68,1322,0,0;QS=1,0;MQ0F=0 PL 0,15,147 17 2758 . T <*> 0 . DP=5;I16=3,2,0,0,160,5916,0,0,269,15241,0,0,70,1340,0,0;QS=1,0;MQ0F=0 PL 0,15,140 @@ -2782,7 +2781,7 @@ 17 2760 . T <*> 0 . DP=5;I16=3,2,0,0,172,6448,0,0,269,15241,0,0,74,1400,0,0;QS=1,0;MQ0F=0 PL 0,15,150 17 2761 . T <*> 0 . DP=5;I16=3,2,0,0,170,6570,0,0,269,15241,0,0,76,1442,0,0;QS=1,0;MQ0F=0 PL 0,15,148 17 2762 . T <*> 0 . DP=6;I16=3,3,0,0,210,7698,0,0,329,18841,0,0,78,1492,0,0;QS=1,0;MQ0F=0 PL 0,18,177 -17 2763 . C A,<*> 0 . DP=6;I16=3,2,0,1,182,6872,13,169,300,18000,29,841,69,1407,12,144;QS=0.933333,0.0666667,0;SGB=-0.379885;RPBZ=1.46385;MQBZ=-2.23607;MQSBZ=-1;BQBZ=-1.46385;SCBZ=1.73205;FS=0;MQ0F=0 PL 0,5,147,15,150,153 +17 2763 . C A,<*> 0 . DP=6;I16=3,2,0,1,182,6872,13,169,300,18000,29,841,69,1407,12,144;QS=0.933333,0.0666667,0;SGB=-0.379885;RPBZ=1.46385;MQBZ=-2.23607;MQSBZ=-1;BQBZ=-1.46385;SCBZ=1.73205;MQ0F=0 PL 0,5,147,15,150,153 17 2764 . C <*> 0 . DP=6;I16=3,3,0,0,192,7040,0,0,329,18841,0,0,84,1620,0,0;QS=1,0;MQ0F=0 PL 0,18,165 17 2765 . T <*> 0 . DP=6;I16=3,3,0,0,223,8627,0,0,329,18841,0,0,86,1648,0,0;QS=1,0;MQ0F=0 PL 0,18,189 17 2766 . C <*> 0 . DP=7;I16=3,4,0,0,226,8350,0,0,389,22441,0,0,88,1684,0,0;QS=1,0;MQ0F=0 PL 0,21,186 @@ -2840,7 +2839,7 @@ 17 2818 . G <*> 0 . DP=7;I16=4,3,0,0,258,9646,0,0,420,25200,0,0,147,3567,0,0;QS=1,0;MQ0F=0 PL 0,21,208 17 2819 . G <*> 0 . DP=7;I16=4,3,0,0,243,8655,0,0,420,25200,0,0,147,3529,0,0;QS=1,0;MQ0F=0 PL 0,21,196 17 2820 . G <*> 0 . DP=7;I16=4,3,0,0,234,8150,0,0,420,25200,0,0,147,3495,0,0;QS=1,0;MQ0F=0 PL 0,21,188 -17 2821 . A G,<*> 0 . DP=8;I16=4,3,0,1,210,6834,2,4,420,25200,60,3600,147,3465,25,625;QS=0.981308,0.0186916,0;SGB=-0.379885;RPBZ=-1.5367;MQBZ=0;MQSBZ=0;BQBZ=-1.54604;SCBZ=1.75;FS=0;MQ0F=0 PL 0,15,164,21,167,164 +17 2821 . A G,<*> 0 . DP=8;I16=4,3,0,1,210,6834,2,4,420,25200,60,3600,147,3465,25,625;QS=0.981308,0.0186916,0;SGB=-0.379885;RPBZ=-1.5367;MQBZ=0;MQSBZ=0;BQBZ=-1.54604;SCBZ=1.75;MQ0F=0 PL 0,15,164,21,167,164 17 2822 . C <*> 0 . DP=8;I16=4,4,0,0,216,6518,0,0,480,28800,0,0,172,4064,0,0;QS=1,0;MQ0F=0 PL 0,24,172 17 2823 . C <*> 0 . DP=8;I16=4,4,0,0,251,8419,0,0,480,28800,0,0,172,4042,0,0;QS=1,0;MQ0F=0 PL 0,24,197 17 2824 . C <*> 0 . DP=8;I16=4,4,0,0,276,10170,0,0,480,28800,0,0,172,4024,0,0;QS=1,0;MQ0F=0 PL 0,24,215 @@ -2885,7 +2884,7 @@ 17 2863 . G <*> 0 . DP=7;I16=2,5,0,0,250,9198,0,0,420,25200,0,0,118,2682,0,0;QS=1,0;MQ0F=0 PL 0,21,195 17 2864 . G <*> 0 . DP=7;I16=2,5,0,0,235,8639,0,0,420,25200,0,0,115,2649,0,0;QS=1,0;MQ0F=0 PL 0,21,188 17 2865 . G <*> 0 . DP=7;I16=2,5,0,0,238,8596,0,0,420,25200,0,0,112,2622,0,0;QS=1,0;MQ0F=0 PL 0,21,188 -17 2866 . T G,<*> 0 . DP=6;I16=1,4,1,0,179,6567,2,4,300,18000,60,3600,100,2500,10,100;QS=0.978142,0.0218579,0;SGB=-0.379885;RPBZ=0.87831;MQBZ=0;MQSBZ=0;BQBZ=-1.46385;SCBZ=-0.447214;FS=0;MQ0F=0 PL 0,10,141,15,144,141 +17 2866 . T G,<*> 0 . DP=6;I16=1,4,1,0,179,6567,2,4,300,18000,60,3600,100,2500,10,100;QS=0.978142,0.0218579,0;SGB=-0.379885;RPBZ=0.87831;MQBZ=0;MQSBZ=0;BQBZ=-1.46385;SCBZ=-0.447214;MQ0F=0 PL 0,10,141,15,144,141 17 2867 . G <*> 0 . DP=5;I16=2,3,0,0,172,6102,0,0,300,18000,0,0,109,2581,0,0;QS=1,0;MQ0F=0 PL 0,15,150 17 2868 . T <*> 0 . DP=5;I16=2,3,0,0,179,6849,0,0,300,18000,0,0,108,2564,0,0;QS=1,0;MQ0F=0 PL 0,15,157 17 2869 . C <*> 0 . DP=5;I16=2,3,0,0,189,7277,0,0,300,18000,0,0,107,2549,0,0;QS=1,0;MQ0F=0 PL 0,15,165 @@ -3015,7 +3014,7 @@ 17 2993 . G <*> 0 . DP=4;I16=2,2,0,0,134,4698,0,0,240,14400,0,0,100,2500,0,0;QS=1,0;MQ0F=0 PL 0,12,123 17 2994 . G <*> 0 . DP=4;I16=2,2,0,0,127,4217,0,0,240,14400,0,0,99,2451,0,0;QS=1,0;MQ0F=0 PL 0,12,116 17 2995 . G <*> 0 . DP=4;I16=2,2,0,0,146,5388,0,0,240,14400,0,0,98,2404,0,0;QS=1,0;MQ0F=0 PL 0,12,134 -17 2996 . T G,<*> 0 . DP=4;I16=1,2,1,0,114,4428,1,1,180,10800,60,3600,75,1875,22,484;QS=0.966102,0.0338983,0;SGB=-0.379885;RPBZ=1.34164;MQBZ=0;MQSBZ=0;BQBZ=-1.41421;SCBZ=0;FS=0;MQ0F=0 PL 0,5,101,9,104,101 +17 2996 . T G,<*> 0 . DP=4;I16=1,2,1,0,114,4428,1,1,180,10800,60,3600,75,1875,22,484;QS=0.966102,0.0338983,0;SGB=-0.379885;RPBZ=1.34164;MQBZ=0;MQSBZ=0;BQBZ=-1.41421;SCBZ=0;MQ0F=0 PL 0,5,101,9,104,101 17 2997 . C <*> 0 . DP=4;I16=2,2,0,0,125,4001,0,0,240,14400,0,0,96,2316,0,0;QS=1,0;MQ0F=0 PL 0,12,115 17 2998 . C <*> 0 . DP=4;I16=2,2,0,0,134,4610,0,0,240,14400,0,0,95,2275,0,0;QS=1,0;MQ0F=0 PL 0,12,123 17 2999 . A <*> 0 . DP=4;I16=2,2,0,0,148,5574,0,0,240,14400,0,0,94,2236,0,0;QS=1,0;MQ0F=0 PL 0,12,136 @@ -3079,7 +3078,7 @@ 17 3057 . C <*> 0 . DP=4;I16=2,2,0,0,105,3419,0,0,240,14400,0,0,65,1303,0,0;QS=1,0;MQ0F=0 PL 0,12,99 17 3058 . C <*> 0 . DP=4;I16=2,2,0,0,125,4207,0,0,240,14400,0,0,64,1318,0,0;QS=1,0;MQ0F=0 PL 0,12,116 17 3059 . T <*> 0 . DP=4;I16=2,2,0,0,109,3705,0,0,240,14400,0,0,63,1339,0,0;QS=1,0;MQ0F=0 PL 0,12,103 -17 3060 . G C,<*> 0 . DP=5;I16=2,2,0,1,126,4164,2,4,240,14400,60,3600,61,1315,25,625;QS=0.969231,0.0307692,0;SGB=-0.379885;RPBZ=-1.41421;MQBZ=0;MQSBZ=0;BQBZ=-1.41421;SCBZ=1.22474;FS=0;MQ0F=0 PL 0,8,110,12,113,110 +17 3060 . G C,<*> 0 . DP=5;I16=2,2,0,1,126,4164,2,4,240,14400,60,3600,61,1315,25,625;QS=0.969231,0.0307692,0;SGB=-0.379885;RPBZ=-1.41421;MQBZ=0;MQSBZ=0;BQBZ=-1.41421;SCBZ=1.22474;MQ0F=0 PL 0,8,110,12,113,110 17 3061 . C <*> 0 . DP=5;I16=2,3,0,0,164,5458,0,0,300,18000,0,0,84,1920,0,0;QS=1,0;MQ0F=0 PL 0,15,143 17 3062 . C <*> 0 . DP=5;I16=2,3,0,0,153,4913,0,0,300,18000,0,0,82,1904,0,0;QS=1,0;MQ0F=0 PL 0,15,134 17 3063 . C <*> 0 . DP=5;I16=2,3,0,0,149,4995,0,0,300,18000,0,0,80,1892,0,0;QS=1,0;MQ0F=0 PL 0,15,133 @@ -3088,7 +3087,7 @@ 17 3066 . A <*> 0 . DP=4;I16=1,3,0,0,115,3749,0,0,240,14400,0,0,76,1876,0,0;QS=1,0;MQ0F=0 PL 0,12,104 17 3067 . T <*> 0 . DP=4;I16=1,3,0,0,114,3570,0,0,240,14400,0,0,75,1875,0,0;QS=1,0;MQ0F=0 PL 0,12,103 17 3068 . G <*> 0 . DP=3;I16=1,2,0,0,88,2790,0,0,180,10800,0,0,75,1875,0,0;QS=1,0;MQ0F=0 PL 0,9,84 -17 3069 . G C,<*> 0 . DP=3;I16=1,1,0,1,57,1889,1,1,120,7200,60,3600,50,1250,25,625;QS=0.934426,0.0655738,0;SGB=-0.379885;RPBZ=-1.22474;MQBZ=0;MQSBZ=0;BQBZ=-1.22474;SCBZ=1.22474;FS=0;MQ0F=0 PL 0,3,51,6,54,52 +17 3069 . G C,<*> 0 . DP=3;I16=1,1,0,1,57,1889,1,1,120,7200,60,3600,50,1250,25,625;QS=0.934426,0.0655738,0;SGB=-0.379885;RPBZ=-1.22474;MQBZ=0;MQSBZ=0;BQBZ=-1.22474;SCBZ=1.22474;MQ0F=0 PL 0,3,51,6,54,52 17 3070 . C <*> 0 . DP=3;I16=1,2,0,0,100,3454,0,0,180,10800,0,0,75,1875,0,0;QS=1,0;MQ0F=0 PL 0,9,95 17 3071 . C <*> 0 . DP=3;I16=1,2,0,0,104,3656,0,0,180,10800,0,0,75,1875,0,0;QS=1,0;MQ0F=0 PL 0,9,98 17 3072 . C <*> 0 . DP=3;I16=1,2,0,0,112,4230,0,0,180,10800,0,0,75,1875,0,0;QS=1,0;MQ0F=0 PL 0,9,106 @@ -3123,7 +3122,7 @@ 17 3101 . C <*> 0 . DP=5;I16=2,3,0,0,186,6930,0,0,300,18000,0,0,78,1546,0,0;QS=1,0;MQ0F=0 PL 0,15,161 17 3102 . A <*> 0 . DP=6;I16=3,3,0,0,226,8548,0,0,360,21600,0,0,78,1560,0,0;QS=1,0;MQ0F=0 PL 0,18,189 17 3103 . T <*> 0 . DP=6;I16=3,3,0,0,223,8347,0,0,360,21600,0,0,79,1583,0,0;QS=1,0;MQ0F=0 PL 0,18,187 -17 3104 . C T,<*> 0 . DP=5;I16=1,2,2,0,114,4334,80,3202,180,10800,120,7200,41,765,40,850;QS=0.587629,0.412371,0;VDB=0.78;SGB=-0.453602;RPBZ=0.296174;MQBZ=0;MQSBZ=0;BQBZ=1.48087;SCBZ=-0.816497;FS=0;MQ0F=0 PL 59,0,93,68,99,157 +17 3104 . C T,<*> 0 . DP=5;I16=1,2,2,0,114,4334,80,3202,180,10800,120,7200,41,765,40,850;QS=0.587629,0.412371,0;VDB=0.78;SGB=-0.453602;RPBZ=0.296174;MQBZ=0;MQSBZ=0;BQBZ=1.48087;SCBZ=-0.816497;MQ0F=0 PL 59,0,93,68,99,157 17 3105 . T <*> 0 . DP=5;I16=3,2,0,0,195,7621,0,0,300,18000,0,0,83,1655,0,0;QS=1,0;MQ0F=0 PL 0,15,169 17 3106 . G <*> 0 . DP=5;I16=3,2,0,0,193,7461,0,0,300,18000,0,0,85,1703,0,0;QS=1,0;MQ0F=0 PL 0,15,167 17 3107 . T <*> 0 . DP=6;I16=3,3,0,0,233,9067,0,0,360,21600,0,0,87,1759,0,0;QS=1,0;MQ0F=0 PL 0,18,195 @@ -3285,11 +3284,11 @@ 17 3263 . G <*> 0 . DP=4;I16=2,2,0,0,160,6442,0,0,240,14400,0,0,67,1291,0,0;QS=1,0;MQ0F=0 PL 0,12,146 17 3264 . G <*> 0 . DP=4;I16=2,2,0,0,156,6120,0,0,240,14400,0,0,68,1330,0,0;QS=1,0;MQ0F=0 PL 0,12,143 17 3265 . G <*> 0 . DP=4;I16=2,2,0,0,148,5530,0,0,240,14400,0,0,69,1375,0,0;QS=1,0;MQ0F=0 PL 0,12,136 -17 3266 . T G,<*> 0 . DP=4;I16=1,2,1,0,120,4802,2,4,180,10800,60,3600,61,1345,9,81;QS=0.967742,0.0322581,0;SGB=-0.379885;RPBZ=1.34164;MQBZ=0;MQSBZ=0;BQBZ=-1.34164;SCBZ=1.73205;FS=0;MQ0F=0 PL 0,5,107,9,110,107 +17 3266 . T G,<*> 0 . DP=4;I16=1,2,1,0,120,4802,2,4,180,10800,60,3600,61,1345,9,81;QS=0.967742,0.0322581,0;SGB=-0.379885;RPBZ=1.34164;MQBZ=0;MQSBZ=0;BQBZ=-1.34164;SCBZ=1.73205;MQ0F=0 PL 0,5,107,9,110,107 17 3267 . G <*> 0 . DP=4;I16=2,2,0,0,144,5394,0,0,240,14400,0,0,71,1483,0,0;QS=1,0;MQ0F=0 PL 0,12,133 17 3268 . G <*> 0 . DP=4;I16=2,2,0,0,154,6010,0,0,240,14400,0,0,71,1495,0,0;QS=1,0;MQ0F=0 PL 0,12,142 17 3269 . G <*> 0 . DP=4;I16=2,2,0,0,149,5625,0,0,240,14400,0,0,71,1511,0,0;QS=1,0;MQ0F=0 PL 0,12,137 -17 3270 . T G,<*> 0 . DP=5;I16=2,2,1,0,148,5560,2,4,240,14400,60,3600,65,1457,5,25;QS=0.973684,0.0263158,0;SGB=-0.379885;RPBZ=1.41421;MQBZ=0;MQSBZ=0;BQBZ=-1.41421;SCBZ=2;FS=0;MQ0F=0 PL 0,8,129,12,132,129 +17 3270 . T G,<*> 0 . DP=5;I16=2,2,1,0,148,5560,2,4,240,14400,60,3600,65,1457,5,25;QS=0.973684,0.0263158,0;SGB=-0.379885;RPBZ=1.41421;MQBZ=0;MQSBZ=0;BQBZ=-1.41421;SCBZ=2;MQ0F=0 PL 0,8,129,12,132,129 17 3271 . G <*> 0 . DP=4;I16=2,2,0,0,157,6181,0,0,240,14400,0,0,66,1444,0,0;QS=1,0;MQ0F=0 PL 0,12,143 17 3272 . G <*> 0 . DP=4;I16=2,2,0,0,153,5881,0,0,240,14400,0,0,67,1437,0,0;QS=1,0;MQ0F=0 PL 0,12,140 17 3273 . A <*> 0 . DP=4;I16=2,2,0,0,161,6485,0,0,240,14400,0,0,68,1436,0,0;QS=1,0;MQ0F=0 PL 0,12,147 @@ -3335,7 +3334,7 @@ 17 3313 . T <*> 0 . DP=5;I16=4,1,0,0,198,7856,0,0,300,18000,0,0,111,2621,0,0;QS=1,0;MQ0F=0 PL 0,15,161 17 3314 . G <*> 0 . DP=5;I16=4,1,0,0,197,7831,0,0,300,18000,0,0,112,2644,0,0;QS=1,0;MQ0F=0 PL 0,15,161 17 3315 . G <*> 0 . DP=5;I16=4,1,0,0,189,7205,0,0,300,18000,0,0,113,2669,0,0;QS=1,0;MQ0F=0 PL 0,15,155 -17 3316 . T G,<*> 0 . DP=5;I16=3,1,1,0,139,4903,4,16,240,14400,60,3600,89,2071,25,625;QS=0.972028,0.027972,0;SGB=-0.379885;RPBZ=0;MQBZ=0;MQSBZ=0;BQBZ=-1.45095;SCBZ=0;FS=0;MQ0F=0 PL 0,8,116,12,119,116 +17 3316 . T G,<*> 0 . DP=5;I16=3,1,1,0,139,4903,4,16,240,14400,60,3600,89,2071,25,625;QS=0.972028,0.027972,0;SGB=-0.379885;RPBZ=0;MQBZ=0;MQSBZ=0;BQBZ=-1.45095;SCBZ=0;MQ0F=0 PL 0,8,116,12,119,116 17 3317 . G <*> 0 . DP=6;I16=4,2,0,0,203,7051,0,0,360,21600,0,0,115,2725,0,0;QS=1,0;MQ0F=0 PL 0,18,168 17 3318 . A <*> 0 . DP=6;I16=4,2,0,0,225,8557,0,0,360,21600,0,0,116,2708,0,0;QS=1,0;MQ0F=0 PL 0,18,185 17 3319 . A <*> 0 . DP=6;I16=4,2,0,0,230,9112,0,0,360,21600,0,0,117,2697,0,0;QS=1,0;MQ0F=0 PL 0,18,188 @@ -3378,7 +3377,7 @@ 17 3356 . T <*> 0 . DP=6;I16=4,2,0,0,241,9683,0,0,360,21600,0,0,137,3225,0,0;QS=1,0;MQ0F=0 PL 0,18,195 17 3357 . G <*> 0 . DP=6;I16=4,2,0,0,235,9245,0,0,360,21600,0,0,137,3245,0,0;QS=1,0;MQ0F=0 PL 0,18,192 17 3358 . G <*> 0 . DP=6;I16=4,2,0,0,228,8744,0,0,360,21600,0,0,137,3269,0,0;QS=1,0;MQ0F=0 PL 0,18,187 -17 3359 . T G,<*> 0 . DP=6;I16=3,2,1,0,185,6969,2,4,300,18000,60,3600,125,3125,11,121;QS=0.978836,0.021164,0;SGB=-0.379885;RPBZ=1.46385;MQBZ=0;MQSBZ=0;BQBZ=-1.46385;SCBZ=0;FS=0;MQ0F=0 PL 0,10,155,15,158,155 +17 3359 . T G,<*> 0 . DP=6;I16=3,2,1,0,185,6969,2,4,300,18000,60,3600,125,3125,11,121;QS=0.978836,0.021164,0;SGB=-0.379885;RPBZ=1.46385;MQBZ=0;MQSBZ=0;BQBZ=-1.46385;SCBZ=0;MQ0F=0 PL 0,10,155,15,158,155 17 3360 . G <*> 0 . DP=6;I16=4,2,0,0,211,7669,0,0,360,21600,0,0,135,3225,0,0;QS=1,0;MQ0F=0 PL 0,18,175 17 3361 . G <*> 0 . DP=6;I16=4,2,0,0,211,7655,0,0,360,21600,0,0,134,3206,0,0;QS=1,0;MQ0F=0 PL 0,18,175 17 3362 . C <*> 0 . DP=6;I16=4,2,0,0,210,7526,0,0,360,21600,0,0,133,3189,0,0;QS=1,0;MQ0F=0 PL 0,18,173 @@ -3527,7 +3526,7 @@ 17 3505 . A <*> 0 . DP=6;I16=1,5,0,0,217,8043,0,0,329,18841,0,0,104,2160,0,0;QS=1,0;MQ0F=0 PL 0,18,163 17 3506 . A <*> 0 . DP=6;I16=1,5,0,0,221,8287,0,0,329,18841,0,0,105,2181,0,0;QS=1,0;MQ0F=0 PL 0,18,168 17 3507 . T <*> 0 . DP=6;I16=1,5,0,0,201,7061,0,0,329,18841,0,0,106,2208,0,0;QS=1,0;MQ0F=0 PL 0,18,153 -17 3508 . C A,<*> 0 . DP=6;I16=0,5,1,0,164,5506,2,4,300,18000,29,841,82,1616,25,625;QS=0.97619,0.0238095,0;SGB=-0.379885;RPBZ=1.46385;MQBZ=-2.23607;MQSBZ=2.23607;BQBZ=-1.46385;SCBZ=1.73205;FS=0;MQ0F=0 PL 0,10,113,15,116,114 +17 3508 . C A,<*> 0 . DP=6;I16=0,5,1,0,164,5506,2,4,300,18000,29,841,82,1616,25,625;QS=0.97619,0.0238095,0;SGB=-0.379885;RPBZ=1.46385;MQBZ=-2.23607;MQSBZ=2.23607;BQBZ=-1.46385;SCBZ=1.73205;MQ0F=0 PL 0,10,113,15,116,114 17 3509 . A <*> 0 . DP=5;I16=0,5,0,0,171,6123,0,0,300,18000,0,0,83,1655,0,0;QS=1,0;MQ0F=0 PL 0,15,125 17 3510 . C <*> 0 . DP=5;I16=0,5,0,0,163,5573,0,0,300,18000,0,0,84,1700,0,0;QS=1,0;MQ0F=0 PL 0,15,119 17 3511 . A <*> 0 . DP=5;I16=0,5,0,0,153,5207,0,0,300,18000,0,0,85,1751,0,0;QS=1,0;MQ0F=0 PL 0,15,115 @@ -3606,7 +3605,7 @@ 17 3584 . G <*> 0 . DP=7;I16=4,3,0,0,271,10633,0,0,420,25200,0,0,121,2629,0,0;QS=1,0;MQ0F=0 PL 0,21,218 17 3585 . A <*> 0 . DP=8;I16=5,3,0,0,301,11477,0,0,480,28800,0,0,121,2633,0,0;QS=1,0;MQ0F=0 PL 0,24,229 17 3586 . A <*> 0 . DP=8;I16=5,3,0,0,308,11984,0,0,480,28800,0,0,122,2646,0,0;QS=1,0;MQ0F=0 PL 0,24,234 -17 3587 . G A,<*> 0 . DP=8;I16=0,0,5,3,0,0,314,12410,0,0,480,28800,0,0,123,2669;QS=0,1,0;VDB=0.92727;SGB=-0.651104;MQSBZ=0;FS=0;MQ0F=0 PL 240,24,0,240,24,240 +17 3587 . G A,<*> 0 . DP=8;I16=0,0,5,3,0,0,314,12410,0,0,480,28800,0,0,123,2669;QS=0,1,0;VDB=0.92727;SGB=-0.651104;MQSBZ=0;MQ0F=0 PL 240,24,0,240,24,240 17 3588 . A <*> 0 . DP=8;I16=5,3,0,0,313,12383,0,0,480,28800,0,0,123,2651,0,0;QS=1,0;MQ0F=0 PL 0,24,239 17 3589 . A <*> 0 . DP=8;I16=5,3,0,0,293,10975,0,0,480,28800,0,0,123,2641,0,0;QS=1,0;MQ0F=0 PL 0,24,224 17 3590 . A <*> 0 . DP=8;I16=5,3,0,0,296,11288,0,0,480,28800,0,0,123,2639,0,0;QS=1,0;MQ0F=0 PL 0,24,227 @@ -3629,7 +3628,7 @@ 17 3607 . A <*> 0 . DP=9;I16=6,3,0,0,321,11705,0,0,540,32400,0,0,142,3018,0,0;QS=1,0;MQ0F=0 PL 0,27,232 17 3608 . A <*> 0 . DP=9;I16=6,3,0,0,316,11960,0,0,540,32400,0,0,145,3081,0,0;QS=1,0;MQ0F=0 PL 0,27,233 17 3609 . A <*> 0 . DP=9;I16=6,3,0,0,328,12274,0,0,540,32400,0,0,147,3107,0,0;QS=1,0;MQ0F=0 PL 0,27,238 -17 3610 . C A,<*> 0 . DP=9;I16=5,3,1,0,292,10792,8,64,480,28800,60,3600,124,2520,25,625;QS=0.973333,0.0266667,0;SGB=-0.379885;RPBZ=-0.387298;MQBZ=0;MQSBZ=0;BQBZ=-1.62549;SCBZ=-0.53033;FS=0;MQ0F=0 PL 0,17,213,24,216,214 +17 3610 . C A,<*> 0 . DP=9;I16=5,3,1,0,292,10792,8,64,480,28800,60,3600,124,2520,25,625;QS=0.973333,0.0266667,0;SGB=-0.379885;RPBZ=-0.387298;MQBZ=0;MQSBZ=0;BQBZ=-1.62549;SCBZ=-0.53033;MQ0F=0 PL 0,17,213,24,216,214 17 3611 . C <*> 0 . DP=9;I16=6,3,0,0,316,12098,0,0,540,32400,0,0,150,3144,0,0;QS=1,0;MQ0F=0 PL 0,27,234 17 3612 . A <*> 0 . DP=9;I16=6,3,0,0,341,13619,0,0,540,32400,0,0,151,3153,0,0;QS=1,0;MQ0F=0 PL 0,27,251 17 3613 . G <*> 0 . DP=9;I16=6,3,0,0,306,11050,0,0,540,32400,0,0,152,3172,0,0;QS=1,0;MQ0F=0 PL 0,27,226 @@ -3661,12 +3660,12 @@ 17 3639 . G <*> 0 . DP=9;I16=6,3,0,0,308,10662,0,0,540,32400,0,0,175,4019,0,0;QS=1,0;MQ0F=0 PL 0,27,221 17 3640 . T <*> 0 . DP=9;I16=6,3,0,0,315,11283,0,0,540,32400,0,0,175,3975,0,0;QS=1,0;MQ0F=0 PL 0,27,229 17 3641 . G <*> 0 . DP=9;I16=6,3,0,0,309,10867,0,0,540,32400,0,0,175,3939,0,0;QS=1,0;MQ0F=0 PL 0,27,224 -17 3642 . T G,<*> 0 . DP=9;I16=5,3,1,0,293,11005,3,9,480,28800,60,3600,150,3286,25,625;QS=0.986532,0.013468,0;SGB=-0.379885;RPBZ=0.387298;MQBZ=0;MQSBZ=0;BQBZ=-1.55569;SCBZ=-0.53033;FS=0;MQ0F=0 PL 0,18,219,24,222,219 +17 3642 . T G,<*> 0 . DP=9;I16=5,3,1,0,293,11005,3,9,480,28800,60,3600,150,3286,25,625;QS=0.986532,0.013468,0;SGB=-0.379885;RPBZ=0.387298;MQBZ=0;MQSBZ=0;BQBZ=-1.55569;SCBZ=-0.53033;MQ0F=0 PL 0,18,219,24,222,219 17 3643 . T <*> 0 . DP=9;I16=6,3,0,0,312,11318,0,0,540,32400,0,0,175,3891,0,0;QS=1,0;MQ0F=0 PL 0,27,230 17 3644 . T <*> 0 . DP=9;I16=6,3,0,0,316,12098,0,0,540,32400,0,0,175,3879,0,0;QS=1,0;MQ0F=0 PL 0,27,237 17 3645 . T <*> 0 . DP=9;I16=6,3,0,0,326,12228,0,0,540,32400,0,0,175,3875,0,0;QS=1,0;MQ0F=0 PL 0,27,239 17 3646 . C <*> 0 . DP=9;I16=6,3,0,0,252,7724,0,0,540,32400,0,0,175,3879,0,0;QS=1,0;MQ0F=0 PL 0,27,188 -17 3647 . G T,<*> 0 . DP=9;I16=5,3,1,0,214,7092,12,144,480,28800,60,3600,150,3266,25,625;QS=0.947368,0.0526316,0;SGB=-0.379885;RPBZ=0.387298;MQBZ=0;MQSBZ=0;BQBZ=-1.1619;SCBZ=-0.53033;FS=0;MQ0F=0 PL 0,14,162,24,165,165 +17 3647 . G T,<*> 0 . DP=9;I16=5,3,1,0,214,7092,12,144,480,28800,60,3600,150,3266,25,625;QS=0.947368,0.0526316,0;SGB=-0.379885;RPBZ=0.387298;MQBZ=0;MQSBZ=0;BQBZ=-1.1619;SCBZ=-0.53033;MQ0F=0 PL 0,14,162,24,165,165 17 3648 . A <*> 0 . DP=9;I16=6,3,0,0,304,11112,0,0,540,32400,0,0,175,3911,0,0;QS=1,0;MQ0F=0 PL 0,27,227 17 3649 . C <*> 0 . DP=9;I16=6,3,0,0,309,10981,0,0,540,32400,0,0,175,3939,0,0;QS=1,0;MQ0F=0 PL 0,27,226 17 3650 . A <*> 0 . DP=9;I16=6,3,0,0,335,12925,0,0,540,32400,0,0,175,3975,0,0;QS=1,0;MQ0F=0 PL 0,27,246 @@ -3681,7 +3680,7 @@ 17 3659 . T <*> 0 . DP=7;I16=5,2,0,0,235,8387,0,0,420,25200,0,0,169,4101,0,0;QS=1,0;MQ0F=0 PL 0,21,186 17 3660 . G <*> 0 . DP=7;I16=5,2,0,0,215,7415,0,0,420,25200,0,0,169,4095,0,0;QS=1,0;MQ0F=0 PL 0,21,174 17 3661 . T <*> 0 . DP=7;I16=5,2,0,0,234,8550,0,0,420,25200,0,0,168,4044,0,0;QS=1,0;MQ0F=0 PL 0,21,188 -17 3662 . T G,<*> 0 . DP=7;I16=4,2,1,0,222,8532,10,100,360,21600,60,3600,146,3558,21,441;QS=0.956897,0.0431034,0;SGB=-0.379885;RPBZ=1;MQBZ=0;MQSBZ=0;BQBZ=-1.51357;SCBZ=-0.408248;FS=0;MQ0F=0 PL 0,10,175,18,178,178 +17 3662 . T G,<*> 0 . DP=7;I16=4,2,1,0,222,8532,10,100,360,21600,60,3600,146,3558,21,441;QS=0.956897,0.0431034,0;SGB=-0.379885;RPBZ=1;MQBZ=0;MQSBZ=0;BQBZ=-1.51357;SCBZ=-0.408248;MQ0F=0 PL 0,10,175,18,178,178 17 3663 . A <*> 0 . DP=7;I16=5,2,0,0,231,8235,0,0,420,25200,0,0,166,3960,0,0;QS=1,0;MQ0F=0 PL 0,21,183 17 3664 . T <*> 0 . DP=7;I16=5,2,0,0,250,9272,0,0,420,25200,0,0,165,3927,0,0;QS=1,0;MQ0F=0 PL 0,21,196 17 3665 . A <*> 0 . DP=7;I16=5,2,0,0,271,10551,0,0,420,25200,0,0,163,3849,0,0;QS=1,0;MQ0F=0 PL 0,21,208 @@ -3738,11 +3737,11 @@ 17 3716 . T <*> 0 . DP=6;I16=5,1,0,0,218,8322,0,0,337,19369,0,0,124,2760,0,0;QS=1,0;MQ0F=0 PL 0,18,164 17 3717 . C <*> 0 . DP=6;I16=5,1,0,0,222,8600,0,0,337,19369,0,0,123,2729,0,0;QS=1,0;MQ0F=0 PL 0,18,168 17 3718 . T <*> 0 . DP=6;I16=5,1,0,0,223,9053,0,0,337,19369,0,0,122,2704,0,0;QS=1,0;MQ0F=0 PL 0,18,165 -17 3719 . A T,<*> 0 . DP=6;I16=5,0,0,1,200,8050,12,144,300,18000,37,1369,96,2060,25,625;QS=0.943396,0.0566038,0;SGB=-0.379885;RPBZ=-0.87831;MQBZ=-2.23607;MQSBZ=-2.23607;BQBZ=-1.46385;SCBZ=0;FS=0;MQ0F=0 PL 0,5,133,15,136,137 +17 3719 . A T,<*> 0 . DP=6;I16=5,0,0,1,200,8050,12,144,300,18000,37,1369,96,2060,25,625;QS=0.943396,0.0566038,0;SGB=-0.379885;RPBZ=-0.87831;MQBZ=-2.23607;MQSBZ=-2.23607;BQBZ=-1.46385;SCBZ=0;MQ0F=0 PL 0,5,133,15,136,137 17 3720 . C <*> 0 . DP=6;I16=5,1,0,0,212,7920,0,0,337,19369,0,0,120,2672,0,0;QS=1,0;MQ0F=0 PL 0,18,158 -17 3721 . A C,<*> 0 . DP=6;I16=5,0,0,1,205,8415,4,16,300,18000,37,1369,94,2040,25,625;QS=0.980861,0.0191388,0;SGB=-0.379885;RPBZ=-0.87831;MQBZ=-2.23607;MQSBZ=-2.23607;BQBZ=-1.46385;SCBZ=0;FS=0;MQ0F=0 PL 0,10,140,15,143,140 +17 3721 . A C,<*> 0 . DP=6;I16=5,0,0,1,205,8415,4,16,300,18000,37,1369,94,2040,25,625;QS=0.980861,0.0191388,0;SGB=-0.379885;RPBZ=-0.87831;MQBZ=-2.23607;MQSBZ=-2.23607;BQBZ=-1.46385;SCBZ=0;MQ0F=0 PL 0,10,140,15,143,140 17 3722 . C <*> 0 . DP=6;I16=5,1,0,0,220,8352,0,0,337,19369,0,0,118,2664,0,0;QS=1,0;MQ0F=0 PL 0,18,165 -17 3723 . A G,<*> 0 . DP=6;I16=5,0,0,1,205,8419,8,64,300,18000,37,1369,92,2044,25,625;QS=0.962441,0.0375587,0;SGB=-0.379885;RPBZ=-0.87831;MQBZ=-2.23607;MQSBZ=-2.23607;BQBZ=-1.50756;SCBZ=0;FS=0;MQ0F=0 PL 0,8,138,15,141,140 +17 3723 . A G,<*> 0 . DP=6;I16=5,0,0,1,205,8419,8,64,300,18000,37,1369,92,2044,25,625;QS=0.962441,0.0375587,0;SGB=-0.379885;RPBZ=-0.87831;MQBZ=-2.23607;MQSBZ=-2.23607;BQBZ=-1.50756;SCBZ=0;MQ0F=0 PL 0,8,138,15,141,140 17 3724 . C <*> 0 . DP=6;I16=5,1,0,0,222,8374,0,0,337,19369,0,0,116,2680,0,0;QS=1,0;MQ0F=0 PL 0,18,169 17 3725 . T <*> 0 . DP=6;I16=5,1,0,0,249,10441,0,0,337,19369,0,0,115,2697,0,0;QS=1,0;MQ0F=0 PL 0,18,190 17 3726 . G <*> 0 . DP=6;I16=5,1,0,0,215,8133,0,0,337,19369,0,0,113,2669,0,0;QS=1,0;MQ0F=0 PL 0,18,166 @@ -3783,7 +3782,7 @@ 17 3761 . A <*> 0 . DP=6;I16=4,2,0,0,230,9010,0,0,337,19369,0,0,97,2101,0,0;QS=1,0;MQ0F=0 PL 0,18,188 17 3762 . C <*> 0 . DP=6;I16=4,2,0,0,198,7636,0,0,337,19369,0,0,96,2064,0,0;QS=1,0;MQ0F=0 PL 0,18,161 17 3763 . C <*> 0 . DP=6;I16=4,2,0,0,226,8912,0,0,337,19369,0,0,94,1984,0,0;QS=1,0;MQ0F=0 PL 0,18,186 -17 3764 . A C,<*> 0 . DP=6;I16=4,1,0,1,204,8328,8,64,300,18000,37,1369,69,1383,23,529;QS=0.962264,0.0377358,0;SGB=-0.379885;RPBZ=0.29277;MQBZ=-2.23607;MQSBZ=-1.41421;BQBZ=-1.55543;SCBZ=0;FS=0;MQ0F=0 PL 0,8,159,15,162,161 +17 3764 . A C,<*> 0 . DP=6;I16=4,1,0,1,204,8328,8,64,300,18000,37,1369,69,1383,23,529;QS=0.962264,0.0377358,0;SGB=-0.379885;RPBZ=0.29277;MQBZ=-2.23607;MQSBZ=-1.41421;BQBZ=-1.55543;SCBZ=0;MQ0F=0 PL 0,8,159,15,162,161 17 3765 . C <*> 0 . DP=6;I16=4,2,0,0,231,8935,0,0,337,19369,0,0,90,1848,0,0;QS=1,0;MQ0F=0 PL 0,18,189 17 3766 . A <*> 0 . DP=6;I16=4,2,0,0,234,9192,0,0,337,19369,0,0,88,1792,0,0;QS=1,0;MQ0F=0 PL 0,18,191 17 3767 . A <*> 0 . DP=6;I16=4,2,0,0,232,9038,0,0,337,19369,0,0,86,1744,0,0;QS=1,0;MQ0F=0 PL 0,18,191 @@ -3922,7 +3921,7 @@ 17 3900 . T <*> 0 . DP=10;I16=2,8,0,0,377,14437,0,0,554,31538,0,0,187,4177,0,0;QS=1,0;MQ0F=0 PL 0,30,240 17 3901 . G <*> 0 . DP=10;I16=2,8,0,0,332,11724,0,0,554,31538,0,0,189,4219,0,0;QS=1,0;MQ0F=0 PL 0,30,218 17 3902 . C <*> 0 . DP=10;I16=2,8,0,0,352,12592,0,0,554,31538,0,0,191,4269,0,0;QS=1,0;MQ0F=0 PL 0,30,217 -17 3903 . A C,<*> 0 . DP=11;I16=2,8,0,1,318,10522,2,4,554,31538,60,3600,193,4327,2,4;QS=0.987421,0.0125786,0;SGB=-0.379885;RPBZ=-1.58114;MQBZ=0.471405;MQSBZ=3.16228;BQBZ=-1.58474;SCBZ=2.011;FS=0;MQ0F=0 PL 0,23,198,30,201,198 +17 3903 . A C,<*> 0 . DP=11;I16=2,8,0,1,318,10522,2,4,554,31538,60,3600,193,4327,2,4;QS=0.987421,0.0125786,0;SGB=-0.379885;RPBZ=-1.58114;MQBZ=0.471405;MQSBZ=3.16228;BQBZ=-1.58474;SCBZ=2.011;MQ0F=0 PL 0,23,198,30,201,198 17 3904 . C <*> 0 . DP=11;I16=2,9,0,0,390,14732,0,0,614,35138,0,0,198,4402,0,0;QS=1,0;MQ0F=0 PL 0,33,243 17 3905 . C <*> 0 . DP=11;I16=2,9,0,0,429,16811,0,0,614,35138,0,0,201,4483,0,0;QS=1,0;MQ0F=0 PL 0,33,255 17 3906 . T <*> 0 . DP=11;I16=2,9,0,0,440,17690,0,0,614,35138,0,0,204,4574,0,0;QS=1,0;MQ0F=0 PL 0,33,253 @@ -3931,7 +3930,7 @@ 17 3909 . T <*> 0 . DP=11;I16=2,9,0,0,395,14975,0,0,614,35138,0,0,211,4811,0,0;QS=1,0;MQ0F=0 PL 0,33,237 17 3910 . A <*> 0 . DP=10;I16=2,8,0,0,351,12613,0,0,554,31538,0,0,213,4845,0,0;QS=1,0;MQ0F=0 PL 0,30,224 17 3911 . C <*> 0 . DP=10;I16=2,8,0,0,338,11622,0,0,554,31538,0,0,215,4887,0,0;QS=1,0;MQ0F=0 PL 0,30,214 -17 3912 . A C,<*> 0 . DP=10;I16=2,7,0,1,319,11431,16,256,494,27938,60,3600,205,4767,11,121;QS=0.951807,0.0481928,0;SGB=-0.379885;RPBZ=-1.5667;MQBZ=0.5;MQSBZ=3;BQBZ=-1.59599;SCBZ=1.07088;FS=0;MQ0F=0 PL 0,14,202,27,205,208 +17 3912 . A C,<*> 0 . DP=10;I16=2,7,0,1,319,11431,16,256,494,27938,60,3600,205,4767,11,121;QS=0.951807,0.0481928,0;SGB=-0.379885;RPBZ=-1.5667;MQBZ=0.5;MQSBZ=3;BQBZ=-1.59599;SCBZ=1.07088;MQ0F=0 PL 0,14,202,27,205,208 17 3913 . C <*> 0 . DP=10;I16=2,8,0,0,369,14053,0,0,554,31538,0,0,217,4899,0,0;QS=1,0;MQ0F=0 PL 0,30,234 17 3914 . T <*> 0 . DP=10;I16=2,8,0,0,364,13634,0,0,554,31538,0,0,218,4920,0,0;QS=1,0;MQ0F=0 PL 0,30,228 17 3915 . C <*> 0 . DP=10;I16=2,8,0,0,360,13176,0,0,554,31538,0,0,219,4951,0,0;QS=1,0;MQ0F=0 PL 0,30,229 @@ -3955,11 +3954,11 @@ 17 3933 . T <*> 0 . DP=9;I16=2,7,0,0,309,11545,0,0,494,27938,0,0,175,3953,0,0;QS=1,0;MQ0F=0 PL 0,27,218 17 3934 . C <*> 0 . DP=9;I16=2,7,0,0,312,11150,0,0,494,27938,0,0,171,3857,0,0;QS=1,0;MQ0F=0 PL 0,27,212 17 3935 . C <*> 0 . DP=9;I16=2,7,0,0,275,8779,0,0,494,27938,0,0,167,3769,0,0;QS=1,0;MQ0F=0 PL 0,27,185 -17 3936 . A G,<*> 0 . DP=9;I16=0,0,2,7,0,0,312,11304,0,0,494,27938,0,0,163,3689;QS=0,1,0;VDB=0.356759;SGB=-0.662043;MQSBZ=2.82843;FS=0;MQ0F=0 PL 217,27,0,217,27,217 +17 3936 . A G,<*> 0 . DP=9;I16=0,0,2,7,0,0,312,11304,0,0,494,27938,0,0,163,3689;QS=0,1,0;VDB=0.356759;SGB=-0.662043;MQSBZ=2.82843;MQ0F=0 PL 217,27,0,217,27,217 17 3937 . C <*> 0 . DP=8;I16=1,7,0,0,238,7390,0,0,457,26569,0,0,160,3616,0,0;QS=1,0;MQ0F=0 PL 0,24,156 17 3938 . G <*> 0 . DP=8;I16=1,7,0,0,256,8698,0,0,457,26569,0,0,156,3500,0,0;QS=1,0;MQ0F=0 PL 0,24,176 17 3939 . C <*> 0 . DP=8;I16=1,7,0,0,258,8868,0,0,457,26569,0,0,152,3392,0,0;QS=1,0;MQ0F=0 PL 0,24,176 -17 3940 . A C,<*> 0 . DP=8;I16=1,6,0,1,224,7816,4,16,397,22969,60,3600,123,2667,25,625;QS=0.982143,0.0178571,0;SGB=-0.379885;RPBZ=-1.52753;MQBZ=0.377964;MQSBZ=2.64575;BQBZ=-1.52753;SCBZ=-0.377964;FS=0;MQ0F=0 PL 0,15,157,21,160,157 +17 3940 . A C,<*> 0 . DP=8;I16=1,6,0,1,224,7816,4,16,397,22969,60,3600,123,2667,25,625;QS=0.982143,0.0178571,0;SGB=-0.379885;RPBZ=-1.52753;MQBZ=0.377964;MQSBZ=2.64575;BQBZ=-1.52753;SCBZ=-0.377964;MQ0F=0 PL 0,15,157,21,160,157 17 3941 . C <*> 0 . DP=8;I16=1,7,0,0,264,9696,0,0,457,26569,0,0,144,3200,0,0;QS=1,0;MQ0F=0 PL 0,24,181 17 3942 . C <*> 0 . DP=8;I16=1,7,0,0,295,11227,0,0,457,26569,0,0,140,3116,0,0;QS=1,0;MQ0F=0 PL 0,24,195 17 3943 . T <*> 0 . DP=8;I16=1,7,0,0,292,10930,0,0,457,26569,0,0,136,3040,0,0;QS=1,0;MQ0F=0 PL 0,24,195 @@ -3968,7 +3967,7 @@ 17 3946 . T <*> 0 . DP=7;I16=1,6,0,0,221,7929,0,0,397,22969,0,0,126,2856,0,0;QS=1,0;MQ0F=0 PL 0,21,160 17 3947 . A <*> 0 . DP=6;I16=1,5,0,0,193,6675,0,0,337,19369,0,0,124,2806,0,0;QS=1,0;MQ0F=0 PL 0,18,149 17 3948 . C <*> 0 . DP=6;I16=1,5,0,0,202,7182,0,0,337,19369,0,0,122,2760,0,0;QS=1,0;MQ0F=0 PL 0,18,155 -17 3949 . A C,<*> 0 . DP=6;I16=1,4,0,1,152,5110,24,576,277,15769,60,3600,95,2093,25,625;QS=0.861272,0.138728,0;SGB=-0.379885;RPBZ=-1.46385;MQBZ=0.447214;MQSBZ=2.23607;BQBZ=-0.87831;SCBZ=-0.447214;FS=0;MQ0F=0 PL 6,0,110,21,113,126 +17 3949 . A C,<*> 0 . DP=6;I16=1,4,0,1,152,5110,24,576,277,15769,60,3600,95,2093,25,625;QS=0.861272,0.138728,0;SGB=-0.379885;RPBZ=-1.46385;MQBZ=0.447214;MQSBZ=2.23607;BQBZ=-0.87831;SCBZ=-0.447214;MQ0F=0 PL 6,0,110,21,113,126 17 3950 . C <*> 0 . DP=6;I16=1,5,0,0,217,8159,0,0,337,19369,0,0,118,2680,0,0;QS=1,0;MQ0F=0 PL 0,18,168 17 3951 . T <*> 0 . DP=6;I16=1,5,0,0,194,7366,0,0,337,19369,0,0,116,2646,0,0;QS=1,0;MQ0F=0 PL 0,18,154 17 3952 . C <*> 0 . DP=6;I16=1,5,0,0,183,6271,0,0,337,19369,0,0,114,2616,0,0;QS=1,0;MQ0F=0 PL 0,18,146 diff --git a/test/mpileup/mpileup.2.out b/test/mpileup/mpileup.2.out index 30de883c1..ba918adc4 100644 --- a/test/mpileup/mpileup.2.out +++ b/test/mpileup/mpileup.2.out @@ -12,7 +12,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -24,29 +23,29 @@ 17 100 . C <*> 0 . DP=18;I16=16,1,0,0,672,27586,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,189:9:0 0,9,118:3:0 0,15,134:5:0 17 101 . C <*> 0 . DP=18;I16=16,1,0,0,630,24730,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,182:9:0 0,9,108:3:0 0,15,132:5:0 17 102 . C <*> 0 . DP=18;I16=16,1,0,0,676,27812,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,188:9:0 0,9,121:3:0 0,15,139:5:0 -17 103 . T C,<*> 0 . DP=18;I16=15,1,1,0,668,28542,6,36,929,54841,29,841,323,7035,6,36;QS=2.98256,0.0174419,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64924;SCBZ=4;FS=0;MQ0F=0 PL:DP:DV 0,17,184,24,187,185:9:1 0,9,118,9,118,118:3:0 0,15,147,15,147,147:5:0 -17 104 . G C,<*> 0 . DP=18;I16=15,1,1,0,601,24163,3,9,929,54841,29,841,320,6884,7,49;QS=2.98726,0.0127389,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64309;SCBZ=4;FS=0;MQ0F=0 PL:DP:DV 0,18,173,24,176,173:9:1 0,9,101,9,101,101:3:0 0,15,133,15,133,133:5:0 +17 103 . T C,<*> 0 . DP=18;I16=15,1,1,0,668,28542,6,36,929,54841,29,841,323,7035,6,36;QS=2.98256,0.0174419,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64924;SCBZ=4;MQ0F=0 PL:DP:DV 0,17,184,24,187,185:9:1 0,9,118,9,118,118:3:0 0,15,147,15,147,147:5:0 +17 104 . G C,<*> 0 . DP=18;I16=15,1,1,0,601,24163,3,9,929,54841,29,841,320,6884,7,49;QS=2.98726,0.0127389,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64309;SCBZ=4;MQ0F=0 PL:DP:DV 0,18,173,24,176,173:9:1 0,9,101,9,101,101:3:0 0,15,133,15,133,133:5:0 17 105 . G <*> 0 . DP=19;I16=17,1,0,0,603,22351,0,0,1018,59282,0,0,325,6815,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,171:10:0 0,9,106:3:0 0,15,125:5:0 17 106 . G <*> 0 . DP=19;I16=17,1,0,0,636,25058,0,0,1018,59282,0,0,324,6718,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,190:10:0 0,9,92:3:0 0,15,124:5:0 17 107 . C <*> 0 . DP=19;I16=17,1,0,0,686,27952,0,0,1018,59282,0,0,323,6643,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,192:10:0 0,9,119:3:0 0,15,136:5:0 17 108 . C <*> 0 . DP=19;I16=17,1,0,0,681,27429,0,0,1018,59282,0,0,322,6590,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,190:10:0 0,9,119:3:0 0,15,135:5:0 -17 109 . T C,<*> 0 . DP=19;I16=16,1,1,0,716,30648,2,4,989,58441,29,841,309,6415,12,144;QS=2.98922,0.0107817,0;SGB=-0.556633;RPBZ=-0.674966;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.6661;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV 0,20,191,27,194,191:10:1 0,9,120,9,120,120:3:0 0,15,150,15,150,150:5:0 +17 109 . T C,<*> 0 . DP=19;I16=16,1,1,0,716,30648,2,4,989,58441,29,841,309,6415,12,144;QS=2.98922,0.0107817,0;SGB=-0.556633;RPBZ=-0.674966;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.6661;SCBZ=3;MQ0F=0 PL:DP:DV 0,20,191,27,194,191:10:1 0,9,120,9,120,120:3:0 0,15,150,15,150,150:5:0 17 110 . G <*> 0 . DP=19;I16=17,1,0,0,688,28036,0,0,1018,59282,0,0,320,6550,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,194:10:0 0,9,113:3:0 0,15,136:5:0 17 111 . G <*> 0 . DP=19;I16=17,1,0,0,573,21453,0,0,1018,59282,0,0,318,6514,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,167:10:0 0,9,95:3:0 0,15,119:5:0 -17 112 . C G,<*> 0 . DP=19;I16=16,1,1,0,657,26565,2,4,989,58441,29,841,301,6277,15,225;QS=2.98907,0.010929,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65292;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV 0,20,187,27,190,187:10:1 0,9,103,9,103,103:3:0 0,15,135,15,135,135:5:0 -17 113 . A G,<*> 0 . DP=19;I16=16,1,1,0,635,25055,4,16,989,58441,29,841,297,6207,16,256;QS=2.98817,0.0118343,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65205;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV 0,20,172,27,175,172:10:1 0,9,102,9,102,102:3:0 0,15,139,15,139,139:5:0 +17 112 . C G,<*> 0 . DP=19;I16=16,1,1,0,657,26565,2,4,989,58441,29,841,301,6277,15,225;QS=2.98907,0.010929,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65292;SCBZ=3;MQ0F=0 PL:DP:DV 0,20,187,27,190,187:10:1 0,9,103,9,103,103:3:0 0,15,135,15,135,135:5:0 +17 113 . A G,<*> 0 . DP=19;I16=16,1,1,0,635,25055,4,16,989,58441,29,841,297,6207,16,256;QS=2.98817,0.0118343,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65205;SCBZ=3;MQ0F=0 PL:DP:DV 0,20,172,27,175,172:10:1 0,9,102,9,102,102:3:0 0,15,139,15,139,139:5:0 17 114 . C <*> 0 . DP=19;I16=17,1,0,0,660,25876,0,0,1018,59282,0,0,310,6446,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,181:10:0 0,9,113:3:0 0,15,133:5:0 -17 115 . C A,<*> 0 . DP=21;I16=17,2,1,0,688,27426,12,144,1078,62882,29,841,283,5827,25,625;QS=2.88785,0.11215,0;SGB=-0.556633;RPBZ=0.260329;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.47798;SCBZ=-0.418446;FS=0;MQ0F=0 PL:DP:DV 0,30,189,30,189,189:10:0 3,0,86,9,89,93:3:1 0,21,153,21,153,153:7:0 -17 116 . A C,<*> 0 . DP=21;I16=17,2,1,0,705,27791,2,4,1078,62882,29,841,287,6073,19,361;QS=2.98873,0.0112676,0;SGB=-0.556633;RPBZ=0.0867763;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.65814;SCBZ=2.65016;FS=0;MQ0F=0 PL:DP:DV 0,20,179,27,182,179:10:1 0,9,102,9,102,102:3:0 0,21,175,21,175,175:7:0 +17 115 . C A,<*> 0 . DP=21;I16=17,2,1,0,688,27426,12,144,1078,62882,29,841,283,5827,25,625;QS=2.88785,0.11215,0;SGB=-0.556633;RPBZ=0.260329;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.47798;SCBZ=-0.418446;MQ0F=0 PL:DP:DV 0,30,189,30,189,189:10:0 3,0,86,9,89,93:3:1 0,21,153,21,153,153:7:0 +17 116 . A C,<*> 0 . DP=21;I16=17,2,1,0,705,27791,2,4,1078,62882,29,841,287,6073,19,361;QS=2.98873,0.0112676,0;SGB=-0.556633;RPBZ=0.0867763;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.65814;SCBZ=2.65016;MQ0F=0 PL:DP:DV 0,20,179,27,182,179:10:1 0,9,102,9,102,102:3:0 0,21,175,21,175,175:7:0 17 117 . G <*> 0 . DP=21;I16=18,2,0,0,715,28045,0,0,1107,63723,0,0,304,6444,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,185:10:0 0,9,97:3:0 0,21,177:7:0 17 118 . G <*> 0 . DP=20;I16=17,2,0,0,620,23470,0,0,1047,60123,0,0,303,6481,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,175:9:0 0,9,65:3:0 0,21,162:7:0 17 119 . G <*> 0 . DP=19;I16=16,2,0,0,619,23459,0,0,987,56523,0,0,301,6493,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,176:9:0 0,6,76:2:0 0,21,160:7:0 -17 120 . A G,<*> 0 . DP=19;I16=15,2,1,0,646,25392,4,16,958,55682,29,841,277,5999,23,529;QS=2.9873,0.0126984,0;SGB=-0.556633;RPBZ=0.28942;MQBZ=-2.23607;MQSBZ=-1.30384;BQBZ=-1.6486;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV 0,18,171,24,174,171:9:1 0,6,88,6,88,88:2:0 0,21,171,21,171,171:7:0 +17 120 . A G,<*> 0 . DP=19;I16=15,2,1,0,646,25392,4,16,958,55682,29,841,277,5999,23,529;QS=2.9873,0.0126984,0;SGB=-0.556633;RPBZ=0.28942;MQBZ=-2.23607;MQSBZ=-1.30384;BQBZ=-1.6486;SCBZ=3;MQ0F=0 PL:DP:DV 0,18,171,24,174,171:9:1 0,6,88,6,88,88:2:0 0,21,171,21,171,171:7:0 17 121 . G <*> 0 . DP=19;I16=16,2,0,0,650,25148,0,0,987,56523,0,0,298,6534,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,181:9:0 0,6,84:2:0 0,21,168:7:0 17 122 . C <*> 0 . DP=20;I16=17,2,0,0,696,27784,0,0,1047,60123,0,0,296,6560,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,180:9:0 0,9,107:3:0 0,21,178:7:0 17 123 . T <*> 0 . DP=18;I16=15,2,0,0,647,26145,0,0,927,52923,0,0,296,6554,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,170:8:0 0,9,123:3:0 0,18,166:6:0 17 124 . T <*> 0 . DP=19;I16=16,2,0,0,606,22002,0,0,987,56523,0,0,296,6564,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,154:9:0 0,9,114:3:0 0,18,154:6:0 -17 125 . A T,<*> 0 . DP=18;I16=14,2,1,0,589,22565,4,16,898,52082,29,841,272,5916,25,625;QS=2.98444,0.0155642,0;SGB=-0.556633;RPBZ=1.02125;MQBZ=-2.16025;MQSBZ=-1.23956;BQBZ=-1.64106;SCBZ=2.91548;FS=0;MQ0F=0 PL:DP:DV 0,15,149,21,152,149:8:1 0,9,114,9,114,114:3:0 0,18,162,18,162,162:6:0 +17 125 . A T,<*> 0 . DP=18;I16=14,2,1,0,589,22565,4,16,898,52082,29,841,272,5916,25,625;QS=2.98444,0.0155642,0;SGB=-0.556633;RPBZ=1.02125;MQBZ=-2.16025;MQSBZ=-1.23956;BQBZ=-1.64106;SCBZ=2.91548;MQ0F=0 PL:DP:DV 0,15,149,21,152,149:8:1 0,9,114,9,114,114:3:0 0,18,162,18,162,162:6:0 17 126 . A <*> 0 . DP=18;I16=15,2,0,0,629,24725,0,0,927,52923,0,0,298,6536,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,162:8:0 0,9,117:3:0 0,18,174:6:0 17 127 . C <*> 0 . DP=18;I16=15,2,0,0,627,24331,0,0,927,52923,0,0,299,6549,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,163:8:0 0,9,119:3:0 0,18,160:6:0 17 128 . A <*> 0 . DP=18;I16=15,2,0,0,660,26364,0,0,927,52923,0,0,300,6580,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,169:8:0 0,9,121:3:0 0,18,168:6:0 @@ -80,7 +79,7 @@ 17 156 . C <*> 0 . DP=14;I16=12,2,0,0,536,20884,0,0,809,47641,0,0,266,5934,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,163:7:0 0,6,84:2:0 0,15,150:5:0 17 157 . C <*> 0 . DP=14;I16=12,2,0,0,555,22081,0,0,809,47641,0,0,264,5904,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,169:7:0 0,6,85:2:0 0,15,149:5:0 17 158 . T <*> 0 . DP=14;I16=12,2,0,0,568,23154,0,0,809,47641,0,0,262,5886,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,170:7:0 0,6,84:2:0 0,15,159:5:0 -17 159 . A G,<*> 0 . DP=15;I16=12,2,1,0,519,19467,5,25,809,47641,60,3600,260,5880,0,0;QS=2.97076,0.0292398,0;SGB=-0.556633;RPBZ=-1.62019;MQBZ=0.267261;MQSBZ=-2.54951;BQBZ=-1.63041;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,21,157,21,157,157:7:0 0,6,83,6,83,83:2:0 0,10,129,15,132,129:6:1 +17 159 . A G,<*> 0 . DP=15;I16=12,2,1,0,519,19467,5,25,809,47641,60,3600,260,5880,0,0;QS=2.97076,0.0292398,0;SGB=-0.556633;RPBZ=-1.62019;MQBZ=0.267261;MQSBZ=-2.54951;BQBZ=-1.63041;SCBZ=0;MQ0F=0 PL:DP:DV 0,21,157,21,157,157:7:0 0,6,83,6,83,83:2:0 0,10,129,15,132,129:6:1 17 160 . G <*> 0 . DP=15;I16=13,2,0,0,547,20633,0,0,869,51241,0,0,259,5887,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,165:7:0 0,6,85:2:0 0,18,139:6:0 17 161 . A <*> 0 . DP=15;I16=13,2,0,0,568,21610,0,0,869,51241,0,0,258,5908,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,157:7:0 0,6,83:2:0 0,18,162:6:0 17 162 . A <*> 0 . DP=15;I16=13,2,0,0,558,21206,0,0,869,51241,0,0,255,5843,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,147:7:0 0,6,87:2:0 0,18,167:6:0 @@ -111,7 +110,7 @@ 17 187 . C <*> 0 . DP=14;I16=13,1,0,0,511,18979,0,0,809,47641,0,0,266,5952,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,18,147:6:0 0,3,38:1:0 0,21,172:7:0 17 188 . C <*> 0 . DP=14;I16=13,1,0,0,496,18042,0,0,809,47641,0,0,267,5989,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,18,147:6:0 0,3,37:1:0 0,21,162:7:0 17 189 . C <*> 0 . DP=15;I16=13,2,0,0,552,20504,0,0,838,48482,0,0,268,6040,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,18,152:6:0 0,6,67:2:0 0,21,167:7:0 -17 190 . A C,<*> 0 . DP=15;I16=12,2,1,0,500,18230,5,25,778,44882,60,3600,243,5381,25,625;QS=2.97664,0.0233645,0;SGB=-0.556633;RPBZ=0;MQBZ=0.392232;MQSBZ=-3.74166;BQBZ=-1.63041;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,18,138,18,138,138:6:0 0,6,68,6,68,68:2:0 0,12,153,18,156,153:7:1 +17 190 . A C,<*> 0 . DP=15;I16=12,2,1,0,500,18230,5,25,778,44882,60,3600,243,5381,25,625;QS=2.97664,0.0233645,0;SGB=-0.556633;RPBZ=0;MQBZ=0.392232;MQSBZ=-3.74166;BQBZ=-1.63041;SCBZ=0;MQ0F=0 PL:DP:DV 0,18,138,18,138,138:6:0 0,6,68,6,68,68:2:0 0,12,153,18,156,153:7:1 17 191 . T <*> 0 . DP=15;I16=13,2,0,0,534,19276,0,0,838,48482,0,0,267,5939,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,18,143:6:0 0,6,67:2:0 0,21,169:7:0 17 192 . G <*> 0 . DP=15;I16=13,2,0,0,499,17439,0,0,838,48482,0,0,266,5890,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,18,143:6:0 0,6,67:2:0 0,21,151:7:0 17 193 . T <*> 0 . DP=15;I16=13,2,0,0,505,17811,0,0,838,48482,0,0,265,5859,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,18,140:6:0 0,6,63:2:0 0,21,157:7:0 @@ -144,10 +143,10 @@ 17 220 . G <*> 0 . DP=14;I16=11,3,0,0,495,18407,0,0,747,42123,0,0,267,6079,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,188:7:0 0,9,88:3:0 0,12,84:4:0 17 221 . A <*> 0 . DP=14;I16=11,3,0,0,488,17688,0,0,747,42123,0,0,267,6135,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,176:7:0 0,9,89:3:0 0,12,101:4:0 17 222 . A <*> 0 . DP=14;I16=11,3,0,0,479,17747,0,0,747,42123,0,0,267,6203,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,186:7:0 0,9,89:3:0 0,12,73:4:0 -17 223 . G T,<*> 0 . DP=13;I16=9,3,1,0,412,14782,8,64,627,34923,60,3600,243,5657,25,625;QS=2.96596,0.0340426,0;SGB=-0.556633;RPBZ=1.07052;MQBZ=0.547723;MQSBZ=-3.4641;BQBZ=-1.60577;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,11,166,18,169,167:7:1 0,6,53,6,53,53:2:0 0,12,81,12,81,81:4:0 +17 223 . G T,<*> 0 . DP=13;I16=9,3,1,0,412,14782,8,64,627,34923,60,3600,243,5657,25,625;QS=2.96596,0.0340426,0;SGB=-0.556633;RPBZ=1.07052;MQBZ=0.547723;MQSBZ=-3.4641;BQBZ=-1.60577;SCBZ=0;MQ0F=0 PL:DP:DV 0,11,166,18,169,167:7:1 0,6,53,6,53,53:2:0 0,12,81,12,81,81:4:0 17 224 . G <*> 0 . DP=12;I16=9,3,0,0,379,12759,0,0,627,34923,0,0,270,6370,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,18,168:6:0 0,6,50:2:0 0,12,70:4:0 17 225 . C <*> 0 . DP=12;I16=9,3,0,0,390,13960,0,0,627,34923,0,0,272,6466,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,18,165:6:0 0,6,48:2:0 0,12,86:4:0 -17 226 . A G,C,<*> 0 . DP=13;I16=8,3,1,1,381,13669,6,18,567,31323,89,4441,248,5894,44,986;QS=2.94293,0.0392157,0.0178571,0;VDB=0.84;SGB=-2.62246;RPBZ=-0.592157;MQBZ=-0.615457;MQSBZ=-3.4641;BQBZ=-2.17723;SCBZ=2.34521;FS=0;MQ0F=0 PL:DP:DV 0,18,159,12,162,159,18,159,162,159:7:1 0,6,53,6,53,53,6,53,53,53:2:0 0,5,79,9,82,80,9,82,80,80:4:1 +17 226 . A G,C,<*> 0 . DP=13;I16=8,3,1,1,381,13669,6,18,567,31323,89,4441,248,5894,44,986;QS=2.94293,0.0392157,0.0178571,0;VDB=0.84;SGB=-2.62246;RPBZ=-0.592157;MQBZ=-0.615457;MQSBZ=-3.4641;BQBZ=-2.17723;SCBZ=2.34521;MQ0F=0 PL:DP:DV 0,18,159,12,162,159,18,159,162,159:7:1 0,6,53,6,53,53,6,53,53,53:2:0 0,5,79,9,82,80,9,82,80,80:4:1 17 227 . C <*> 0 . DP=13;I16=9,4,0,0,412,14342,0,0,656,35764,0,0,292,6878,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,190:7:0 0,6,53:2:0 0,12,75:4:0 17 228 . C <*> 0 . DP=13;I16=9,4,0,0,417,14381,0,0,656,35764,0,0,292,6884,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,187:7:0 0,6,45:2:0 0,12,96:4:0 17 229 . G <*> 0 . DP=13;I16=9,4,0,0,368,11524,0,0,656,35764,0,0,292,6898,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,145:7:0 0,6,53:2:0 0,12,70:4:0 @@ -158,7 +157,7 @@ 17 234 . A <*> 0 . DP=14;I16=10,4,0,0,502,18390,0,0,716,39364,0,0,292,6988,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,185:7:0 0,6,53:2:0 0,15,123:5:0 17 235 . A <*> 0 . DP=14;I16=10,4,0,0,488,17796,0,0,716,39364,0,0,291,6951,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,21,186:7:0 0,6,53:2:0 0,15,115:5:0 17 236 . G <*> 0 . DP=15;I16=11,4,0,0,501,17481,0,0,776,42964,0,0,290,6924,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,206:8:0 0,6,53:2:0 0,15,103:5:0 -17 237 . A C,<*> 0 . DP=14;I16=9,4,1,0,465,16877,8,64,656,35764,60,3600,266,6282,25,625;QS=2.93162,0.0683761,0;SGB=-0.556633;RPBZ=1.11754;MQBZ=0.632456;MQSBZ=-3.60555;BQBZ=-1.61959;SCBZ=-0.27735;FS=0;MQ0F=0 PL:DP:DV 0,24,206,24,206,206:8:0 0,6,53,6,53,53:2:0 0,3,84,9,87,87:4:1 +17 237 . A C,<*> 0 . DP=14;I16=9,4,1,0,465,16877,8,64,656,35764,60,3600,266,6282,25,625;QS=2.93162,0.0683761,0;SGB=-0.556633;RPBZ=1.11754;MQBZ=0.632456;MQSBZ=-3.60555;BQBZ=-1.61959;SCBZ=-0.27735;MQ0F=0 PL:DP:DV 0,24,206,24,206,206:8:0 0,6,53,6,53,53:2:0 0,3,84,9,87,87:4:1 17 238 . C <*> 0 . DP=14;I16=10,4,0,0,482,17238,0,0,716,39364,0,0,292,6900,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,24,211:8:0 0,6,53:2:0 0,12,82:4:0 17 239 . A <*> 0 . DP=15;I16=10,5,0,0,525,19155,0,0,776,42964,0,0,292,6852,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,223:9:0 0,6,50:2:0 0,12,108:4:0 17 240 . C <*> 0 . DP=15;I16=10,5,0,0,512,17930,0,0,776,42964,0,0,292,6764,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,220:9:0 0,6,53:2:0 0,12,106:4:0 @@ -188,18 +187,18 @@ 17 264 . C <*> 0 . DP=22;I16=10,12,0,0,821,31325,0,0,1049,54897,0,0,386,8326,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,15,104:5:0 0,18,172:6:0 17 265 . A <*> 0 . DP=21;I16=9,12,0,0,800,31906,0,0,989,51297,0,0,390,8380,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,15,114:5:0 0,15,129:5:0 17 266 . G <*> 0 . DP=21;I16=9,12,0,0,754,28204,0,0,989,51297,0,0,394,8458,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,15,99:5:0 0,15,138:5:0 -17 267 . T G,<*> 0 . DP=21;I16=9,11,0,1,739,27465,8,64,960,50456,29,841,373,7935,25,625;QS=2.94203,0.057971,0;SGB=-0.556633;RPBZ=-0.330396;MQBZ=-1.23153;MQSBZ=-3.3021;BQBZ=-1.66282;SCBZ=2.91633;FS=0;MQ0F=0 PL:DP:DV 0,33,254,33,254,254:11:0 0,6,93,12,96,96:5:1 0,15,149,15,149,149:5:0 +17 267 . T G,<*> 0 . DP=21;I16=9,11,0,1,739,27465,8,64,960,50456,29,841,373,7935,25,625;QS=2.94203,0.057971,0;SGB=-0.556633;RPBZ=-0.330396;MQBZ=-1.23153;MQSBZ=-3.3021;BQBZ=-1.66282;SCBZ=2.91633;MQ0F=0 PL:DP:DV 0,33,254,33,254,254:11:0 0,6,93,12,96,96:5:1 0,15,149,15,149,149:5:0 17 268 . T <*> 0 . DP=21;I16=9,12,0,0,748,27708,0,0,989,51297,0,0,402,8686,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,238:11:0 0,15,110:5:0 0,15,156:5:0 17 269 . C <*> 0 . DP=22;I16=9,13,0,0,767,28641,0,0,1018,52138,0,0,406,8836,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,15,91:5:0 0,15,154:5:0 17 270 . C <*> 0 . DP=22;I16=9,13,0,0,766,28210,0,0,1018,52138,0,0,410,8962,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,15,98:5:0 0,15,143:5:0 17 271 . T <*> 0 . DP=22;I16=9,13,0,0,847,32935,0,0,1018,52138,0,0,413,9065,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,15,113:5:0 0,15,152:5:0 17 272 . C <*> 0 . DP=22;I16=9,13,0,0,815,31449,0,0,1018,52138,0,0,415,9143,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,15,97:5:0 0,15,149:5:0 -17 273 . T C,<*> 0 . DP=22;I16=9,12,0,1,798,30664,5,25,989,51297,29,841,392,8620,25,625;QS=2.96094,0.0390625,0;SGB=-0.556633;RPBZ=-0.236567;MQBZ=-1.16701;MQSBZ=-3.42286;BQBZ=-1.66779;SCBZ=3.00076;FS=0;MQ0F=0 PL:DP:DV 0,36,255,36,255,255:12:0 0,7,89,12,92,90:5:1 0,15,161,15,161,161:5:0 +17 273 . T C,<*> 0 . DP=22;I16=9,12,0,1,798,30664,5,25,989,51297,29,841,392,8620,25,625;QS=2.96094,0.0390625,0;SGB=-0.556633;RPBZ=-0.236567;MQBZ=-1.16701;MQSBZ=-3.42286;BQBZ=-1.66779;SCBZ=3.00076;MQ0F=0 PL:DP:DV 0,36,255,36,255,255:12:0 0,7,89,12,92,90:5:1 0,15,161,15,161,161:5:0 17 274 . C <*> 0 . DP=22;I16=9,13,0,0,767,28193,0,0,1018,52138,0,0,419,9371,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,15,101:5:0 0,15,144:5:0 17 275 . C <*> 0 . DP=20;I16=7,13,0,0,768,29994,0,0,898,44938,0,0,423,9519,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,15,114:5:0 0,12,122:4:0 17 276 . A <*> 0 . DP=20;I16=7,13,0,0,805,32931,0,0,898,44938,0,0,424,9538,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,253:11:0 0,15,122:5:0 0,12,124:4:0 17 277 . G <*> 0 . DP=20;I16=7,13,0,0,764,29732,0,0,898,44938,0,0,425,9579,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,15,114:5:0 0,12,121:4:0 -17 278 . A C,<*> 0 . DP=21;I16=6,14,1,0,722,26452,7,49,867,42179,60,3600,415,9521,11,121;QS=2.97935,0.020649,0;SGB=-0.556633;RPBZ=1.65198;MQBZ=1.0247;MQSBZ=-3.24037;BQBZ=-1.66667;SCBZ=-0.324037;FS=0;MQ0F=0 PL:DP:DV 0,22,231,30,234,231:11:1 0,18,123,18,123,123:6:0 0,12,121,12,121,121:4:0 +17 278 . A C,<*> 0 . DP=21;I16=6,14,1,0,722,26452,7,49,867,42179,60,3600,415,9521,11,121;QS=2.97935,0.020649,0;SGB=-0.556633;RPBZ=1.65198;MQBZ=1.0247;MQSBZ=-3.24037;BQBZ=-1.66667;SCBZ=-0.324037;MQ0F=0 PL:DP:DV 0,22,231,30,234,231:11:1 0,18,123,18,123,123:6:0 0,12,121,12,121,121:4:0 17 279 . A <*> 0 . DP=22;I16=7,15,0,0,786,28694,0,0,956,46620,0,0,427,9677,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,18,123:6:0 0,12,122:4:0 17 280 . A <*> 0 . DP=22;I16=7,15,0,0,815,31561,0,0,956,46620,0,0,428,9684,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,253:12:0 0,18,130:6:0 0,12,129:4:0 17 281 . G <*> 0 . DP=22;I16=7,15,0,0,820,31416,0,0,956,46620,0,0,428,9662,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,18,122:6:0 0,12,123:4:0 @@ -218,13 +217,13 @@ 17 294 . A <*> 0 . DP=26;I16=10,16,0,0,931,33937,0,0,1227,63779,0,0,443,9785,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,252:12:0 0,24,201:8:0 0,18,161:6:0 17 295 . C <*> 0 . DP=25;I16=10,15,0,0,909,34117,0,0,1198,62938,0,0,447,9833,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,183:8:0 0,18,159:6:0 17 296 . A <*> 0 . DP=25;I16=10,15,0,0,874,31846,0,0,1198,62938,0,0,451,9905,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,169:8:0 0,18,169:6:0 -17 297 . C G,<*> 0 . DP=25;I16=9,15,1,0,901,34305,4,16,1138,59338,60,3600,445,9901,10,100;QS=2.98261,0.0173913,0;SGB=-0.556633;RPBZ=-1.24856;MQBZ=0.806872;MQSBZ=-3.22749;BQBZ=-1.67542;SCBZ=-0.368383;FS=0;MQ0F=0 PL:DP:DV 0,33,255,33,255,255:11:0 0,15,168,21,171,168:8:1 0,18,161,18,161,161:6:0 +17 297 . C G,<*> 0 . DP=25;I16=9,15,1,0,901,34305,4,16,1138,59338,60,3600,445,9901,10,100;QS=2.98261,0.0173913,0;SGB=-0.556633;RPBZ=-1.24856;MQBZ=0.806872;MQSBZ=-3.22749;BQBZ=-1.67542;SCBZ=-0.368383;MQ0F=0 PL:DP:DV 0,33,255,33,255,255:11:0 0,15,168,21,171,168:8:1 0,18,161,18,161,161:6:0 17 298 . A <*> 0 . DP=26;I16=11,15,0,0,936,34652,0,0,1258,66538,0,0,459,10121,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,184:8:0 0,21,191:7:0 17 299 . C <*> 0 . DP=27;I16=11,15,0,0,971,36863,0,0,1258,66538,0,0,464,10266,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,193:8:0 0,21,189:7:0 17 300 . A <*> 0 . DP=27;I16=11,15,0,0,1001,39455,0,0,1258,66538,0,0,469,10437,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,204:8:0 0,21,210:7:0 17 301 . G <*> 0 . DP=25;I16=10,14,0,0,928,36116,0,0,1169,62097,0,0,476,10632,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,255:10:0 0,21,195:7:0 0,21,196:7:0 17 302 . T <*> 0 . DP=25;I16=10,14,0,0,879,32885,0,0,1169,62097,0,0,483,10849,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,231:10:0 0,21,172:7:0 0,21,202:7:0 -17 302 . T TA 0 . INDEL;IDV=7;IMF=1;DP=25;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.539485,2.46052;VDB=0.241622;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.22749;BQBZ=-1.67542;SCBZ=-0.268121;FS=0;MQ0F=0 PL:DP:DV 161,0,99:11:6 158,0,14:7:6 201,21,0:7:7 +17 302 . T TA 0 . INDEL;IDV=7;IMF=1;DP=25;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.539485,2.46052;VDB=0.241622;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.22749;BQBZ=-1.67542;SCBZ=-0.268121;MQ0F=0 PL:DP:DV 161,0,99:11:6 158,0,14:7:6 201,21,0:7:7 17 303 . G <*> 0 . DP=25;I16=10,15,0,0,968,37972,0,0,1229,65697,0,0,497,11181,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,21,197:7:0 0,21,195:7:0 17 304 . C <*> 0 . DP=27;I16=11,16,0,0,991,37005,0,0,1318,70138,0,0,503,11359,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,206:8:0 0,24,200:8:0 17 305 . C <*> 0 . DP=27;I16=11,16,0,0,1057,41761,0,0,1318,70138,0,0,510,11508,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,213:8:0 0,24,211:8:0 @@ -257,9 +256,9 @@ 17 332 . A <*> 0 . DP=32;I16=14,18,0,0,1156,42666,0,0,1649,90897,0,0,560,12178,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,27,214:9:0 0,33,255:11:0 17 333 . A <*> 0 . DP=32;I16=14,18,0,0,1141,41987,0,0,1649,90897,0,0,558,12064,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,27,223:9:0 0,33,255:11:0 17 334 . A <*> 0 . DP=32;I16=14,18,0,0,1162,43328,0,0,1649,90897,0,0,556,11986,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,27,221:9:0 0,33,255:11:0 -17 335 . A G,<*> 0 . DP=32;I16=13,18,1,0,1084,40336,4,16,1589,87297,60,3600,555,11943,0,0;QS=2.98919,0.0108108,0;SGB=-0.556633;RPBZ=-1.67936;MQBZ=0.622171;MQSBZ=-2.25492;BQBZ=-1.68602;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV 0,33,252,33,252,252:11:0 0,27,219,27,219,219:9:0 0,25,245,33,248,245:12:1 +17 335 . A G,<*> 0 . DP=32;I16=13,18,1,0,1084,40336,4,16,1589,87297,60,3600,555,11943,0,0;QS=2.98919,0.0108108,0;SGB=-0.556633;RPBZ=-1.67936;MQBZ=0.622171;MQSBZ=-2.25492;BQBZ=-1.68602;SCBZ=-0.258065;MQ0F=0 PL:DP:DV 0,33,252,33,252,252:11:0 0,27,219,27,219,219:9:0 0,25,245,33,248,245:12:1 17 336 . A <*> 0 . DP=32;I16=14,18,0,0,1094,39794,0,0,1649,90897,0,0,555,11935,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,27,212:9:0 0,36,255:12:0 -17 337 . C A,<*> 0 . DP=32;I16=14,17,0,1,1125,42481,5,25,1612,89528,37,1369,536,11590,18,324;QS=2.98113,0.0188679,0;SGB=-0.556633;RPBZ=0.812593;MQBZ=-1.03695;MQSBZ=-2.25492;BQBZ=-1.68353;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV 0,33,255,33,255,255:11:0 0,17,195,24,198,195:9:1 0,36,255,36,255,255:12:0 +17 337 . C A,<*> 0 . DP=32;I16=14,17,0,1,1125,42481,5,25,1612,89528,37,1369,536,11590,18,324;QS=2.98113,0.0188679,0;SGB=-0.556633;RPBZ=0.812593;MQBZ=-1.03695;MQSBZ=-2.25492;BQBZ=-1.68353;SCBZ=-0.258065;MQ0F=0 PL:DP:DV 0,33,255,33,255,255:11:0 0,17,195,24,198,195:9:1 0,36,255,36,255,255:12:0 17 338 . T <*> 0 . DP=30;I16=14,16,0,0,1190,47898,0,0,1560,86456,0,0,554,11878,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,255:10:0 0,24,226:8:0 0,36,255:12:0 17 339 . C <*> 0 . DP=31;I16=14,17,0,0,1130,43210,0,0,1589,87297,0,0,554,11874,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,185:8:0 0,36,255:12:0 17 340 . C <*> 0 . DP=31;I16=14,17,0,0,1196,47044,0,0,1589,87297,0,0,554,11852,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,221:8:0 0,36,255:12:0 @@ -277,11 +276,11 @@ 17 352 . A <*> 0 . DP=31;I16=16,15,0,0,1162,45664,0,0,1651,92815,0,0,569,13029,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,27,230:9:0 0,33,255:11:0 17 353 . G <*> 0 . DP=29;I16=15,14,0,0,1109,43095,0,0,1562,88374,0,0,570,13064,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,255:10:0 0,27,231:9:0 0,30,255:10:0 17 354 . A <*> 0 . DP=28;I16=14,14,0,0,1078,42938,0,0,1502,84774,0,0,571,13075,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,225:9:0 0,27,244:9:0 0,30,255:10:0 -17 355 . G T,<*> 0 . DP=28;I16=14,13,0,1,1001,37907,41,1681,1442,81174,60,3600,547,12487,25,625;QS=2.875,0.125,0;SGB=-0.556633;RPBZ=0.185772;MQBZ=0.520126;MQSBZ=-1.7696;BQBZ=0.683978;SCBZ=-0.27735;FS=0;MQ0F=0 PL:DP:DV 14,0,200,38,203,231:9:1 0,27,222,27,222,222:9:0 0,30,255,30,255,255:10:0 +17 355 . G T,<*> 0 . DP=28;I16=14,13,0,1,1001,37907,41,1681,1442,81174,60,3600,547,12487,25,625;QS=2.875,0.125,0;SGB=-0.556633;RPBZ=0.185772;MQBZ=0.520126;MQSBZ=-1.7696;BQBZ=0.683978;SCBZ=-0.27735;MQ0F=0 PL:DP:DV 14,0,200,38,203,231:9:1 0,27,222,27,222,222:9:0 0,30,255,30,255,255:10:0 17 356 . G <*> 0 . DP=27;I16=14,13,0,0,993,37481,0,0,1465,83405,0,0,574,13174,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,27,228:9:0 0,24,201:8:0 0,30,255:10:0 17 357 . C <*> 0 . DP=28;I16=15,13,0,0,1026,39496,0,0,1525,87005,0,0,575,13209,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,255:10:0 0,24,205:8:0 0,30,252:10:0 17 358 . A <*> 0 . DP=28;I16=15,13,0,0,1050,40518,0,0,1525,87005,0,0,576,13216,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,254:10:0 0,24,197:8:0 0,30,255:10:0 -17 359 . G T,<*> 0 . DP=29;I16=15,13,0,1,1085,42761,10,100,1525,87005,60,3600,552,12620,25,625;QS=2.96032,0.0396825,0;SGB=-0.556633;RPBZ=-0.119611;MQBZ=0.456435;MQSBZ=-1.53333;BQBZ=-1.68246;SCBZ=5.2915;FS=0;MQ0F=0 PL:DP:DV 0,30,255,30,255,255:10:0 0,13,178,21,181,180:8:1 0,33,255,33,255,255:11:0 +17 359 . G T,<*> 0 . DP=29;I16=15,13,0,1,1085,42761,10,100,1525,87005,60,3600,552,12620,25,625;QS=2.96032,0.0396825,0;SGB=-0.556633;RPBZ=-0.119611;MQBZ=0.456435;MQSBZ=-1.53333;BQBZ=-1.68246;SCBZ=5.2915;MQ0F=0 PL:DP:DV 0,30,255,30,255,255:10:0 0,13,178,21,181,180:8:1 0,33,255,33,255,255:11:0 17 360 . A <*> 0 . DP=29;I16=15,14,0,0,1111,43259,0,0,1585,90605,0,0,579,13297,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,252:10:0 0,24,220:8:0 0,33,255:11:0 17 361 . A <*> 0 . DP=29;I16=15,14,0,0,1116,43442,0,0,1585,90605,0,0,579,13273,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,252:10:0 0,24,219:8:0 0,33,255:11:0 17 362 . A <*> 0 . DP=29;I16=16,13,0,0,1104,42700,0,0,1585,90605,0,0,580,13272,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,218:8:0 0,30,255:10:0 @@ -291,13 +290,13 @@ 17 366 . A <*> 0 . DP=29;I16=16,13,0,0,1090,41562,0,0,1585,90605,0,0,581,13167,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,211:8:0 0,30,255:10:0 17 367 . T <*> 0 . DP=29;I16=16,13,0,0,1055,39149,0,0,1585,90605,0,0,579,13093,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,204:8:0 0,30,255:10:0 17 368 . A <*> 0 . DP=29;I16=16,13,0,0,1054,39632,0,0,1585,90605,0,0,576,12998,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,208:8:0 0,30,255:10:0 -17 369 . T G,<*> 0 . DP=28;I16=16,11,0,1,1037,40275,6,36,1496,86164,60,3600,548,12256,25,625;QS=2.97683,0.023166,0;SGB=-0.556633;RPBZ=0.12395;MQBZ=0.408248;MQSBZ=-1.37784;BQBZ=-1.68703;SCBZ=5.19615;FS=0;MQ0F=0 PL:DP:DV 0,30,250,30,250,250:10:0 0,15,189,21,192,190:8:1 0,30,255,30,255,255:10:0 +17 369 . T G,<*> 0 . DP=28;I16=16,11,0,1,1037,40275,6,36,1496,86164,60,3600,548,12256,25,625;QS=2.97683,0.023166,0;SGB=-0.556633;RPBZ=0.12395;MQBZ=0.408248;MQSBZ=-1.37784;BQBZ=-1.68703;SCBZ=5.19615;MQ0F=0 PL:DP:DV 0,30,250,30,250,250:10:0 0,15,189,21,192,190:8:1 0,30,255,30,255,255:10:0 17 370 . C <*> 0 . DP=28;I16=16,12,0,0,1045,40219,0,0,1556,89764,0,0,570,12790,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,255:10:0 0,24,201:8:0 0,30,255:10:0 17 371 . T <*> 0 . DP=29;I16=16,13,0,0,1155,46591,0,0,1616,93364,0,0,567,12725,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,30,255:10:0 0,24,227:8:0 0,33,255:11:0 17 372 . C <*> 0 . DP=30;I16=16,14,0,0,1139,44019,0,0,1676,96964,0,0,564,12636,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,215:8:0 0,33,255:11:0 17 373 . A <*> 0 . DP=30;I16=16,14,0,0,1142,44118,0,0,1676,96964,0,0,561,12525,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,220:8:0 0,33,255:11:0 17 374 . T <*> 0 . DP=30;I16=16,14,0,0,1098,41180,0,0,1676,96964,0,0,556,12344,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,33,255:11:0 0,24,221:8:0 0,33,255:11:0 -17 375 . A T,<*> 0 . DP=31;I16=17,13,0,1,1138,43798,14,196,1676,96964,60,3600,547,12177,4,16;QS=2.9661,0.0338983,0;SGB=-0.556633;RPBZ=-1.45432;MQBZ=0.3849;MQSBZ=-1.26404;BQBZ=-1.68488;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,36,255,36,255,255:12:0 0,24,218,24,218,218:8:0 0,18,255,30,255,255:11:1 +17 375 . A T,<*> 0 . DP=31;I16=17,13,0,1,1138,43798,14,196,1676,96964,60,3600,547,12177,4,16;QS=2.9661,0.0338983,0;SGB=-0.556633;RPBZ=-1.45432;MQBZ=0.3849;MQSBZ=-1.26404;BQBZ=-1.68488;SCBZ=0;MQ0F=0 PL:DP:DV 0,36,255,36,255,255:12:0 0,24,218,24,218,218:8:0 0,18,255,30,255,255:11:1 17 376 . G <*> 0 . DP=31;I16=17,14,0,0,1131,42581,0,0,1736,100564,0,0,547,12073,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,24,220:8:0 0,33,255:11:0 17 377 . T <*> 0 . DP=31;I16=17,14,0,0,1116,41750,0,0,1736,100564,0,0,543,11985,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,24,211:8:0 0,33,255:11:0 17 378 . T <*> 0 . DP=30;I16=18,12,0,0,1098,41066,0,0,1707,99723,0,0,541,11927,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,39,255:13:0 0,21,186:7:0 0,30,255:10:0 @@ -306,7 +305,7 @@ 17 381 . T <*> 0 . DP=29;I16=18,11,0,0,1167,47337,0,0,1678,98882,0,0,537,11729,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,21,211:7:0 0,30,255:10:0 17 382 . T <*> 0 . DP=29;I16=18,11,0,0,1062,40514,0,0,1678,98882,0,0,535,11693,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,21,182:7:0 0,30,255:10:0 17 383 . T <*> 0 . DP=29;I16=18,11,0,0,1059,39847,0,0,1678,98882,0,0,532,11638,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,36,255:12:0 0,21,172:7:0 0,30,255:10:0 -17 384 . A C,<*> 0 . DP=31;I16=19,11,0,1,1077,39885,4,16,1738,102482,60,3600,504,10988,25,625;QS=2.98419,0.0158103,0;SGB=-0.556633;RPBZ=0.615229;MQBZ=0.262613;MQSBZ=-0.333409;BQBZ=-1.68746;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,39,255,39,255,255:13:0 0,15,171,21,174,171:8:1 0,30,255,30,255,255:10:0 +17 384 . A C,<*> 0 . DP=31;I16=19,11,0,1,1077,39885,4,16,1738,102482,60,3600,504,10988,25,625;QS=2.98419,0.0158103,0;SGB=-0.556633;RPBZ=0.615229;MQBZ=0.262613;MQSBZ=-0.333409;BQBZ=-1.68746;SCBZ=0;MQ0F=0 PL:DP:DV 0,39,255,39,255,255:13:0 0,15,171,21,174,171:8:1 0,30,255,30,255,255:10:0 17 385 . C <*> 0 . DP=31;I16=19,12,0,0,1118,41180,0,0,1798,106082,0,0,527,11569,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,39,255:13:0 0,24,186:8:0 0,30,255:10:0 17 386 . T <*> 0 . DP=30;I16=18,12,0,0,1158,45592,0,0,1738,102482,0,0,526,11556,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,39,255:13:0 0,21,191:7:0 0,30,255:10:0 17 387 . T <*> 0 . DP=30;I16=18,12,0,0,1105,41821,0,0,1738,102482,0,0,525,11573,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,39,255:13:0 0,21,187:7:0 0,30,255:10:0 @@ -323,7 +322,7 @@ 17 398 . A <*> 0 . DP=28;I16=17,11,0,0,1025,38361,0,0,1587,92523,0,0,524,11850,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,39,255:13:0 0,15,144:5:0 0,30,255:10:0 17 399 . A <*> 0 . DP=28;I16=17,11,0,0,1023,38949,0,0,1587,92523,0,0,526,11900,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,39,255:13:0 0,15,140:5:0 0,30,255:10:0 17 400 . A <*> 0 . DP=29;I16=17,12,0,0,1070,40554,0,0,1647,96123,0,0,526,11828,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,39,255:13:0 0,15,159:5:0 0,33,255:11:0 -17 401 . A C,<*> 0 . DP=29;I16=17,11,0,1,1063,41001,8,64,1587,92523,60,3600,501,11113,25,625;QS=2.97985,0.0201511,0;SGB=-0.556633;RPBZ=-0.478622;MQBZ=0.339683;MQSBZ=0.29364;BQBZ=-1.68267;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,39,255,39,255,255:13:0 0,15,160,15,160,160:5:0 0,22,255,30,255,255:11:1 +17 401 . A C,<*> 0 . DP=29;I16=17,11,0,1,1063,41001,8,64,1587,92523,60,3600,501,11113,25,625;QS=2.97985,0.0201511,0;SGB=-0.556633;RPBZ=-0.478622;MQBZ=0.339683;MQSBZ=0.29364;BQBZ=-1.68267;SCBZ=0;MQ0F=0 PL:DP:DV 0,39,255,39,255,255:13:0 0,15,160,15,160,160:5:0 0,22,255,30,255,255:11:1 17 402 . T <*> 0 . DP=29;I16=17,12,0,0,1076,40740,0,0,1647,96123,0,0,526,11680,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,39,255:13:0 0,15,149:5:0 0,33,255:11:0 17 403 . T <*> 0 . DP=29;I16=17,12,0,0,1085,40985,0,0,1647,96123,0,0,526,11654,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,39,255:13:0 0,15,148:5:0 0,33,255:11:0 17 404 . G <*> 0 . DP=29;I16=17,12,0,0,1074,40524,0,0,1647,96123,0,0,525,11609,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,39,255:13:0 0,15,131:5:0 0,33,255:11:0 @@ -334,7 +333,7 @@ 17 409 . T <*> 0 . DP=29;I16=17,12,0,0,1100,42734,0,0,1678,98882,0,0,525,11503,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,42,255:14:0 0,12,131:4:0 0,33,255:11:0 17 410 . T <*> 0 . DP=29;I16=17,12,0,0,1035,38325,0,0,1678,98882,0,0,524,11432,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,42,255:14:0 0,12,125:4:0 0,33,255:11:0 17 411 . T <*> 0 . DP=29;I16=17,12,0,0,1022,37928,0,0,1678,98882,0,0,522,11342,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,42,255:14:0 0,12,111:4:0 0,33,255:11:0 -17 412 . C T,<*> 0 . DP=30;I16=17,12,1,0,1094,42458,14,196,1678,98882,60,3600,495,10659,25,625;QS=2.97455,0.0254545,0;SGB=-0.556633;RPBZ=-0.40473;MQBZ=0.267261;MQSBZ=-0.293785;BQBZ=-1.6942;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,30,255,42,255,255:15:1 0,12,124,12,124,124:4:0 0,33,255,33,255,255:11:0 +17 412 . C T,<*> 0 . DP=30;I16=17,12,1,0,1094,42458,14,196,1678,98882,60,3600,495,10659,25,625;QS=2.97455,0.0254545,0;SGB=-0.556633;RPBZ=-0.40473;MQBZ=0.267261;MQSBZ=-0.293785;BQBZ=-1.6942;SCBZ=0;MQ0F=0 PL:DP:DV 0,30,255,42,255,255:15:1 0,12,124,12,124,124:4:0 0,33,255,33,255,255:11:0 17 413 . A <*> 0 . DP=31;I16=18,13,0,0,1189,45985,0,0,1798,106082,0,0,520,11258,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,9,102:3:0 0,33,255:11:0 17 414 . T <*> 0 . DP=30;I16=18,12,0,0,1151,44355,0,0,1738,102482,0,0,523,11265,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,9,109:3:0 0,33,255:11:0 17 415 . G <*> 0 . DP=30;I16=18,12,0,0,1131,43175,0,0,1738,102482,0,0,526,11306,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,9,110:3:0 0,33,255:11:0 @@ -359,7 +358,7 @@ 17 434 . T <*> 0 . DP=29;I16=15,14,0,0,1036,37654,0,0,1647,96123,0,0,561,12567,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,9,98:3:0 0,30,243:10:0 17 435 . A <*> 0 . DP=29;I16=15,14,0,0,1035,38091,0,0,1647,96123,0,0,562,12596,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,9,103:3:0 0,30,237:10:0 17 436 . T <*> 0 . DP=28;I16=14,14,0,0,998,36220,0,0,1587,92523,0,0,564,12654,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,9,110:3:0 0,27,223:9:0 -17 437 . T G,<*> 0 . DP=28;I16=13,14,1,0,990,36832,6,36,1558,91682,29,841,549,12435,16,256;QS=2.9781,0.0218978,0;SGB=-0.556633;RPBZ=-1.36214;MQBZ=-2.88675;MQSBZ=0.6;BQBZ=-1.67909;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,48,255,48,255,255:16:0 0,9,109,9,109,109:3:0 0,17,200,24,203,201:9:1 +17 437 . T G,<*> 0 . DP=28;I16=13,14,1,0,990,36832,6,36,1558,91682,29,841,549,12435,16,256;QS=2.9781,0.0218978,0;SGB=-0.556633;RPBZ=-1.36214;MQBZ=-2.88675;MQSBZ=0.6;BQBZ=-1.67909;SCBZ=0;MQ0F=0 PL:DP:DV 0,48,255,48,255,255:16:0 0,9,109,9,109,109:3:0 0,17,200,24,203,201:9:1 17 438 . A <*> 0 . DP=28;I16=14,14,0,0,984,35784,0,0,1587,92523,0,0,565,12707,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,9,107:3:0 0,27,220:9:0 17 439 . C <*> 0 . DP=28;I16=14,14,0,0,1055,40273,0,0,1587,92523,0,0,563,12649,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,9,107:3:0 0,27,224:9:0 17 440 . A <*> 0 . DP=28;I16=14,14,0,0,1095,43251,0,0,1587,92523,0,0,561,12615,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,9,115:3:0 0,27,247:9:0 @@ -387,13 +386,13 @@ 17 462 . G <*> 0 . DP=32;I16=18,13,0,0,1169,46001,0,0,1775,103851,0,0,577,12669,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,12,131:4:0 0,30,241:10:0 17 463 . G <*> 0 . DP=32;I16=18,13,0,0,1095,41573,0,0,1775,103851,0,0,583,12729,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,12,126:4:0 0,30,221:10:0 17 464 . A <*> 0 . DP=32;I16=18,13,0,0,1100,41724,0,0,1775,103851,0,0,589,12821,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,12,148:4:0 0,30,217:10:0 -17 465 . C T,<*> 0 . DP=33;I16=19,12,0,1,1173,45601,4,16,1775,103851,60,3600,589,12909,6,36;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.67982;MQBZ=0.321288;MQSBZ=0.341466;BQBZ=-1.68493;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,51,255,51,255,255:17:0 0,15,158,15,158,158:5:0 0,20,224,27,227,224:10:1 +17 465 . C T,<*> 0 . DP=33;I16=19,12,0,1,1173,45601,4,16,1775,103851,60,3600,589,12909,6,36;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.67982;MQBZ=0.321288;MQSBZ=0.341466;BQBZ=-1.68493;SCBZ=0;MQ0F=0 PL:DP:DV 0,51,255,51,255,255:17:0 0,15,158,15,158,158:5:0 0,20,224,27,227,224:10:1 17 466 . A <*> 0 . DP=34;I16=20,13,0,0,1268,49686,0,0,1895,111051,0,0,602,13102,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,15,173:5:0 0,30,255:10:0 17 467 . A <*> 0 . DP=34;I16=20,13,0,0,1246,48610,0,0,1895,111051,0,0,608,13194,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,15,177:5:0 0,30,251:10:0 17 468 . A <*> 0 . DP=35;I16=21,13,0,0,1253,48095,0,0,1955,114651,0,0,613,13273,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,15,174:5:0 0,30,251:10:0 17 469 . A <*> 0 . DP=35;I16=21,13,0,0,1260,49028,0,0,1955,114651,0,0,618,13340,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,15,165:5:0 0,30,255:10:0 17 470 . G <*> 0 . DP=35;I16=21,13,0,0,1265,48879,0,0,1955,114651,0,0,623,13445,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,15,167:5:0 0,30,238:10:0 -17 471 . T G,C,<*> 0 . DP=36;I16=21,12,0,2,1220,46380,18,162,1918,113282,97,4969,611,13281,16,256;QS=2.94529,0.0273556,0.0273556,0;VDB=0.96;SGB=0.346553;RPBZ=0.497712;MQBZ=-1.9761;MQSBZ=0.312094;BQBZ=-2.35032;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,57,255,57,255,255,57,255,255,255:19:0 0,15,169,15,169,169,15,169,169,169:5:0 0,19,219,19,221,219,27,222,222,221:11:2 +17 471 . T G,C,<*> 0 . DP=36;I16=21,12,0,2,1220,46380,18,162,1918,113282,97,4969,611,13281,16,256;QS=2.94529,0.0273556,0.0273556,0;VDB=0.96;SGB=0.346553;RPBZ=0.497712;MQBZ=-1.9761;MQSBZ=0.312094;BQBZ=-2.35032;SCBZ=0;MQ0F=0 PL:DP:DV 0,57,255,57,255,255,57,255,255,255:19:0 0,15,169,15,169,169,15,169,169,169:5:0 0,19,219,19,221,219,27,222,222,221:11:2 17 472 . T <*> 0 . DP=35;I16=21,13,0,0,1234,46640,0,0,1955,114651,0,0,633,13665,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,15,172:5:0 0,30,241:10:0 17 473 . G <*> 0 . DP=35;I16=21,13,0,0,1303,51953,0,0,1955,114651,0,0,638,13780,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,15,159:5:0 0,30,250:10:0 17 474 . G <*> 0 . DP=36;I16=22,13,0,0,1279,49235,0,0,2015,118251,0,0,642,13884,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,15,146:5:0 0,33,255:11:0 @@ -410,7 +409,7 @@ 17 485 . G <*> 0 . DP=35;I16=23,12,0,0,1329,51411,0,0,2015,118251,0,0,669,14931,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,18,160:6:0 0,33,255:11:0 17 486 . A <*> 0 . DP=34;I16=22,12,0,0,1313,51667,0,0,1955,114651,0,0,671,14989,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,18,173:6:0 0,33,255:11:0 17 487 . G <*> 0 . DP=34;I16=22,12,0,0,1300,50304,0,0,1955,114651,0,0,672,15030,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,18,169:6:0 0,33,255:11:0 -17 488 . A G,<*> 0 . DP=35;I16=22,12,1,0,1278,48412,4,16,1986,117410,29,841,646,14380,25,625;QS=2.98947,0.0105263,0;SGB=-0.556633;RPBZ=0.594463;MQBZ=-3.36505;MQSBZ=0.10737;BQBZ=-1.69552;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,54,255,54,255,255:18:0 0,18,177,18,177,177:6:0 0,23,255,30,255,255:11:1 +17 488 . A G,<*> 0 . DP=35;I16=22,12,1,0,1278,48412,4,16,1986,117410,29,841,646,14380,25,625;QS=2.98947,0.0105263,0;SGB=-0.556633;RPBZ=0.594463;MQBZ=-3.36505;MQSBZ=0.10737;BQBZ=-1.69552;SCBZ=0;MQ0F=0 PL:DP:DV 0,54,255,54,255,255:18:0 0,18,177,18,177,177:6:0 0,23,255,30,255,255:11:1 17 489 . A <*> 0 . DP=35;I16=23,12,0,0,1264,46916,0,0,2015,118251,0,0,671,15015,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,18,175:6:0 0,33,255:11:0 17 490 . A <*> 0 . DP=36;I16=24,12,0,0,1332,50280,0,0,2075,121851,0,0,671,15061,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,188:7:0 0,33,255:11:0 17 491 . T <*> 0 . DP=36;I16=24,12,0,0,1284,46802,0,0,2075,121851,0,0,671,15093,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,178:7:0 0,33,255:11:0 @@ -434,9 +433,9 @@ 17 509 . C <*> 0 . DP=34;I16=24,10,0,0,1272,48272,0,0,1986,117410,0,0,640,14430,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,186:7:0 0,27,241:9:0 17 510 . A <*> 0 . DP=34;I16=23,11,0,0,1211,44827,0,0,1986,117410,0,0,638,14398,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,21,187:7:0 0,24,221:8:0 17 511 . A <*> 0 . DP=34;I16=23,11,0,0,1238,46516,0,0,1986,117410,0,0,637,14395,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,21,195:7:0 0,24,233:8:0 -17 512 . A C,<*> 0 . DP=33;I16=22,10,0,1,1133,41513,13,169,1866,110210,60,3600,628,14340,9,81;QS=2.97766,0.0223368,0;SGB=-0.556633;RPBZ=-1.47079;MQBZ=0.253876;MQSBZ=-0.461593;BQBZ=-1.68442;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,39,255,51,255,255:18:1 0,21,183,21,183,183:7:0 0,24,231,24,231,231:8:0 -17 513 . A T,<*> 0 . DP=32;I16=21,10,1,0,1125,42283,12,144,1806,106610,60,3600,623,14249,15,225;QS=2.97966,0.020339,0;SGB=-0.556633;RPBZ=-1.24609;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.57376;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,37,255,48,255,255:17:1 0,21,177,21,177,177:7:0 0,24,233,24,233,233:8:0 -17 514 . A T,<*> 0 . DP=32;I16=22,9,0,1,1086,40204,16,256,1806,106610,60,3600,627,14381,11,121;QS=2.97127,0.0287253,0;SGB=-0.556633;RPBZ=-1.4628;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.46657;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,34,255,48,255,255:17:1 0,21,172,21,172,172:7:0 0,24,235,24,235,235:8:0 +17 512 . A C,<*> 0 . DP=33;I16=22,10,0,1,1133,41513,13,169,1866,110210,60,3600,628,14340,9,81;QS=2.97766,0.0223368,0;SGB=-0.556633;RPBZ=-1.47079;MQBZ=0.253876;MQSBZ=-0.461593;BQBZ=-1.68442;SCBZ=0;MQ0F=0 PL:DP:DV 0,39,255,51,255,255:18:1 0,21,183,21,183,183:7:0 0,24,231,24,231,231:8:0 +17 513 . A T,<*> 0 . DP=32;I16=21,10,1,0,1125,42283,12,144,1806,106610,60,3600,623,14249,15,225;QS=2.97966,0.020339,0;SGB=-0.556633;RPBZ=-1.24609;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.57376;SCBZ=0;MQ0F=0 PL:DP:DV 0,37,255,48,255,255:17:1 0,21,177,21,177,177:7:0 0,24,233,24,233,233:8:0 +17 514 . A T,<*> 0 . DP=32;I16=22,9,0,1,1086,40204,16,256,1806,106610,60,3600,627,14381,11,121;QS=2.97127,0.0287253,0;SGB=-0.556633;RPBZ=-1.4628;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.46657;SCBZ=0;MQ0F=0 PL:DP:DV 0,34,255,48,255,255:17:1 0,21,172,21,172,172:7:0 0,24,235,24,235,235:8:0 17 515 . C <*> 0 . DP=32;I16=22,10,0,0,1050,37704,0,0,1866,110210,0,0,638,14554,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,21,169:7:0 0,24,211:8:0 17 516 . C <*> 0 . DP=32;I16=22,10,0,0,1109,40651,0,0,1866,110210,0,0,637,14579,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,21,187:7:0 0,24,215:8:0 17 517 . T <*> 0 . DP=33;I16=23,10,0,0,1269,49995,0,0,1926,113810,0,0,636,14626,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,201:7:0 0,24,242:8:0 @@ -445,7 +444,7 @@ 17 520 . T <*> 0 . DP=36;I16=25,11,0,0,1243,45051,0,0,2106,124610,0,0,638,14818,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,63,255:21:0 0,21,180:7:0 0,24,223:8:0 17 521 . C <*> 0 . DP=34;I16=25,9,0,0,1281,49527,0,0,1986,117410,0,0,641,14875,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,60,255:20:0 0,21,191:7:0 0,21,204:7:0 17 522 . A <*> 0 . DP=32;I16=24,8,0,0,1158,43228,0,0,1897,112969,0,0,646,14960,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,60,255:20:0 0,21,185:7:0 0,15,170:5:0 -17 523 . T G,<*> 0 . DP=32;I16=23,8,1,0,1184,45708,15,225,1837,109369,60,3600,626,14446,25,625;QS=2.9794,0.0206044,0;SGB=-0.556633;RPBZ=1.13742;MQBZ=0.179605;MQSBZ=-1.73205;BQBZ=-1.68805;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,44,255,57,255,255:20:1 0,21,191,21,191,191:7:0 0,15,166,15,166,166:5:0 +17 523 . T G,<*> 0 . DP=32;I16=23,8,1,0,1184,45708,15,225,1837,109369,60,3600,626,14446,25,625;QS=2.9794,0.0206044,0;SGB=-0.556633;RPBZ=1.13742;MQBZ=0.179605;MQSBZ=-1.73205;BQBZ=-1.68805;SCBZ=0;MQ0F=0 PL:DP:DV 0,44,255,57,255,255:20:1 0,21,191,21,191,191:7:0 0,15,166,15,166,166:5:0 17 524 . T <*> 0 . DP=32;I16=24,8,0,0,1096,39618,0,0,1897,112969,0,0,654,15108,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,60,255:20:0 0,21,194:7:0 0,15,150:5:0 17 525 . G <*> 0 . DP=32;I16=24,8,0,0,1188,45718,0,0,1897,112969,0,0,656,15120,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,60,255:20:0 0,21,188:7:0 0,15,133:5:0 17 526 . C <*> 0 . DP=32;I16=24,8,0,0,1154,44014,0,0,1897,112969,0,0,658,15156,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,60,255:20:0 0,21,185:7:0 0,15,137:5:0 @@ -457,7 +456,7 @@ 17 532 . T <*> 0 . DP=32;I16=25,7,0,0,1161,43607,0,0,1897,112969,0,0,649,14477,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,21,181:7:0 0,18,192:6:0 17 533 . C <*> 0 . DP=32;I16=25,7,0,0,1154,44084,0,0,1897,112969,0,0,644,14274,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,21,178:7:0 0,18,180:6:0 17 534 . T <*> 0 . DP=31;I16=24,7,0,0,1222,49526,0,0,1837,109369,0,0,640,14104,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,205:7:0 0,18,205:6:0 -17 535 . A G,<*> 0 . DP=31;I16=24,6,0,1,1080,39870,8,64,1777,105769,60,3600,611,13341,25,625;QS=2.98623,0.0137694,0;SGB=-0.556633;RPBZ=-0.894788;MQBZ=0.182574;MQSBZ=-1.85164;BQBZ=-1.6854;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,21,194,21,194,194:7:0 0,18,189,18,189,189:6:0 +17 535 . A G,<*> 0 . DP=31;I16=24,6,0,1,1080,39870,8,64,1777,105769,60,3600,611,13341,25,625;QS=2.98623,0.0137694,0;SGB=-0.556633;RPBZ=-0.894788;MQBZ=0.182574;MQSBZ=-1.85164;BQBZ=-1.6854;SCBZ=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,21,194,21,194,194:7:0 0,18,189,18,189,189:6:0 17 536 . C <*> 0 . DP=31;I16=24,7,0,0,1095,40551,0,0,1837,109369,0,0,631,13809,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,184:7:0 0,18,157:6:0 17 537 . C <*> 0 . DP=31;I16=24,7,0,0,1049,38677,0,0,1837,109369,0,0,626,13682,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,172:7:0 0,18,183:6:0 17 538 . A <*> 0 . DP=31;I16=24,7,0,0,1138,42478,0,0,1837,109369,0,0,620,13536,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,189:7:0 0,18,181:6:0 @@ -470,8 +469,8 @@ 17 545 . A <*> 0 . DP=33;I16=25,8,0,0,1197,44795,0,0,1926,113810,0,0,587,12951,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,24,196:8:0 0,18,184:6:0 17 546 . A <*> 0 . DP=32;I16=24,8,0,0,1136,41758,0,0,1866,110210,0,0,580,12802,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,21,166:7:0 0,18,193:6:0 17 547 . A <*> 0 . DP=32;I16=24,8,0,0,1159,43539,0,0,1866,110210,0,0,572,12634,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,57,255:19:0 0,21,180:7:0 0,18,195:6:0 -17 548 . A C,<*> 0 . DP=33;I16=23,9,1,0,1153,42673,9,81,1866,110210,60,3600,561,12489,3,9;QS=2.98607,0.0139319,0;SGB=-0.556633;RPBZ=1.57584;MQBZ=0.253876;MQSBZ=-2.34521;BQBZ=-1.68939;SCBZ=3.80814;FS=0;MQ0F=0 PL:DP:DV 0,44,255,54,255,255:19:1 0,21,181,21,181,181:7:0 0,21,211,21,211,211:7:0 -17 549 . T G,<*> 0 . DP=32;I16=23,8,0,1,1135,42143,20,400,1806,106610,60,3600,532,11720,25,625;QS=2.96918,0.0308166,0;SGB=-0.556633;RPBZ=-0.487556;MQBZ=0.258065;MQSBZ=-2.29695;BQBZ=-1.68602;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV 0,34,255,51,255,255:18:1 0,21,168,21,168,168:7:0 0,21,208,21,208,208:7:0 +17 548 . A C,<*> 0 . DP=33;I16=23,9,1,0,1153,42673,9,81,1866,110210,60,3600,561,12489,3,9;QS=2.98607,0.0139319,0;SGB=-0.556633;RPBZ=1.57584;MQBZ=0.253876;MQSBZ=-2.34521;BQBZ=-1.68939;SCBZ=3.80814;MQ0F=0 PL:DP:DV 0,44,255,54,255,255:19:1 0,21,181,21,181,181:7:0 0,21,211,21,211,211:7:0 +17 549 . T G,<*> 0 . DP=32;I16=23,8,0,1,1135,42143,20,400,1806,106610,60,3600,532,11720,25,625;QS=2.96918,0.0308166,0;SGB=-0.556633;RPBZ=-0.487556;MQBZ=0.258065;MQSBZ=-2.29695;BQBZ=-1.68602;SCBZ=-0.258065;MQ0F=0 PL:DP:DV 0,34,255,51,255,255:18:1 0,21,168,21,168,168:7:0 0,21,208,21,208,208:7:0 17 550 . T <*> 0 . DP=32;I16=23,9,0,0,1056,37314,0,0,1866,110210,0,0,549,12177,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,150:7:0 0,21,220:7:0 17 551 . G <*> 0 . DP=31;I16=22,9,0,0,1121,41639,0,0,1806,106610,0,0,541,12045,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,21,172:7:0 0,21,208:7:0 17 552 . C <*> 0 . DP=30;I16=21,9,0,0,1093,41365,0,0,1746,103010,0,0,535,11947,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,21,167:7:0 0,21,208:7:0 @@ -481,14 +480,14 @@ 17 556 . C <*> 0 . DP=29;I16=20,9,0,0,1055,39195,0,0,1709,101641,0,0,509,11219,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,18,158:6:0 0,18,186:6:0 17 557 . A <*> 0 . DP=27;I16=18,9,0,0,987,36749,0,0,1589,94441,0,0,506,11074,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,45,255:15:0 0,18,157:6:0 0,18,186:6:0 17 558 . A <*> 0 . DP=27;I16=18,9,0,0,956,35872,0,0,1589,94441,0,0,502,10906,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,45,255:15:0 0,18,153:6:0 0,18,177:6:0 -17 559 . C A,<*> 0 . DP=27;I16=18,8,0,1,915,33775,14,196,1560,93600,29,841,473,10141,25,625;QS=2.92708,0.0729167,0;SGB=-0.556633;RPBZ=-1.02726;MQBZ=-5.09902;MQSBZ=-1.41421;BQBZ=-1.54776;SCBZ=5.09902;FS=0;MQ0F=0 PL:DP:DV 0,45,255,45,255,255:15:0 0,4,116,15,119,123:6:1 0,18,169,18,169,169:6:0 +17 559 . C A,<*> 0 . DP=27;I16=18,8,0,1,915,33775,14,196,1560,93600,29,841,473,10141,25,625;QS=2.92708,0.0729167,0;SGB=-0.556633;RPBZ=-1.02726;MQBZ=-5.09902;MQSBZ=-1.41421;BQBZ=-1.54776;SCBZ=5.09902;MQ0F=0 PL:DP:DV 0,45,255,45,255,255:15:0 0,4,116,15,119,123:6:1 0,18,169,18,169,169:6:0 17 560 . C <*> 0 . DP=28;I16=19,9,0,0,992,36552,0,0,1649,98041,0,0,494,10654,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,45,255:15:0 0,18,160:6:0 0,21,181:7:0 17 561 . A <*> 0 . DP=28;I16=19,9,0,0,973,35555,0,0,1649,98041,0,0,491,10571,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,45,255:15:0 0,18,158:6:0 0,21,194:7:0 17 562 . C <*> 0 . DP=28;I16=19,9,0,0,1014,38392,0,0,1649,98041,0,0,488,10518,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,45,255:15:0 0,18,153:6:0 0,21,187:7:0 17 563 . A <*> 0 . DP=27;I16=18,9,0,0,903,32513,0,0,1589,94441,0,0,485,10445,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,45,255:15:0 0,15,149:5:0 0,21,179:7:0 17 564 . C <*> 0 . DP=27;I16=18,9,0,0,859,28747,0,0,1589,94441,0,0,482,10402,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,45,255:15:0 0,15,121:5:0 0,21,182:7:0 17 565 . G <*> 0 . DP=30;I16=18,12,0,0,842,27104,0,0,1769,105241,0,0,479,10389,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,18,100:6:0 0,21,154:7:0 -17 566 . C A,<*> 0 . DP=29;I16=16,12,1,0,920,33998,9,81,1649,98041,60,3600,454,9734,25,625;QS=2.98321,0.016791,0;SGB=-0.556633;RPBZ=0.239193;MQBZ=0.188982;MQSBZ=-1.19024;BQBZ=-1.43942;SCBZ=-0.188982;FS=0;MQ0F=0 PL:DP:DV 0,38,255,48,255,255:17:1 0,15,155,15,155,155:5:0 0,21,170,21,170,170:7:0 +17 566 . C A,<*> 0 . DP=29;I16=16,12,1,0,920,33998,9,81,1649,98041,60,3600,454,9734,25,625;QS=2.98321,0.016791,0;SGB=-0.556633;RPBZ=0.239193;MQBZ=0.188982;MQSBZ=-1.19024;BQBZ=-1.43942;SCBZ=-0.188982;MQ0F=0 PL:DP:DV 0,38,255,48,255,255:17:1 0,15,155,15,155,155:5:0 0,21,170,21,170,170:7:0 17 567 . C <*> 0 . DP=30;I16=17,13,0,0,956,34312,0,0,1769,105241,0,0,496,10638,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,18,156:6:0 0,21,194:7:0 17 568 . C <*> 0 . DP=29;I16=16,13,0,0,1060,40304,0,0,1709,101641,0,0,497,10663,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,18,179:6:0 0,21,193:7:0 17 569 . T <*> 0 . DP=30;I16=16,13,0,0,1061,41321,0,0,1709,101641,0,0,497,10671,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,18,190:6:0 0,21,213:7:0 @@ -496,15 +495,15 @@ 17 571 . C <*> 0 . DP=31;I16=17,13,0,0,1069,40739,0,0,1769,105241,0,0,497,10783,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,18,159:6:0 0,21,193:7:0 17 572 . A <*> 0 . DP=31;I16=18,12,0,0,1092,41268,0,0,1769,105241,0,0,499,10887,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,21,204:7:0 0,18,175:6:0 17 573 . A <*> 0 . DP=31;I16=18,12,0,0,1060,38698,0,0,1769,105241,0,0,501,10975,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,21,201:7:0 0,18,178:6:0 -17 574 . C A,<*> 0 . DP=31;I16=18,11,0,1,1088,41328,15,225,1740,104400,29,841,478,10422,25,625;QS=2.94071,0.0592885,0;SGB=-0.556633;RPBZ=-0.173514;MQBZ=-5.38516;MQSBZ=-1.22474;BQBZ=-1.68578;SCBZ=3.60588;FS=0;MQ0F=0 PL:DP:DV 0,48,255,48,255,255:16:0 0,9,170,21,173,177:8:1 0,18,173,18,173,173:6:0 -17 575 . T C,<*> 0 . DP=30;I16=17,11,0,1,1048,41548,9,81,1680,100800,29,841,480,10426,25,625;QS=2.96786,0.0321429,0;SGB=-0.556633;RPBZ=-0.119685;MQBZ=-5.2915;MQSBZ=-1.19024;BQBZ=-1.68121;SCBZ=3.53589;FS=0;MQ0F=0 PL:DP:DV 0,48,255,48,255,255:16:0 0,13,200,21,203,202:8:1 0,15,163,15,163,163:5:0 +17 574 . C A,<*> 0 . DP=31;I16=18,11,0,1,1088,41328,15,225,1740,104400,29,841,478,10422,25,625;QS=2.94071,0.0592885,0;SGB=-0.556633;RPBZ=-0.173514;MQBZ=-5.38516;MQSBZ=-1.22474;BQBZ=-1.68578;SCBZ=3.60588;MQ0F=0 PL:DP:DV 0,48,255,48,255,255:16:0 0,9,170,21,173,177:8:1 0,18,173,18,173,173:6:0 +17 575 . T C,<*> 0 . DP=30;I16=17,11,0,1,1048,41548,9,81,1680,100800,29,841,480,10426,25,625;QS=2.96786,0.0321429,0;SGB=-0.556633;RPBZ=-0.119685;MQBZ=-5.2915;MQSBZ=-1.19024;BQBZ=-1.68121;SCBZ=3.53589;MQ0F=0 PL:DP:DV 0,48,255,48,255,255:16:0 0,13,200,21,203,202:8:1 0,15,163,15,163,163:5:0 17 576 . G <*> 0 . DP=30;I16=17,12,0,0,1043,39581,0,0,1709,101641,0,0,507,11087,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,24,208:8:0 0,15,151:5:0 17 577 . G <*> 0 . DP=30;I16=17,12,0,0,997,37255,0,0,1709,101641,0,0,509,11155,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,24,204:8:0 0,15,146:5:0 17 578 . G <*> 0 . DP=29;I16=16,13,0,0,975,34803,0,0,1709,101641,0,0,520,11286,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,48,255:16:0 0,24,198:8:0 0,15,151:5:0 17 579 . G <*> 0 . DP=30;I16=16,14,0,0,1038,38820,0,0,1769,105241,0,0,523,11335,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,24,224:8:0 0,15,144:5:0 -17 580 . A C,<*> 0 . DP=30;I16=15,14,1,0,1060,39178,16,256,1709,101641,60,3600,510,11078,17,289;QS=2.97338,0.0266223,0;SGB=-0.556633;RPBZ=1.32953;MQBZ=0.185695;MQSBZ=-1.06904;BQBZ=-1.69093;SCBZ=-0.267102;FS=0;MQ0F=0 PL:DP:DV 0,34,255,48,255,255:17:1 0,24,221,24,221,221:8:0 0,15,155,15,155,155:5:0 +17 580 . A C,<*> 0 . DP=30;I16=15,14,1,0,1060,39178,16,256,1709,101641,60,3600,510,11078,17,289;QS=2.97338,0.0266223,0;SGB=-0.556633;RPBZ=1.32953;MQBZ=0.185695;MQSBZ=-1.06904;BQBZ=-1.69093;SCBZ=-0.267102;MQ0F=0 PL:DP:DV 0,34,255,48,255,255:17:1 0,24,221,24,221,221:8:0 0,15,155,15,155,155:5:0 17 581 . A <*> 0 . DP=31;I16=16,15,0,0,1083,39215,0,0,1829,108841,0,0,530,11384,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,24,223:8:0 0,15,153:5:0 -17 582 . C G,<*> 0 . DP=31;I16=15,15,1,0,1080,39870,8,64,1769,105241,60,3600,519,11211,15,225;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.34259;MQBZ=0.182574;MQSBZ=-1.0328;BQBZ=-1.68266;SCBZ=-0.262467;FS=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,24,207,24,207,207:8:0 0,15,151,15,151,151:5:0 +17 582 . C G,<*> 0 . DP=31;I16=15,15,1,0,1080,39870,8,64,1769,105241,60,3600,519,11211,15,225;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.34259;MQBZ=0.182574;MQSBZ=-1.0328;BQBZ=-1.68266;SCBZ=-0.262467;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,24,207,24,207,207:8:0 0,15,151,15,151,151:5:0 17 583 . T <*> 0 . DP=30;I16=16,14,0,0,1135,43913,0,0,1769,105241,0,0,539,11523,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,24,238:8:0 0,15,163:5:0 17 584 . C <*> 0 . DP=31;I16=17,14,0,0,1069,39521,0,0,1798,106082,0,0,544,11644,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,24,209:8:0 0,15,157:5:0 17 585 . A <*> 0 . DP=31;I16=17,14,0,0,1096,39866,0,0,1798,106082,0,0,549,11751,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,24,211:8:0 0,15,157:5:0 @@ -515,10 +514,10 @@ 17 590 . C <*> 0 . DP=32;I16=17,15,0,0,1103,41355,0,0,1858,109682,0,0,574,12576,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,24,194:8:0 0,18,175:6:0 17 591 . A <*> 0 . DP=31;I16=16,15,0,0,1164,44088,0,0,1798,106082,0,0,579,12695,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,209:7:0 0,18,188:6:0 17 592 . A <*> 0 . DP=31;I16=16,15,0,0,1121,42193,0,0,1798,106082,0,0,583,12795,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,215:7:0 0,18,182:6:0 -17 593 . C A,<*> 0 . DP=31;I16=16,14,0,1,1071,39925,7,49,1769,105241,29,841,561,12253,25,625;QS=2.97021,0.0297872,0;SGB=-0.556633;RPBZ=0.559355;MQBZ=-3.80789;MQSBZ=-0.0464238;BQBZ=-1.57464;SCBZ=3.67454;FS=0;MQ0F=0 PL:DP:DV 0,54,255,54,255,255:18:0 0,12,184,18,187,185:7:1 0,18,174,18,174,174:6:0 -17 594 . A G,<*> 0 . DP=33;I16=16,16,1,0,1161,42757,4,16,1858,109682,60,3600,572,12672,15,225;QS=2.99359,0.00641026,0;SGB=-0.556633;RPBZ=-0.998367;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68954;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:DV 0,42,255,51,255,255:18:1 0,21,205,21,205,205:7:0 0,24,213,24,213,213:8:0 +17 593 . C A,<*> 0 . DP=31;I16=16,14,0,1,1071,39925,7,49,1769,105241,29,841,561,12253,25,625;QS=2.97021,0.0297872,0;SGB=-0.556633;RPBZ=0.559355;MQBZ=-3.80789;MQSBZ=-0.0464238;BQBZ=-1.57464;SCBZ=3.67454;MQ0F=0 PL:DP:DV 0,54,255,54,255,255:18:0 0,12,184,18,187,185:7:1 0,18,174,18,174,174:6:0 +17 594 . A G,<*> 0 . DP=33;I16=16,16,1,0,1161,42757,4,16,1858,109682,60,3600,572,12672,15,225;QS=2.99359,0.00641026,0;SGB=-0.556633;RPBZ=-0.998367;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68954;SCBZ=-0.253876;MQ0F=0 PL:DP:DV 0,42,255,51,255,255:18:1 0,21,205,21,205,205:7:0 0,24,213,24,213,213:8:0 17 595 . A <*> 0 . DP=33;I16=17,16,0,0,1136,40412,0,0,1918,113282,0,0,589,12905,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,198:7:0 0,24,218:8:0 -17 596 . A G,<*> 0 . DP=33;I16=16,16,1,0,1061,37187,8,64,1858,109682,60,3600,590,12952,1,1;QS=2.98564,0.0143627,0;SGB=-0.556633;RPBZ=1.68146;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68357;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,21,169,21,169,169:7:0 0,24,231,24,231,231:8:0 +17 596 . A G,<*> 0 . DP=33;I16=16,16,1,0,1061,37187,8,64,1858,109682,60,3600,590,12952,1,1;QS=2.98564,0.0143627,0;SGB=-0.556633;RPBZ=1.68146;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68357;SCBZ=-0.253876;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,21,169,21,169,169:7:0 0,24,231,24,231,231:8:0 17 597 . C <*> 0 . DP=33;I16=17,16,0,0,1196,44890,0,0,1918,113282,0,0,592,12990,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,54,255:18:0 0,21,204:7:0 0,24,220:8:0 17 598 . T <*> 0 . DP=33;I16=16,17,0,0,1219,47333,0,0,1918,113282,0,0,597,13029,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,21,217:7:0 0,27,242:9:0 17 599 . T <*> 0 . DP=33;I16=16,17,0,0,1182,43598,0,0,1918,113282,0,0,599,13095,0,0;QS=3,0;MQ0F=0 PL:DP:DV 0,51,255:17:0 0,21,197:7:0 0,27,247:9:0 diff --git a/test/mpileup/mpileup.3.out b/test/mpileup/mpileup.3.out index 89c6c0607..abfe1509f 100644 --- a/test/mpileup/mpileup.3.out +++ b/test/mpileup/mpileup.3.out @@ -12,7 +12,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= diff --git a/test/mpileup/mpileup.4.out b/test/mpileup/mpileup.4.out index 061f8975f..942558a4d 100644 --- a/test/mpileup/mpileup.4.out +++ b/test/mpileup/mpileup.4.out @@ -12,7 +12,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -28,29 +27,29 @@ 17 100 . C <*> 0 . DP=18;DPR=17,0;I16=16,1,0,0,672,27586,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,189:9:0:0:9,0,0,0:9,0 0,9,118:3:0:0:2,1,0,0:3,0 0,15,134:5:0:0:5,0,0,0:5,0 17 101 . C <*> 0 . DP=18;DPR=17,0;I16=16,1,0,0,630,24730,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,182:9:0:0:9,0,0,0:9,0 0,9,108:3:0:0:2,1,0,0:3,0 0,15,132:5:0:0:5,0,0,0:5,0 17 102 . C <*> 0 . DP=18;DPR=17,0;I16=16,1,0,0,676,27812,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,188:9:0:0:9,0,0,0:9,0 0,9,121:3:0:0:2,1,0,0:3,0 0,15,139:5:0:0:5,0,0,0:5,0 -17 103 . T C,<*> 0 . DP=18;DPR=16,1,0;I16=15,1,1,0,668,28542,6,36,929,54841,29,841,323,7035,6,36;QS=2.98256,0.0174419,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64924;SCBZ=4;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,17,184,24,187,185:9:1:0:8,0,1,0:8,1,0 0,9,118,9,118,118:3:0:0:2,1,0,0:3,0,0 0,15,147,15,147,147:5:0:0:5,0,0,0:5,0,0 -17 104 . G C,<*> 0 . DP=18;DPR=16,1,0;I16=15,1,1,0,601,24163,3,9,929,54841,29,841,320,6884,7,49;QS=2.98726,0.0127389,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64309;SCBZ=4;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,173,24,176,173:9:1:0:8,0,1,0:8,1,0 0,9,101,9,101,101:3:0:0:2,1,0,0:3,0,0 0,15,133,15,133,133:5:0:0:5,0,0,0:5,0,0 +17 103 . T C,<*> 0 . DP=18;DPR=16,1,0;I16=15,1,1,0,668,28542,6,36,929,54841,29,841,323,7035,6,36;QS=2.98256,0.0174419,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64924;SCBZ=4;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,17,184,24,187,185:9:1:0:8,0,1,0:8,1,0 0,9,118,9,118,118:3:0:0:2,1,0,0:3,0,0 0,15,147,15,147,147:5:0:0:5,0,0,0:5,0,0 +17 104 . G C,<*> 0 . DP=18;DPR=16,1,0;I16=15,1,1,0,601,24163,3,9,929,54841,29,841,320,6884,7,49;QS=2.98726,0.0127389,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64309;SCBZ=4;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,173,24,176,173:9:1:0:8,0,1,0:8,1,0 0,9,101,9,101,101:3:0:0:2,1,0,0:3,0,0 0,15,133,15,133,133:5:0:0:5,0,0,0:5,0,0 17 105 . G <*> 0 . DP=19;DPR=18,0;I16=17,1,0,0,603,22351,0,0,1018,59282,0,0,325,6815,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,171:10:0:0:10,0,0,0:10,0 0,9,106:3:0:0:2,1,0,0:3,0 0,15,125:5:0:0:5,0,0,0:5,0 17 106 . G <*> 0 . DP=19;DPR=18,0;I16=17,1,0,0,636,25058,0,0,1018,59282,0,0,324,6718,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,190:10:0:0:10,0,0,0:10,0 0,9,92:3:0:0:2,1,0,0:3,0 0,15,124:5:0:0:5,0,0,0:5,0 17 107 . C <*> 0 . DP=19;DPR=18,0;I16=17,1,0,0,686,27952,0,0,1018,59282,0,0,323,6643,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,192:10:0:0:10,0,0,0:10,0 0,9,119:3:0:0:2,1,0,0:3,0 0,15,136:5:0:0:5,0,0,0:5,0 17 108 . C <*> 0 . DP=19;DPR=18,0;I16=17,1,0,0,681,27429,0,0,1018,59282,0,0,322,6590,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,190:10:0:0:10,0,0,0:10,0 0,9,119:3:0:0:2,1,0,0:3,0 0,15,135:5:0:0:5,0,0,0:5,0 -17 109 . T C,<*> 0 . DP=19;DPR=17,1,0;I16=16,1,1,0,716,30648,2,4,989,58441,29,841,309,6415,12,144;QS=2.98922,0.0107817,0;SGB=-0.556633;RPBZ=-0.674966;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.6661;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,20,191,27,194,191:10:1:0:9,0,1,0:9,1,0 0,9,120,9,120,120:3:0:0:2,1,0,0:3,0,0 0,15,150,15,150,150:5:0:0:5,0,0,0:5,0,0 +17 109 . T C,<*> 0 . DP=19;DPR=17,1,0;I16=16,1,1,0,716,30648,2,4,989,58441,29,841,309,6415,12,144;QS=2.98922,0.0107817,0;SGB=-0.556633;RPBZ=-0.674966;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.6661;SCBZ=3;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,20,191,27,194,191:10:1:0:9,0,1,0:9,1,0 0,9,120,9,120,120:3:0:0:2,1,0,0:3,0,0 0,15,150,15,150,150:5:0:0:5,0,0,0:5,0,0 17 110 . G <*> 0 . DP=19;DPR=18,0;I16=17,1,0,0,688,28036,0,0,1018,59282,0,0,320,6550,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,194:10:0:0:10,0,0,0:10,0 0,9,113:3:0:0:2,1,0,0:3,0 0,15,136:5:0:0:5,0,0,0:5,0 17 111 . G <*> 0 . DP=19;DPR=18,0;I16=17,1,0,0,573,21453,0,0,1018,59282,0,0,318,6514,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,167:10:0:0:10,0,0,0:10,0 0,9,95:3:0:0:2,1,0,0:3,0 0,15,119:5:0:0:5,0,0,0:5,0 -17 112 . C G,<*> 0 . DP=19;DPR=17,1,0;I16=16,1,1,0,657,26565,2,4,989,58441,29,841,301,6277,15,225;QS=2.98907,0.010929,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65292;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,20,187,27,190,187:10:1:0:9,0,1,0:9,1,0 0,9,103,9,103,103:3:0:0:2,1,0,0:3,0,0 0,15,135,15,135,135:5:0:0:5,0,0,0:5,0,0 -17 113 . A G,<*> 0 . DP=19;DPR=17,1,0;I16=16,1,1,0,635,25055,4,16,989,58441,29,841,297,6207,16,256;QS=2.98817,0.0118343,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65205;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,20,172,27,175,172:10:1:0:9,0,1,0:9,1,0 0,9,102,9,102,102:3:0:0:2,1,0,0:3,0,0 0,15,139,15,139,139:5:0:0:5,0,0,0:5,0,0 +17 112 . C G,<*> 0 . DP=19;DPR=17,1,0;I16=16,1,1,0,657,26565,2,4,989,58441,29,841,301,6277,15,225;QS=2.98907,0.010929,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65292;SCBZ=3;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,20,187,27,190,187:10:1:0:9,0,1,0:9,1,0 0,9,103,9,103,103:3:0:0:2,1,0,0:3,0,0 0,15,135,15,135,135:5:0:0:5,0,0,0:5,0,0 +17 113 . A G,<*> 0 . DP=19;DPR=17,1,0;I16=16,1,1,0,635,25055,4,16,989,58441,29,841,297,6207,16,256;QS=2.98817,0.0118343,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65205;SCBZ=3;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,20,172,27,175,172:10:1:0:9,0,1,0:9,1,0 0,9,102,9,102,102:3:0:0:2,1,0,0:3,0,0 0,15,139,15,139,139:5:0:0:5,0,0,0:5,0,0 17 114 . C <*> 0 . DP=19;DPR=18,0;I16=17,1,0,0,660,25876,0,0,1018,59282,0,0,310,6446,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,181:10:0:0:10,0,0,0:10,0 0,9,113:3:0:0:2,1,0,0:3,0 0,15,133:5:0:0:5,0,0,0:5,0 -17 115 . C A,<*> 0 . DP=21;DPR=19,1,0;I16=17,2,1,0,688,27426,12,144,1078,62882,29,841,283,5827,25,625;QS=2.88785,0.11215,0;SGB=-0.556633;RPBZ=0.260329;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.47798;SCBZ=-0.418446;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,189,30,189,189:10:0:0:10,0,0,0:10,0,0 3,0,86,9,89,93:3:1:0:1,1,1,0:2,1,0 0,21,153,21,153,153:7:0:0:6,1,0,0:7,0,0 -17 116 . A C,<*> 0 . DP=21;DPR=19,1,0;I16=17,2,1,0,705,27791,2,4,1078,62882,29,841,287,6073,19,361;QS=2.98873,0.0112676,0;SGB=-0.556633;RPBZ=0.0867763;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.65814;SCBZ=2.65016;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,20,179,27,182,179:10:1:0:9,0,1,0:9,1,0 0,9,102,9,102,102:3:0:0:2,1,0,0:3,0,0 0,21,175,21,175,175:7:0:0:6,1,0,0:7,0,0 +17 115 . C A,<*> 0 . DP=21;DPR=19,1,0;I16=17,2,1,0,688,27426,12,144,1078,62882,29,841,283,5827,25,625;QS=2.88785,0.11215,0;SGB=-0.556633;RPBZ=0.260329;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.47798;SCBZ=-0.418446;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,189,30,189,189:10:0:0:10,0,0,0:10,0,0 3,0,86,9,89,93:3:1:0:1,1,1,0:2,1,0 0,21,153,21,153,153:7:0:0:6,1,0,0:7,0,0 +17 116 . A C,<*> 0 . DP=21;DPR=19,1,0;I16=17,2,1,0,705,27791,2,4,1078,62882,29,841,287,6073,19,361;QS=2.98873,0.0112676,0;SGB=-0.556633;RPBZ=0.0867763;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.65814;SCBZ=2.65016;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,20,179,27,182,179:10:1:0:9,0,1,0:9,1,0 0,9,102,9,102,102:3:0:0:2,1,0,0:3,0,0 0,21,175,21,175,175:7:0:0:6,1,0,0:7,0,0 17 117 . G <*> 0 . DP=21;DPR=20,0;I16=18,2,0,0,715,28045,0,0,1107,63723,0,0,304,6444,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,185:10:0:0:10,0,0,0:10,0 0,9,97:3:0:0:2,1,0,0:3,0 0,21,177:7:0:0:6,1,0,0:7,0 17 118 . G <*> 0 . DP=20;DPR=19,0;I16=17,2,0,0,620,23470,0,0,1047,60123,0,0,303,6481,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,175:9:0:0:9,0,0,0:9,0 0,9,65:3:0:0:2,1,0,0:3,0 0,21,162:7:0:0:6,1,0,0:7,0 17 119 . G <*> 0 . DP=19;DPR=18,0;I16=16,2,0,0,619,23459,0,0,987,56523,0,0,301,6493,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,176:9:0:0:9,0,0,0:9,0 0,6,76:2:0:0:1,1,0,0:2,0 0,21,160:7:0:0:6,1,0,0:7,0 -17 120 . A G,<*> 0 . DP=19;DPR=17,1,0;I16=15,2,1,0,646,25392,4,16,958,55682,29,841,277,5999,23,529;QS=2.9873,0.0126984,0;SGB=-0.556633;RPBZ=0.28942;MQBZ=-2.23607;MQSBZ=-1.30384;BQBZ=-1.6486;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,171,24,174,171:9:1:0:8,0,1,0:8,1,0 0,6,88,6,88,88:2:0:0:1,1,0,0:2,0,0 0,21,171,21,171,171:7:0:0:6,1,0,0:7,0,0 +17 120 . A G,<*> 0 . DP=19;DPR=17,1,0;I16=15,2,1,0,646,25392,4,16,958,55682,29,841,277,5999,23,529;QS=2.9873,0.0126984,0;SGB=-0.556633;RPBZ=0.28942;MQBZ=-2.23607;MQSBZ=-1.30384;BQBZ=-1.6486;SCBZ=3;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,171,24,174,171:9:1:0:8,0,1,0:8,1,0 0,6,88,6,88,88:2:0:0:1,1,0,0:2,0,0 0,21,171,21,171,171:7:0:0:6,1,0,0:7,0,0 17 121 . G <*> 0 . DP=19;DPR=18,0;I16=16,2,0,0,650,25148,0,0,987,56523,0,0,298,6534,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,181:9:0:0:9,0,0,0:9,0 0,6,84:2:0:0:1,1,0,0:2,0 0,21,168:7:0:0:6,1,0,0:7,0 17 122 . C <*> 0 . DP=20;DPR=19,0;I16=17,2,0,0,696,27784,0,0,1047,60123,0,0,296,6560,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,180:9:0:0:9,0,0,0:9,0 0,9,107:3:0:0:2,1,0,0:3,0 0,21,178:7:0:0:6,1,0,0:7,0 17 123 . T <*> 0 . DP=18;DPR=17,0;I16=15,2,0,0,647,26145,0,0,927,52923,0,0,296,6554,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,24,170:8:0:0:8,0,0,0:8,0 0,9,123:3:0:0:2,1,0,0:3,0 0,18,166:6:0:0:5,1,0,0:6,0 17 124 . T <*> 0 . DP=19;DPR=18,0;I16=16,2,0,0,606,22002,0,0,987,56523,0,0,296,6564,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,154:9:0:0:9,0,0,0:9,0 0,9,114:3:0:0:2,1,0,0:3,0 0,18,154:6:0:0:5,1,0,0:6,0 -17 125 . A T,<*> 0 . DP=18;DPR=16,1,0;I16=14,2,1,0,589,22565,4,16,898,52082,29,841,272,5916,25,625;QS=2.98444,0.0155642,0;SGB=-0.556633;RPBZ=1.02125;MQBZ=-2.16025;MQSBZ=-1.23956;BQBZ=-1.64106;SCBZ=2.91548;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,15,149,21,152,149:8:1:0:7,0,1,0:7,1,0 0,9,114,9,114,114:3:0:0:2,1,0,0:3,0,0 0,18,162,18,162,162:6:0:0:5,1,0,0:6,0,0 +17 125 . A T,<*> 0 . DP=18;DPR=16,1,0;I16=14,2,1,0,589,22565,4,16,898,52082,29,841,272,5916,25,625;QS=2.98444,0.0155642,0;SGB=-0.556633;RPBZ=1.02125;MQBZ=-2.16025;MQSBZ=-1.23956;BQBZ=-1.64106;SCBZ=2.91548;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,15,149,21,152,149:8:1:0:7,0,1,0:7,1,0 0,9,114,9,114,114:3:0:0:2,1,0,0:3,0,0 0,18,162,18,162,162:6:0:0:5,1,0,0:6,0,0 17 126 . A <*> 0 . DP=18;DPR=17,0;I16=15,2,0,0,629,24725,0,0,927,52923,0,0,298,6536,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,24,162:8:0:0:8,0,0,0:8,0 0,9,117:3:0:0:2,1,0,0:3,0 0,18,174:6:0:0:5,1,0,0:6,0 17 127 . C <*> 0 . DP=18;DPR=17,0;I16=15,2,0,0,627,24331,0,0,927,52923,0,0,299,6549,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,24,163:8:0:0:8,0,0,0:8,0 0,9,119:3:0:0:2,1,0,0:3,0 0,18,160:6:0:0:5,1,0,0:6,0 17 128 . A <*> 0 . DP=18;DPR=17,0;I16=15,2,0,0,660,26364,0,0,927,52923,0,0,300,6580,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,24,169:8:0:0:8,0,0,0:8,0 0,9,121:3:0:0:2,1,0,0:3,0 0,18,168:6:0:0:5,1,0,0:6,0 @@ -84,7 +83,7 @@ 17 156 . C <*> 0 . DP=14;DPR=14,0;I16=12,2,0,0,536,20884,0,0,809,47641,0,0,266,5934,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,163:7:0:0:7,0,0,0:7,0 0,6,84:2:0:0:1,1,0,0:2,0 0,15,150:5:0:0:4,1,0,0:5,0 17 157 . C <*> 0 . DP=14;DPR=14,0;I16=12,2,0,0,555,22081,0,0,809,47641,0,0,264,5904,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,169:7:0:0:7,0,0,0:7,0 0,6,85:2:0:0:1,1,0,0:2,0 0,15,149:5:0:0:4,1,0,0:5,0 17 158 . T <*> 0 . DP=14;DPR=14,0;I16=12,2,0,0,568,23154,0,0,809,47641,0,0,262,5886,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,170:7:0:0:7,0,0,0:7,0 0,6,84:2:0:0:1,1,0,0:2,0 0,15,159:5:0:0:4,1,0,0:5,0 -17 159 . A G,<*> 0 . DP=15;DPR=14,1,0;I16=12,2,1,0,519,19467,5,25,809,47641,60,3600,260,5880,0,0;QS=2.97076,0.0292398,0;SGB=-0.556633;RPBZ=-1.62019;MQBZ=0.267261;MQSBZ=-2.54951;BQBZ=-1.63041;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,157,21,157,157:7:0:0:7,0,0,0:7,0,0 0,6,83,6,83,83:2:0:0:1,1,0,0:2,0,0 0,10,129,15,132,129:6:1:0:4,1,1,0:5,1,0 +17 159 . A G,<*> 0 . DP=15;DPR=14,1,0;I16=12,2,1,0,519,19467,5,25,809,47641,60,3600,260,5880,0,0;QS=2.97076,0.0292398,0;SGB=-0.556633;RPBZ=-1.62019;MQBZ=0.267261;MQSBZ=-2.54951;BQBZ=-1.63041;SCBZ=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,157,21,157,157:7:0:0:7,0,0,0:7,0,0 0,6,83,6,83,83:2:0:0:1,1,0,0:2,0,0 0,10,129,15,132,129:6:1:0:4,1,1,0:5,1,0 17 160 . G <*> 0 . DP=15;DPR=15,0;I16=13,2,0,0,547,20633,0,0,869,51241,0,0,259,5887,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,165:7:0:0:7,0,0,0:7,0 0,6,85:2:0:0:1,1,0,0:2,0 0,18,139:6:0:0:5,1,0,0:6,0 17 161 . A <*> 0 . DP=15;DPR=15,0;I16=13,2,0,0,568,21610,0,0,869,51241,0,0,258,5908,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,157:7:0:0:7,0,0,0:7,0 0,6,83:2:0:0:1,1,0,0:2,0 0,18,162:6:0:0:5,1,0,0:6,0 17 162 . A <*> 0 . DP=15;DPR=15,0;I16=13,2,0,0,558,21206,0,0,869,51241,0,0,255,5843,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,147:7:0:0:7,0,0,0:7,0 0,6,87:2:0:0:1,1,0,0:2,0 0,18,167:6:0:0:5,1,0,0:6,0 @@ -115,7 +114,7 @@ 17 187 . C <*> 0 . DP=14;DPR=14,0;I16=13,1,0,0,511,18979,0,0,809,47641,0,0,266,5952,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,147:6:0:0:6,0,0,0:6,0 0,3,38:1:0:0:1,0,0,0:1,0 0,21,172:7:0:0:6,1,0,0:7,0 17 188 . C <*> 0 . DP=14;DPR=14,0;I16=13,1,0,0,496,18042,0,0,809,47641,0,0,267,5989,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,147:6:0:0:6,0,0,0:6,0 0,3,37:1:0:0:1,0,0,0:1,0 0,21,162:7:0:0:6,1,0,0:7,0 17 189 . C <*> 0 . DP=15;DPR=15,0;I16=13,2,0,0,552,20504,0,0,838,48482,0,0,268,6040,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,152:6:0:0:6,0,0,0:6,0 0,6,67:2:0:0:1,1,0,0:2,0 0,21,167:7:0:0:6,1,0,0:7,0 -17 190 . A C,<*> 0 . DP=15;DPR=14,1,0;I16=12,2,1,0,500,18230,5,25,778,44882,60,3600,243,5381,25,625;QS=2.97664,0.0233645,0;SGB=-0.556633;RPBZ=0;MQBZ=0.392232;MQSBZ=-3.74166;BQBZ=-1.63041;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,138,18,138,138:6:0:0:6,0,0,0:6,0,0 0,6,68,6,68,68:2:0:0:1,1,0,0:2,0,0 0,12,153,18,156,153:7:1:0:5,1,1,0:6,1,0 +17 190 . A C,<*> 0 . DP=15;DPR=14,1,0;I16=12,2,1,0,500,18230,5,25,778,44882,60,3600,243,5381,25,625;QS=2.97664,0.0233645,0;SGB=-0.556633;RPBZ=0;MQBZ=0.392232;MQSBZ=-3.74166;BQBZ=-1.63041;SCBZ=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,138,18,138,138:6:0:0:6,0,0,0:6,0,0 0,6,68,6,68,68:2:0:0:1,1,0,0:2,0,0 0,12,153,18,156,153:7:1:0:5,1,1,0:6,1,0 17 191 . T <*> 0 . DP=15;DPR=15,0;I16=13,2,0,0,534,19276,0,0,838,48482,0,0,267,5939,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,143:6:0:0:6,0,0,0:6,0 0,6,67:2:0:0:1,1,0,0:2,0 0,21,169:7:0:0:6,1,0,0:7,0 17 192 . G <*> 0 . DP=15;DPR=15,0;I16=13,2,0,0,499,17439,0,0,838,48482,0,0,266,5890,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,143:6:0:0:6,0,0,0:6,0 0,6,67:2:0:0:1,1,0,0:2,0 0,21,151:7:0:0:6,1,0,0:7,0 17 193 . T <*> 0 . DP=15;DPR=15,0;I16=13,2,0,0,505,17811,0,0,838,48482,0,0,265,5859,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,140:6:0:0:6,0,0,0:6,0 0,6,63:2:0:0:1,1,0,0:2,0 0,21,157:7:0:0:6,1,0,0:7,0 @@ -148,10 +147,10 @@ 17 220 . G <*> 0 . DP=14;DPR=14,0;I16=11,3,0,0,495,18407,0,0,747,42123,0,0,267,6079,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,188:7:0:0:6,1,0,0:7,0 0,9,88:3:0:0:1,2,0,0:3,0 0,12,84:4:0:0:4,0,0,0:4,0 17 221 . A <*> 0 . DP=14;DPR=14,0;I16=11,3,0,0,488,17688,0,0,747,42123,0,0,267,6135,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,176:7:0:0:6,1,0,0:7,0 0,9,89:3:0:0:1,2,0,0:3,0 0,12,101:4:0:0:4,0,0,0:4,0 17 222 . A <*> 0 . DP=14;DPR=14,0;I16=11,3,0,0,479,17747,0,0,747,42123,0,0,267,6203,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,186:7:0:0:6,1,0,0:7,0 0,9,89:3:0:0:1,2,0,0:3,0 0,12,73:4:0:0:4,0,0,0:4,0 -17 223 . G T,<*> 0 . DP=13;DPR=12,1,0;I16=9,3,1,0,412,14782,8,64,627,34923,60,3600,243,5657,25,625;QS=2.96596,0.0340426,0;SGB=-0.556633;RPBZ=1.07052;MQBZ=0.547723;MQSBZ=-3.4641;BQBZ=-1.60577;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,11,166,18,169,167:7:1:0:5,1,1,0:6,1,0 0,6,53,6,53,53:2:0:0:0,2,0,0:2,0,0 0,12,81,12,81,81:4:0:0:4,0,0,0:4,0,0 +17 223 . G T,<*> 0 . DP=13;DPR=12,1,0;I16=9,3,1,0,412,14782,8,64,627,34923,60,3600,243,5657,25,625;QS=2.96596,0.0340426,0;SGB=-0.556633;RPBZ=1.07052;MQBZ=0.547723;MQSBZ=-3.4641;BQBZ=-1.60577;SCBZ=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,11,166,18,169,167:7:1:0:5,1,1,0:6,1,0 0,6,53,6,53,53:2:0:0:0,2,0,0:2,0,0 0,12,81,12,81,81:4:0:0:4,0,0,0:4,0,0 17 224 . G <*> 0 . DP=12;DPR=12,0;I16=9,3,0,0,379,12759,0,0,627,34923,0,0,270,6370,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,168:6:0:0:5,1,0,0:6,0 0,6,50:2:0:0:0,2,0,0:2,0 0,12,70:4:0:0:4,0,0,0:4,0 17 225 . C <*> 0 . DP=12;DPR=12,0;I16=9,3,0,0,390,13960,0,0,627,34923,0,0,272,6466,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,165:6:0:0:5,1,0,0:6,0 0,6,48:2:0:0:0,2,0,0:2,0 0,12,86:4:0:0:4,0,0,0:4,0 -17 226 . A G,C,<*> 0 . DP=13;DPR=11,1,1,0;I16=8,3,1,1,381,13669,6,18,567,31323,89,4441,248,5894,44,986;QS=2.94293,0.0392157,0.0178571,0;VDB=0.84;SGB=-2.62246;RPBZ=-0.592157;MQBZ=-0.615457;MQSBZ=-3.4641;BQBZ=-2.17723;SCBZ=2.34521;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,159,12,162,159,18,159,162,159:7:1:0:5,1,0,1:6,0,1,0 0,6,53,6,53,53,6,53,53,53:2:0:0:0,2,0,0:2,0,0,0 0,5,79,9,82,80,9,82,80,80:4:1:0:3,0,1,0:3,1,0,0 +17 226 . A G,C,<*> 0 . DP=13;DPR=11,1,1,0;I16=8,3,1,1,381,13669,6,18,567,31323,89,4441,248,5894,44,986;QS=2.94293,0.0392157,0.0178571,0;VDB=0.84;SGB=-2.62246;RPBZ=-0.592157;MQBZ=-0.615457;MQSBZ=-3.4641;BQBZ=-2.17723;SCBZ=2.34521;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,18,159,12,162,159,18,159,162,159:7:1:0:5,1,0,1:6,0,1,0 0,6,53,6,53,53,6,53,53,53:2:0:0:0,2,0,0:2,0,0,0 0,5,79,9,82,80,9,82,80,80:4:1:0:3,0,1,0:3,1,0,0 17 227 . C <*> 0 . DP=13;DPR=13,0;I16=9,4,0,0,412,14342,0,0,656,35764,0,0,292,6878,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,190:7:0:0:5,2,0,0:7,0 0,6,53:2:0:0:0,2,0,0:2,0 0,12,75:4:0:0:4,0,0,0:4,0 17 228 . C <*> 0 . DP=13;DPR=13,0;I16=9,4,0,0,417,14381,0,0,656,35764,0,0,292,6884,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,187:7:0:0:5,2,0,0:7,0 0,6,45:2:0:0:0,2,0,0:2,0 0,12,96:4:0:0:4,0,0,0:4,0 17 229 . G <*> 0 . DP=13;DPR=13,0;I16=9,4,0,0,368,11524,0,0,656,35764,0,0,292,6898,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,145:7:0:0:5,2,0,0:7,0 0,6,53:2:0:0:0,2,0,0:2,0 0,12,70:4:0:0:4,0,0,0:4,0 @@ -162,7 +161,7 @@ 17 234 . A <*> 0 . DP=14;DPR=14,0;I16=10,4,0,0,502,18390,0,0,716,39364,0,0,292,6988,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,185:7:0:0:5,2,0,0:7,0 0,6,53:2:0:0:0,2,0,0:2,0 0,15,123:5:0:0:5,0,0,0:5,0 17 235 . A <*> 0 . DP=14;DPR=14,0;I16=10,4,0,0,488,17796,0,0,716,39364,0,0,291,6951,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,21,186:7:0:0:5,2,0,0:7,0 0,6,53:2:0:0:0,2,0,0:2,0 0,15,115:5:0:0:5,0,0,0:5,0 17 236 . G <*> 0 . DP=15;DPR=15,0;I16=11,4,0,0,501,17481,0,0,776,42964,0,0,290,6924,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,24,206:8:0:0:6,2,0,0:8,0 0,6,53:2:0:0:0,2,0,0:2,0 0,15,103:5:0:0:5,0,0,0:5,0 -17 237 . A C,<*> 0 . DP=14;DPR=13,1,0;I16=9,4,1,0,465,16877,8,64,656,35764,60,3600,266,6282,25,625;QS=2.93162,0.0683761,0;SGB=-0.556633;RPBZ=1.11754;MQBZ=0.632456;MQSBZ=-3.60555;BQBZ=-1.61959;SCBZ=-0.27735;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,24,206,24,206,206:8:0:0:6,2,0,0:8,0,0 0,6,53,6,53,53:2:0:0:0,2,0,0:2,0,0 0,3,84,9,87,87:4:1:0:3,0,1,0:3,1,0 +17 237 . A C,<*> 0 . DP=14;DPR=13,1,0;I16=9,4,1,0,465,16877,8,64,656,35764,60,3600,266,6282,25,625;QS=2.93162,0.0683761,0;SGB=-0.556633;RPBZ=1.11754;MQBZ=0.632456;MQSBZ=-3.60555;BQBZ=-1.61959;SCBZ=-0.27735;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,24,206,24,206,206:8:0:0:6,2,0,0:8,0,0 0,6,53,6,53,53:2:0:0:0,2,0,0:2,0,0 0,3,84,9,87,87:4:1:0:3,0,1,0:3,1,0 17 238 . C <*> 0 . DP=14;DPR=14,0;I16=10,4,0,0,482,17238,0,0,716,39364,0,0,292,6900,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,24,211:8:0:0:6,2,0,0:8,0 0,6,53:2:0:0:0,2,0,0:2,0 0,12,82:4:0:0:4,0,0,0:4,0 17 239 . A <*> 0 . DP=15;DPR=15,0;I16=10,5,0,0,525,19155,0,0,776,42964,0,0,292,6852,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,223:9:0:0:6,3,0,0:9,0 0,6,50:2:0:0:0,2,0,0:2,0 0,12,108:4:0:0:4,0,0,0:4,0 17 240 . C <*> 0 . DP=15;DPR=15,0;I16=10,5,0,0,512,17930,0,0,776,42964,0,0,292,6764,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,220:9:0:0:6,3,0,0:9,0 0,6,53:2:0:0:0,2,0,0:2,0 0,12,106:4:0:0:4,0,0,0:4,0 @@ -192,18 +191,18 @@ 17 264 . C <*> 0 . DP=22;DPR=22,0;I16=10,12,0,0,821,31325,0,0,1049,54897,0,0,386,8326,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:7,4,0,0:11,0 0,15,104:5:0:0:0,5,0,0:5,0 0,18,172:6:0:0:3,3,0,0:6,0 17 265 . A <*> 0 . DP=21;DPR=21,0;I16=9,12,0,0,800,31906,0,0,989,51297,0,0,390,8380,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:7,4,0,0:11,0 0,15,114:5:0:0:0,5,0,0:5,0 0,15,129:5:0:0:2,3,0,0:5,0 17 266 . G <*> 0 . DP=21;DPR=21,0;I16=9,12,0,0,754,28204,0,0,989,51297,0,0,394,8458,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:7,4,0,0:11,0 0,15,99:5:0:0:0,5,0,0:5,0 0,15,138:5:0:0:2,3,0,0:5,0 -17 267 . T G,<*> 0 . DP=21;DPR=20,1,0;I16=9,11,0,1,739,27465,8,64,960,50456,29,841,373,7935,25,625;QS=2.94203,0.057971,0;SGB=-0.556633;RPBZ=-0.330396;MQBZ=-1.23153;MQSBZ=-3.3021;BQBZ=-1.66282;SCBZ=2.91633;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,254,33,254,254:11:0:0:7,4,0,0:11,0,0 0,6,93,12,96,96:5:1:0:0,4,0,1:4,1,0 0,15,149,15,149,149:5:0:0:2,3,0,0:5,0,0 +17 267 . T G,<*> 0 . DP=21;DPR=20,1,0;I16=9,11,0,1,739,27465,8,64,960,50456,29,841,373,7935,25,625;QS=2.94203,0.057971,0;SGB=-0.556633;RPBZ=-0.330396;MQBZ=-1.23153;MQSBZ=-3.3021;BQBZ=-1.66282;SCBZ=2.91633;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,254,33,254,254:11:0:0:7,4,0,0:11,0,0 0,6,93,12,96,96:5:1:0:0,4,0,1:4,1,0 0,15,149,15,149,149:5:0:0:2,3,0,0:5,0,0 17 268 . T <*> 0 . DP=21;DPR=21,0;I16=9,12,0,0,748,27708,0,0,989,51297,0,0,402,8686,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,238:11:0:0:7,4,0,0:11,0 0,15,110:5:0:0:0,5,0,0:5,0 0,15,156:5:0:0:2,3,0,0:5,0 17 269 . C <*> 0 . DP=22;DPR=22,0;I16=9,13,0,0,767,28641,0,0,1018,52138,0,0,406,8836,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:7,5,0,0:12,0 0,15,91:5:0:0:0,5,0,0:5,0 0,15,154:5:0:0:2,3,0,0:5,0 17 270 . C <*> 0 . DP=22;DPR=22,0;I16=9,13,0,0,766,28210,0,0,1018,52138,0,0,410,8962,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:7,5,0,0:12,0 0,15,98:5:0:0:0,5,0,0:5,0 0,15,143:5:0:0:2,3,0,0:5,0 17 271 . T <*> 0 . DP=22;DPR=22,0;I16=9,13,0,0,847,32935,0,0,1018,52138,0,0,413,9065,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:7,5,0,0:12,0 0,15,113:5:0:0:0,5,0,0:5,0 0,15,152:5:0:0:2,3,0,0:5,0 17 272 . C <*> 0 . DP=22;DPR=22,0;I16=9,13,0,0,815,31449,0,0,1018,52138,0,0,415,9143,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:7,5,0,0:12,0 0,15,97:5:0:0:0,5,0,0:5,0 0,15,149:5:0:0:2,3,0,0:5,0 -17 273 . T C,<*> 0 . DP=22;DPR=21,1,0;I16=9,12,0,1,798,30664,5,25,989,51297,29,841,392,8620,25,625;QS=2.96094,0.0390625,0;SGB=-0.556633;RPBZ=-0.236567;MQBZ=-1.16701;MQSBZ=-3.42286;BQBZ=-1.66779;SCBZ=3.00076;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255,36,255,255:12:0:0:7,5,0,0:12,0,0 0,7,89,12,92,90:5:1:0:0,4,0,1:4,1,0 0,15,161,15,161,161:5:0:0:2,3,0,0:5,0,0 +17 273 . T C,<*> 0 . DP=22;DPR=21,1,0;I16=9,12,0,1,798,30664,5,25,989,51297,29,841,392,8620,25,625;QS=2.96094,0.0390625,0;SGB=-0.556633;RPBZ=-0.236567;MQBZ=-1.16701;MQSBZ=-3.42286;BQBZ=-1.66779;SCBZ=3.00076;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255,36,255,255:12:0:0:7,5,0,0:12,0,0 0,7,89,12,92,90:5:1:0:0,4,0,1:4,1,0 0,15,161,15,161,161:5:0:0:2,3,0,0:5,0,0 17 274 . C <*> 0 . DP=22;DPR=22,0;I16=9,13,0,0,767,28193,0,0,1018,52138,0,0,419,9371,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:7,5,0,0:12,0 0,15,101:5:0:0:0,5,0,0:5,0 0,15,144:5:0:0:2,3,0,0:5,0 17 275 . C <*> 0 . DP=20;DPR=20,0;I16=7,13,0,0,768,29994,0,0,898,44938,0,0,423,9519,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,15,114:5:0:0:0,5,0,0:5,0 0,12,122:4:0:0:1,3,0,0:4,0 17 276 . A <*> 0 . DP=20;DPR=20,0;I16=7,13,0,0,805,32931,0,0,898,44938,0,0,424,9538,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,253:11:0:0:6,5,0,0:11,0 0,15,122:5:0:0:0,5,0,0:5,0 0,12,124:4:0:0:1,3,0,0:4,0 17 277 . G <*> 0 . DP=20;DPR=20,0;I16=7,13,0,0,764,29732,0,0,898,44938,0,0,425,9579,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,15,114:5:0:0:0,5,0,0:5,0 0,12,121:4:0:0:1,3,0,0:4,0 -17 278 . A C,<*> 0 . DP=21;DPR=20,1,0;I16=6,14,1,0,722,26452,7,49,867,42179,60,3600,415,9521,11,121;QS=2.97935,0.020649,0;SGB=-0.556633;RPBZ=1.65198;MQBZ=1.0247;MQSBZ=-3.24037;BQBZ=-1.66667;SCBZ=-0.324037;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,22,231,30,234,231:11:1:0:5,5,1,0:10,1,0 0,18,123,18,123,123:6:0:0:0,6,0,0:6,0,0 0,12,121,12,121,121:4:0:0:1,3,0,0:4,0,0 +17 278 . A C,<*> 0 . DP=21;DPR=20,1,0;I16=6,14,1,0,722,26452,7,49,867,42179,60,3600,415,9521,11,121;QS=2.97935,0.020649,0;SGB=-0.556633;RPBZ=1.65198;MQBZ=1.0247;MQSBZ=-3.24037;BQBZ=-1.66667;SCBZ=-0.324037;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,22,231,30,234,231:11:1:0:5,5,1,0:10,1,0 0,18,123,18,123,123:6:0:0:0,6,0,0:6,0,0 0,12,121,12,121,121:4:0:0:1,3,0,0:4,0,0 17 279 . A <*> 0 . DP=22;DPR=22,0;I16=7,15,0,0,786,28694,0,0,956,46620,0,0,427,9677,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:6,6,0,0:12,0 0,18,123:6:0:0:0,6,0,0:6,0 0,12,122:4:0:0:1,3,0,0:4,0 17 280 . A <*> 0 . DP=22;DPR=22,0;I16=7,15,0,0,815,31561,0,0,956,46620,0,0,428,9684,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,253:12:0:0:6,6,0,0:12,0 0,18,130:6:0:0:0,6,0,0:6,0 0,12,129:4:0:0:1,3,0,0:4,0 17 281 . G <*> 0 . DP=22;DPR=22,0;I16=7,15,0,0,820,31416,0,0,956,46620,0,0,428,9662,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:6,6,0,0:12,0 0,18,122:6:0:0:0,6,0,0:6,0 0,12,123:4:0:0:1,3,0,0:4,0 @@ -222,13 +221,13 @@ 17 294 . A <*> 0 . DP=26;DPR=26,0;I16=10,16,0,0,931,33937,0,0,1227,63779,0,0,443,9785,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,252:12:0:0:6,6,0,0:12,0 0,24,201:8:0:0:3,5,0,0:8,0 0,18,161:6:0:0:1,5,0,0:6,0 17 295 . C <*> 0 . DP=25;DPR=25,0;I16=10,15,0,0,909,34117,0,0,1198,62938,0,0,447,9833,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,183:8:0:0:3,5,0,0:8,0 0,18,159:6:0:0:1,5,0,0:6,0 17 296 . A <*> 0 . DP=25;DPR=25,0;I16=10,15,0,0,874,31846,0,0,1198,62938,0,0,451,9905,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,169:8:0:0:3,5,0,0:8,0 0,18,169:6:0:0:1,5,0,0:6,0 -17 297 . C G,<*> 0 . DP=25;DPR=24,1,0;I16=9,15,1,0,901,34305,4,16,1138,59338,60,3600,445,9901,10,100;QS=2.98261,0.0173913,0;SGB=-0.556633;RPBZ=-1.24856;MQBZ=0.806872;MQSBZ=-3.22749;BQBZ=-1.67542;SCBZ=-0.368383;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255,33,255,255:11:0:0:6,5,0,0:11,0,0 0,15,168,21,171,168:8:1:0:2,5,1,0:7,1,0 0,18,161,18,161,161:6:0:0:1,5,0,0:6,0,0 +17 297 . C G,<*> 0 . DP=25;DPR=24,1,0;I16=9,15,1,0,901,34305,4,16,1138,59338,60,3600,445,9901,10,100;QS=2.98261,0.0173913,0;SGB=-0.556633;RPBZ=-1.24856;MQBZ=0.806872;MQSBZ=-3.22749;BQBZ=-1.67542;SCBZ=-0.368383;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255,33,255,255:11:0:0:6,5,0,0:11,0,0 0,15,168,21,171,168:8:1:0:2,5,1,0:7,1,0 0,18,161,18,161,161:6:0:0:1,5,0,0:6,0,0 17 298 . A <*> 0 . DP=26;DPR=26,0;I16=11,15,0,0,936,34652,0,0,1258,66538,0,0,459,10121,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,184:8:0:0:3,5,0,0:8,0 0,21,191:7:0:0:2,5,0,0:7,0 17 299 . C <*> 0 . DP=27;DPR=26,0;I16=11,15,0,0,971,36863,0,0,1258,66538,0,0,464,10266,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,193:8:0:0:3,5,0,0:8,0 0,21,189:7:0:0:2,5,0,0:7,0 17 300 . A <*> 0 . DP=27;DPR=26,0;I16=11,15,0,0,1001,39455,0,0,1258,66538,0,0,469,10437,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,204:8:0:0:3,5,0,0:8,0 0,21,210:7:0:0:2,5,0,0:7,0 17 301 . G <*> 0 . DP=25;DPR=24,0;I16=10,14,0,0,928,36116,0,0,1169,62097,0,0,476,10632,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,255:10:0:0:5,5,0,0:10,0 0,21,195:7:0:0:3,4,0,0:7,0 0,21,196:7:0:0:2,5,0,0:7,0 17 302 . T <*> 0 . DP=25;DPR=24,0;I16=10,14,0,0,879,32885,0,0,1169,62097,0,0,483,10849,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,231:10:0:0:5,5,0,0:10,0 0,21,172:7:0:0:3,4,0,0:7,0 0,21,202:7:0:0:2,5,0,0:7,0 -17 302 . T TA 0 . INDEL;IDV=7;IMF=1;DP=25;DPR=6,19;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.539485,2.46052;VDB=0.241622;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.22749;BQBZ=-1.67542;SCBZ=-0.268121;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 161,0,99:11:6:6:1,4,4,2:5,6 158,0,14:7:6:0:1,0,2,4:1,6 201,21,0:7:7:0:0,0,2,5:0,7 +17 302 . T TA 0 . INDEL;IDV=7;IMF=1;DP=25;DPR=6,19;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.539485,2.46052;VDB=0.241622;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.22749;BQBZ=-1.67542;SCBZ=-0.268121;MQ0F=0 PL:DP:DV:SP:DP4:DPR 161,0,99:11:6:6:1,4,4,2:5,6 158,0,14:7:6:0:1,0,2,4:1,6 201,21,0:7:7:0:0,0,2,5:0,7 17 303 . G <*> 0 . DP=25;DPR=25,0;I16=10,15,0,0,968,37972,0,0,1229,65697,0,0,497,11181,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:5,6,0,0:11,0 0,21,197:7:0:0:3,4,0,0:7,0 0,21,195:7:0:0:2,5,0,0:7,0 17 304 . C <*> 0 . DP=27;DPR=27,0;I16=11,16,0,0,991,37005,0,0,1318,70138,0,0,503,11359,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:5,6,0,0:11,0 0,24,206:8:0:0:4,4,0,0:8,0 0,24,200:8:0:0:2,6,0,0:8,0 17 305 . C <*> 0 . DP=27;DPR=27,0;I16=11,16,0,0,1057,41761,0,0,1318,70138,0,0,510,11508,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:5,6,0,0:11,0 0,24,213:8:0:0:4,4,0,0:8,0 0,24,211:8:0:0:2,6,0,0:8,0 @@ -261,9 +260,9 @@ 17 332 . A <*> 0 . DP=32;DPR=32,0;I16=14,18,0,0,1156,42666,0,0,1649,90897,0,0,560,12178,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:6,6,0,0:12,0 0,27,214:9:0:0:4,5,0,0:9,0 0,33,255:11:0:0:4,7,0,0:11,0 17 333 . A <*> 0 . DP=32;DPR=32,0;I16=14,18,0,0,1141,41987,0,0,1649,90897,0,0,558,12064,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:6,6,0,0:12,0 0,27,223:9:0:0:4,5,0,0:9,0 0,33,255:11:0:0:4,7,0,0:11,0 17 334 . A <*> 0 . DP=32;DPR=32,0;I16=14,18,0,0,1162,43328,0,0,1649,90897,0,0,556,11986,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:6,6,0,0:12,0 0,27,221:9:0:0:4,5,0,0:9,0 0,33,255:11:0:0:4,7,0,0:11,0 -17 335 . A G,<*> 0 . DP=32;DPR=31,1,0;I16=13,18,1,0,1084,40336,4,16,1589,87297,60,3600,555,11943,0,0;QS=2.98919,0.0108108,0;SGB=-0.556633;RPBZ=-1.67936;MQBZ=0.622171;MQSBZ=-2.25492;BQBZ=-1.68602;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,252,33,252,252:11:0:0:5,6,0,0:11,0,0 0,27,219,27,219,219:9:0:0:4,5,0,0:9,0,0 0,25,245,33,248,245:12:1:0:4,7,1,0:11,1,0 +17 335 . A G,<*> 0 . DP=32;DPR=31,1,0;I16=13,18,1,0,1084,40336,4,16,1589,87297,60,3600,555,11943,0,0;QS=2.98919,0.0108108,0;SGB=-0.556633;RPBZ=-1.67936;MQBZ=0.622171;MQSBZ=-2.25492;BQBZ=-1.68602;SCBZ=-0.258065;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,252,33,252,252:11:0:0:5,6,0,0:11,0,0 0,27,219,27,219,219:9:0:0:4,5,0,0:9,0,0 0,25,245,33,248,245:12:1:0:4,7,1,0:11,1,0 17 336 . A <*> 0 . DP=32;DPR=32,0;I16=14,18,0,0,1094,39794,0,0,1649,90897,0,0,555,11935,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:5,6,0,0:11,0 0,27,212:9:0:0:4,5,0,0:9,0 0,36,255:12:0:0:5,7,0,0:12,0 -17 337 . C A,<*> 0 . DP=32;DPR=31,1,0;I16=14,17,0,1,1125,42481,5,25,1612,89528,37,1369,536,11590,18,324;QS=2.98113,0.0188679,0;SGB=-0.556633;RPBZ=0.812593;MQBZ=-1.03695;MQSBZ=-2.25492;BQBZ=-1.68353;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255,33,255,255:11:0:0:5,6,0,0:11,0,0 0,17,195,24,198,195:9:1:0:4,4,0,1:8,1,0 0,36,255,36,255,255:12:0:0:5,7,0,0:12,0,0 +17 337 . C A,<*> 0 . DP=32;DPR=31,1,0;I16=14,17,0,1,1125,42481,5,25,1612,89528,37,1369,536,11590,18,324;QS=2.98113,0.0188679,0;SGB=-0.556633;RPBZ=0.812593;MQBZ=-1.03695;MQSBZ=-2.25492;BQBZ=-1.68353;SCBZ=-0.258065;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255,33,255,255:11:0:0:5,6,0,0:11,0,0 0,17,195,24,198,195:9:1:0:4,4,0,1:8,1,0 0,36,255,36,255,255:12:0:0:5,7,0,0:12,0,0 17 338 . T <*> 0 . DP=30;DPR=30,0;I16=14,16,0,0,1190,47898,0,0,1560,86456,0,0,554,11878,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,255:10:0:0:5,5,0,0:10,0 0,24,226:8:0:0:4,4,0,0:8,0 0,36,255:12:0:0:5,7,0,0:12,0 17 339 . C <*> 0 . DP=31;DPR=31,0;I16=14,17,0,0,1130,43210,0,0,1589,87297,0,0,554,11874,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:5,6,0,0:11,0 0,24,185:8:0:0:4,4,0,0:8,0 0,36,255:12:0:0:5,7,0,0:12,0 17 340 . C <*> 0 . DP=31;DPR=31,0;I16=14,17,0,0,1196,47044,0,0,1589,87297,0,0,554,11852,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:5,6,0,0:11,0 0,24,221:8:0:0:4,4,0,0:8,0 0,36,255:12:0:0:5,7,0,0:12,0 @@ -281,11 +280,11 @@ 17 352 . A <*> 0 . DP=31;DPR=31,0;I16=16,15,0,0,1162,45664,0,0,1651,92815,0,0,569,13029,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,27,230:9:0:0:5,4,0,0:9,0 0,33,255:11:0:0:5,6,0,0:11,0 17 353 . G <*> 0 . DP=29;DPR=29,0;I16=15,14,0,0,1109,43095,0,0,1562,88374,0,0,570,13064,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,255:10:0:0:5,5,0,0:10,0 0,27,231:9:0:0:5,4,0,0:9,0 0,30,255:10:0:0:5,5,0,0:10,0 17 354 . A <*> 0 . DP=28;DPR=28,0;I16=14,14,0,0,1078,42938,0,0,1502,84774,0,0,571,13075,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,225:9:0:0:4,5,0,0:9,0 0,27,244:9:0:0:5,4,0,0:9,0 0,30,255:10:0:0:5,5,0,0:10,0 -17 355 . G T,<*> 0 . DP=28;DPR=27,1,0;I16=14,13,0,1,1001,37907,41,1681,1442,81174,60,3600,547,12487,25,625;QS=2.875,0.125,0;SGB=-0.556633;RPBZ=0.185772;MQBZ=0.520126;MQSBZ=-1.7696;BQBZ=0.683978;SCBZ=-0.27735;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 14,0,200,38,203,231:9:1:0:4,4,0,1:8,1,0 0,27,222,27,222,222:9:0:0:5,4,0,0:9,0,0 0,30,255,30,255,255:10:0:0:5,5,0,0:10,0,0 +17 355 . G T,<*> 0 . DP=28;DPR=27,1,0;I16=14,13,0,1,1001,37907,41,1681,1442,81174,60,3600,547,12487,25,625;QS=2.875,0.125,0;SGB=-0.556633;RPBZ=0.185772;MQBZ=0.520126;MQSBZ=-1.7696;BQBZ=0.683978;SCBZ=-0.27735;MQ0F=0 PL:DP:DV:SP:DP4:DPR 14,0,200,38,203,231:9:1:0:4,4,0,1:8,1,0 0,27,222,27,222,222:9:0:0:5,4,0,0:9,0,0 0,30,255,30,255,255:10:0:0:5,5,0,0:10,0,0 17 356 . G <*> 0 . DP=27;DPR=27,0;I16=14,13,0,0,993,37481,0,0,1465,83405,0,0,574,13174,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,27,228:9:0:0:4,5,0,0:9,0 0,24,201:8:0:0:5,3,0,0:8,0 0,30,255:10:0:0:5,5,0,0:10,0 17 357 . C <*> 0 . DP=28;DPR=28,0;I16=15,13,0,0,1026,39496,0,0,1525,87005,0,0,575,13209,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,255:10:0:0:5,5,0,0:10,0 0,24,205:8:0:0:5,3,0,0:8,0 0,30,252:10:0:0:5,5,0,0:10,0 17 358 . A <*> 0 . DP=28;DPR=28,0;I16=15,13,0,0,1050,40518,0,0,1525,87005,0,0,576,13216,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,254:10:0:0:5,5,0,0:10,0 0,24,197:8:0:0:5,3,0,0:8,0 0,30,255:10:0:0:5,5,0,0:10,0 -17 359 . G T,<*> 0 . DP=29;DPR=28,1,0;I16=15,13,0,1,1085,42761,10,100,1525,87005,60,3600,552,12620,25,625;QS=2.96032,0.0396825,0;SGB=-0.556633;RPBZ=-0.119611;MQBZ=0.456435;MQSBZ=-1.53333;BQBZ=-1.68246;SCBZ=5.2915;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,255,30,255,255:10:0:0:5,5,0,0:10,0,0 0,13,178,21,181,180:8:1:0:5,2,0,1:7,1,0 0,33,255,33,255,255:11:0:0:5,6,0,0:11,0,0 +17 359 . G T,<*> 0 . DP=29;DPR=28,1,0;I16=15,13,0,1,1085,42761,10,100,1525,87005,60,3600,552,12620,25,625;QS=2.96032,0.0396825,0;SGB=-0.556633;RPBZ=-0.119611;MQBZ=0.456435;MQSBZ=-1.53333;BQBZ=-1.68246;SCBZ=5.2915;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,255,30,255,255:10:0:0:5,5,0,0:10,0,0 0,13,178,21,181,180:8:1:0:5,2,0,1:7,1,0 0,33,255,33,255,255:11:0:0:5,6,0,0:11,0,0 17 360 . A <*> 0 . DP=29;DPR=29,0;I16=15,14,0,0,1111,43259,0,0,1585,90605,0,0,579,13297,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,252:10:0:0:5,5,0,0:10,0 0,24,220:8:0:0:5,3,0,0:8,0 0,33,255:11:0:0:5,6,0,0:11,0 17 361 . A <*> 0 . DP=29;DPR=29,0;I16=15,14,0,0,1116,43442,0,0,1585,90605,0,0,579,13273,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,252:10:0:0:5,5,0,0:10,0 0,24,219:8:0:0:5,3,0,0:8,0 0,33,255:11:0:0:5,6,0,0:11,0 17 362 . A <*> 0 . DP=29;DPR=29,0;I16=16,13,0,0,1104,42700,0,0,1585,90605,0,0,580,13272,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,218:8:0:0:5,3,0,0:8,0 0,30,255:10:0:0:5,5,0,0:10,0 @@ -295,13 +294,13 @@ 17 366 . A <*> 0 . DP=29;DPR=29,0;I16=16,13,0,0,1090,41562,0,0,1585,90605,0,0,581,13167,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,211:8:0:0:5,3,0,0:8,0 0,30,255:10:0:0:5,5,0,0:10,0 17 367 . T <*> 0 . DP=29;DPR=29,0;I16=16,13,0,0,1055,39149,0,0,1585,90605,0,0,579,13093,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,204:8:0:0:5,3,0,0:8,0 0,30,255:10:0:0:5,5,0,0:10,0 17 368 . A <*> 0 . DP=29;DPR=29,0;I16=16,13,0,0,1054,39632,0,0,1585,90605,0,0,576,12998,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,208:8:0:0:5,3,0,0:8,0 0,30,255:10:0:0:5,5,0,0:10,0 -17 369 . T G,<*> 0 . DP=28;DPR=27,1,0;I16=16,11,0,1,1037,40275,6,36,1496,86164,60,3600,548,12256,25,625;QS=2.97683,0.023166,0;SGB=-0.556633;RPBZ=0.12395;MQBZ=0.408248;MQSBZ=-1.37784;BQBZ=-1.68703;SCBZ=5.19615;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,250,30,250,250:10:0:0:6,4,0,0:10,0,0 0,15,189,21,192,190:8:1:0:5,2,0,1:7,1,0 0,30,255,30,255,255:10:0:0:5,5,0,0:10,0,0 +17 369 . T G,<*> 0 . DP=28;DPR=27,1,0;I16=16,11,0,1,1037,40275,6,36,1496,86164,60,3600,548,12256,25,625;QS=2.97683,0.023166,0;SGB=-0.556633;RPBZ=0.12395;MQBZ=0.408248;MQSBZ=-1.37784;BQBZ=-1.68703;SCBZ=5.19615;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,250,30,250,250:10:0:0:6,4,0,0:10,0,0 0,15,189,21,192,190:8:1:0:5,2,0,1:7,1,0 0,30,255,30,255,255:10:0:0:5,5,0,0:10,0,0 17 370 . C <*> 0 . DP=28;DPR=28,0;I16=16,12,0,0,1045,40219,0,0,1556,89764,0,0,570,12790,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,255:10:0:0:6,4,0,0:10,0 0,24,201:8:0:0:5,3,0,0:8,0 0,30,255:10:0:0:5,5,0,0:10,0 17 371 . T <*> 0 . DP=29;DPR=29,0;I16=16,13,0,0,1155,46591,0,0,1616,93364,0,0,567,12725,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,255:10:0:0:6,4,0,0:10,0 0,24,227:8:0:0:5,3,0,0:8,0 0,33,255:11:0:0:5,6,0,0:11,0 17 372 . C <*> 0 . DP=30;DPR=30,0;I16=16,14,0,0,1139,44019,0,0,1676,96964,0,0,564,12636,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,215:8:0:0:5,3,0,0:8,0 0,33,255:11:0:0:5,6,0,0:11,0 17 373 . A <*> 0 . DP=30;DPR=30,0;I16=16,14,0,0,1142,44118,0,0,1676,96964,0,0,561,12525,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,220:8:0:0:5,3,0,0:8,0 0,33,255:11:0:0:5,6,0,0:11,0 17 374 . T <*> 0 . DP=30;DPR=30,0;I16=16,14,0,0,1098,41180,0,0,1676,96964,0,0,556,12344,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,33,255:11:0:0:6,5,0,0:11,0 0,24,221:8:0:0:5,3,0,0:8,0 0,33,255:11:0:0:5,6,0,0:11,0 -17 375 . A T,<*> 0 . DP=31;DPR=30,1,0;I16=17,13,0,1,1138,43798,14,196,1676,96964,60,3600,547,12177,4,16;QS=2.9661,0.0338983,0;SGB=-0.556633;RPBZ=-1.45432;MQBZ=0.3849;MQSBZ=-1.26404;BQBZ=-1.68488;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255,36,255,255:12:0:0:7,5,0,0:12,0,0 0,24,218,24,218,218:8:0:0:5,3,0,0:8,0,0 0,18,255,30,255,255:11:1:0:5,5,0,1:10,1,0 +17 375 . A T,<*> 0 . DP=31;DPR=30,1,0;I16=17,13,0,1,1138,43798,14,196,1676,96964,60,3600,547,12177,4,16;QS=2.9661,0.0338983,0;SGB=-0.556633;RPBZ=-1.45432;MQBZ=0.3849;MQSBZ=-1.26404;BQBZ=-1.68488;SCBZ=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255,36,255,255:12:0:0:7,5,0,0:12,0,0 0,24,218,24,218,218:8:0:0:5,3,0,0:8,0,0 0,18,255,30,255,255:11:1:0:5,5,0,1:10,1,0 17 376 . G <*> 0 . DP=31;DPR=31,0;I16=17,14,0,0,1131,42581,0,0,1736,100564,0,0,547,12073,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:7,5,0,0:12,0 0,24,220:8:0:0:5,3,0,0:8,0 0,33,255:11:0:0:5,6,0,0:11,0 17 377 . T <*> 0 . DP=31;DPR=31,0;I16=17,14,0,0,1116,41750,0,0,1736,100564,0,0,543,11985,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:7,5,0,0:12,0 0,24,211:8:0:0:5,3,0,0:8,0 0,33,255:11:0:0:5,6,0,0:11,0 17 378 . T <*> 0 . DP=30;DPR=30,0;I16=18,12,0,0,1098,41066,0,0,1707,99723,0,0,541,11927,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255:13:0:0:8,5,0,0:13,0 0,21,186:7:0:0:5,2,0,0:7,0 0,30,255:10:0:0:5,5,0,0:10,0 @@ -310,7 +309,7 @@ 17 381 . T <*> 0 . DP=29;DPR=29,0;I16=18,11,0,0,1167,47337,0,0,1678,98882,0,0,537,11729,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:8,4,0,0:12,0 0,21,211:7:0:0:5,2,0,0:7,0 0,30,255:10:0:0:5,5,0,0:10,0 17 382 . T <*> 0 . DP=29;DPR=29,0;I16=18,11,0,0,1062,40514,0,0,1678,98882,0,0,535,11693,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:8,4,0,0:12,0 0,21,182:7:0:0:5,2,0,0:7,0 0,30,255:10:0:0:5,5,0,0:10,0 17 383 . T <*> 0 . DP=29;DPR=29,0;I16=18,11,0,0,1059,39847,0,0,1678,98882,0,0,532,11638,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,36,255:12:0:0:8,4,0,0:12,0 0,21,172:7:0:0:5,2,0,0:7,0 0,30,255:10:0:0:5,5,0,0:10,0 -17 384 . A C,<*> 0 . DP=31;DPR=30,1,0;I16=19,11,0,1,1077,39885,4,16,1738,102482,60,3600,504,10988,25,625;QS=2.98419,0.0158103,0;SGB=-0.556633;RPBZ=0.615229;MQBZ=0.262613;MQSBZ=-0.333409;BQBZ=-1.68746;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255,39,255,255:13:0:0:8,5,0,0:13,0,0 0,15,171,21,174,171:8:1:0:6,1,0,1:7,1,0 0,30,255,30,255,255:10:0:0:5,5,0,0:10,0,0 +17 384 . A C,<*> 0 . DP=31;DPR=30,1,0;I16=19,11,0,1,1077,39885,4,16,1738,102482,60,3600,504,10988,25,625;QS=2.98419,0.0158103,0;SGB=-0.556633;RPBZ=0.615229;MQBZ=0.262613;MQSBZ=-0.333409;BQBZ=-1.68746;SCBZ=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255,39,255,255:13:0:0:8,5,0,0:13,0,0 0,15,171,21,174,171:8:1:0:6,1,0,1:7,1,0 0,30,255,30,255,255:10:0:0:5,5,0,0:10,0,0 17 385 . C <*> 0 . DP=31;DPR=31,0;I16=19,12,0,0,1118,41180,0,0,1798,106082,0,0,527,11569,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255:13:0:0:8,5,0,0:13,0 0,24,186:8:0:0:6,2,0,0:8,0 0,30,255:10:0:0:5,5,0,0:10,0 17 386 . T <*> 0 . DP=30;DPR=30,0;I16=18,12,0,0,1158,45592,0,0,1738,102482,0,0,526,11556,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255:13:0:0:8,5,0,0:13,0 0,21,191:7:0:0:5,2,0,0:7,0 0,30,255:10:0:0:5,5,0,0:10,0 17 387 . T <*> 0 . DP=30;DPR=30,0;I16=18,12,0,0,1105,41821,0,0,1738,102482,0,0,525,11573,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255:13:0:0:8,5,0,0:13,0 0,21,187:7:0:0:5,2,0,0:7,0 0,30,255:10:0:0:5,5,0,0:10,0 @@ -327,7 +326,7 @@ 17 398 . A <*> 0 . DP=28;DPR=28,0;I16=17,11,0,0,1025,38361,0,0,1587,92523,0,0,524,11850,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255:13:0:0:8,5,0,0:13,0 0,15,144:5:0:0:3,2,0,0:5,0 0,30,255:10:0:0:6,4,0,0:10,0 17 399 . A <*> 0 . DP=28;DPR=28,0;I16=17,11,0,0,1023,38949,0,0,1587,92523,0,0,526,11900,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255:13:0:0:8,5,0,0:13,0 0,15,140:5:0:0:3,2,0,0:5,0 0,30,255:10:0:0:6,4,0,0:10,0 17 400 . A <*> 0 . DP=29;DPR=29,0;I16=17,12,0,0,1070,40554,0,0,1647,96123,0,0,526,11828,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255:13:0:0:8,5,0,0:13,0 0,15,159:5:0:0:3,2,0,0:5,0 0,33,255:11:0:0:6,5,0,0:11,0 -17 401 . A C,<*> 0 . DP=29;DPR=28,1,0;I16=17,11,0,1,1063,41001,8,64,1587,92523,60,3600,501,11113,25,625;QS=2.97985,0.0201511,0;SGB=-0.556633;RPBZ=-0.478622;MQBZ=0.339683;MQSBZ=0.29364;BQBZ=-1.68267;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255,39,255,255:13:0:0:8,5,0,0:13,0,0 0,15,160,15,160,160:5:0:0:3,2,0,0:5,0,0 0,22,255,30,255,255:11:1:0:6,4,0,1:10,1,0 +17 401 . A C,<*> 0 . DP=29;DPR=28,1,0;I16=17,11,0,1,1063,41001,8,64,1587,92523,60,3600,501,11113,25,625;QS=2.97985,0.0201511,0;SGB=-0.556633;RPBZ=-0.478622;MQBZ=0.339683;MQSBZ=0.29364;BQBZ=-1.68267;SCBZ=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255,39,255,255:13:0:0:8,5,0,0:13,0,0 0,15,160,15,160,160:5:0:0:3,2,0,0:5,0,0 0,22,255,30,255,255:11:1:0:6,4,0,1:10,1,0 17 402 . T <*> 0 . DP=29;DPR=29,0;I16=17,12,0,0,1076,40740,0,0,1647,96123,0,0,526,11680,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255:13:0:0:8,5,0,0:13,0 0,15,149:5:0:0:3,2,0,0:5,0 0,33,255:11:0:0:6,5,0,0:11,0 17 403 . T <*> 0 . DP=29;DPR=29,0;I16=17,12,0,0,1085,40985,0,0,1647,96123,0,0,526,11654,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255:13:0:0:8,5,0,0:13,0 0,15,148:5:0:0:3,2,0,0:5,0 0,33,255:11:0:0:6,5,0,0:11,0 17 404 . G <*> 0 . DP=29;DPR=29,0;I16=17,12,0,0,1074,40524,0,0,1647,96123,0,0,525,11609,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255:13:0:0:8,5,0,0:13,0 0,15,131:5:0:0:3,2,0,0:5,0 0,33,255:11:0:0:6,5,0,0:11,0 @@ -338,7 +337,7 @@ 17 409 . T <*> 0 . DP=29;DPR=29,0;I16=17,12,0,0,1100,42734,0,0,1678,98882,0,0,525,11503,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,42,255:14:0:0:8,6,0,0:14,0 0,12,131:4:0:0:2,2,0,0:4,0 0,33,255:11:0:0:7,4,0,0:11,0 17 410 . T <*> 0 . DP=29;DPR=29,0;I16=17,12,0,0,1035,38325,0,0,1678,98882,0,0,524,11432,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,42,255:14:0:0:8,6,0,0:14,0 0,12,125:4:0:0:2,2,0,0:4,0 0,33,255:11:0:0:7,4,0,0:11,0 17 411 . T <*> 0 . DP=29;DPR=29,0;I16=17,12,0,0,1022,37928,0,0,1678,98882,0,0,522,11342,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,42,255:14:0:0:8,6,0,0:14,0 0,12,111:4:0:0:2,2,0,0:4,0 0,33,255:11:0:0:7,4,0,0:11,0 -17 412 . C T,<*> 0 . DP=30;DPR=29,1,0;I16=17,12,1,0,1094,42458,14,196,1678,98882,60,3600,495,10659,25,625;QS=2.97455,0.0254545,0;SGB=-0.556633;RPBZ=-0.40473;MQBZ=0.267261;MQSBZ=-0.293785;BQBZ=-1.6942;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,255,42,255,255:15:1:0:8,6,1,0:14,1,0 0,12,124,12,124,124:4:0:0:2,2,0,0:4,0,0 0,33,255,33,255,255:11:0:0:7,4,0,0:11,0,0 +17 412 . C T,<*> 0 . DP=30;DPR=29,1,0;I16=17,12,1,0,1094,42458,14,196,1678,98882,60,3600,495,10659,25,625;QS=2.97455,0.0254545,0;SGB=-0.556633;RPBZ=-0.40473;MQBZ=0.267261;MQSBZ=-0.293785;BQBZ=-1.6942;SCBZ=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,30,255,42,255,255:15:1:0:8,6,1,0:14,1,0 0,12,124,12,124,124:4:0:0:2,2,0,0:4,0,0 0,33,255,33,255,255:11:0:0:7,4,0,0:11,0,0 17 413 . A <*> 0 . DP=31;DPR=31,0;I16=18,13,0,0,1189,45985,0,0,1798,106082,0,0,520,11258,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:9,8,0,0:17,0 0,9,102:3:0:0:2,1,0,0:3,0 0,33,255:11:0:0:7,4,0,0:11,0 17 414 . T <*> 0 . DP=30;DPR=30,0;I16=18,12,0,0,1151,44355,0,0,1738,102482,0,0,523,11265,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:9,7,0,0:16,0 0,9,109:3:0:0:2,1,0,0:3,0 0,33,255:11:0:0:7,4,0,0:11,0 17 415 . G <*> 0 . DP=30;DPR=30,0;I16=18,12,0,0,1131,43175,0,0,1738,102482,0,0,526,11306,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:9,7,0,0:16,0 0,9,110:3:0:0:2,1,0,0:3,0 0,33,255:11:0:0:7,4,0,0:11,0 @@ -363,7 +362,7 @@ 17 434 . T <*> 0 . DP=29;DPR=29,0;I16=15,14,0,0,1036,37654,0,0,1647,96123,0,0,561,12567,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:8,8,0,0:16,0 0,9,98:3:0:0:2,1,0,0:3,0 0,30,243:10:0:0:5,5,0,0:10,0 17 435 . A <*> 0 . DP=29;DPR=29,0;I16=15,14,0,0,1035,38091,0,0,1647,96123,0,0,562,12596,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:8,8,0,0:16,0 0,9,103:3:0:0:2,1,0,0:3,0 0,30,237:10:0:0:5,5,0,0:10,0 17 436 . T <*> 0 . DP=28;DPR=28,0;I16=14,14,0,0,998,36220,0,0,1587,92523,0,0,564,12654,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:8,8,0,0:16,0 0,9,110:3:0:0:2,1,0,0:3,0 0,27,223:9:0:0:4,5,0,0:9,0 -17 437 . T G,<*> 0 . DP=28;DPR=27,1,0;I16=13,14,1,0,990,36832,6,36,1558,91682,29,841,549,12435,16,256;QS=2.9781,0.0218978,0;SGB=-0.556633;RPBZ=-1.36214;MQBZ=-2.88675;MQSBZ=0.6;BQBZ=-1.67909;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255,48,255,255:16:0:0:8,8,0,0:16,0,0 0,9,109,9,109,109:3:0:0:2,1,0,0:3,0,0 0,17,200,24,203,201:9:1:0:3,5,1,0:8,1,0 +17 437 . T G,<*> 0 . DP=28;DPR=27,1,0;I16=13,14,1,0,990,36832,6,36,1558,91682,29,841,549,12435,16,256;QS=2.9781,0.0218978,0;SGB=-0.556633;RPBZ=-1.36214;MQBZ=-2.88675;MQSBZ=0.6;BQBZ=-1.67909;SCBZ=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255,48,255,255:16:0:0:8,8,0,0:16,0,0 0,9,109,9,109,109:3:0:0:2,1,0,0:3,0,0 0,17,200,24,203,201:9:1:0:3,5,1,0:8,1,0 17 438 . A <*> 0 . DP=28;DPR=28,0;I16=14,14,0,0,984,35784,0,0,1587,92523,0,0,565,12707,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:8,8,0,0:16,0 0,9,107:3:0:0:2,1,0,0:3,0 0,27,220:9:0:0:4,5,0,0:9,0 17 439 . C <*> 0 . DP=28;DPR=28,0;I16=14,14,0,0,1055,40273,0,0,1587,92523,0,0,563,12649,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:8,8,0,0:16,0 0,9,107:3:0:0:2,1,0,0:3,0 0,27,224:9:0:0:4,5,0,0:9,0 17 440 . A <*> 0 . DP=28;DPR=28,0;I16=14,14,0,0,1095,43251,0,0,1587,92523,0,0,561,12615,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:8,8,0,0:16,0 0,9,115:3:0:0:2,1,0,0:3,0 0,27,247:9:0:0:4,5,0,0:9,0 @@ -391,13 +390,13 @@ 17 462 . G <*> 0 . DP=32;DPR=31,0;I16=18,13,0,0,1169,46001,0,0,1775,103851,0,0,577,12669,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:10,7,0,0:17,0 0,12,131:4:0:0:3,1,0,0:4,0 0,30,241:10:0:0:5,5,0,0:10,0 17 463 . G <*> 0 . DP=32;DPR=31,0;I16=18,13,0,0,1095,41573,0,0,1775,103851,0,0,583,12729,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:10,7,0,0:17,0 0,12,126:4:0:0:3,1,0,0:4,0 0,30,221:10:0:0:5,5,0,0:10,0 17 464 . A <*> 0 . DP=32;DPR=31,0;I16=18,13,0,0,1100,41724,0,0,1775,103851,0,0,589,12821,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:10,7,0,0:17,0 0,12,148:4:0:0:3,1,0,0:4,0 0,30,217:10:0:0:5,5,0,0:10,0 -17 465 . C T,<*> 0 . DP=33;DPR=31,1,0;I16=19,12,0,1,1173,45601,4,16,1775,103851,60,3600,589,12909,6,36;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.67982;MQBZ=0.321288;MQSBZ=0.341466;BQBZ=-1.68493;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255,51,255,255:17:0:0:10,7,0,0:17,0,0 0,15,158,15,158,158:5:0:0:4,1,0,0:5,0,0 0,20,224,27,227,224:10:1:0:5,4,0,1:9,1,0 +17 465 . C T,<*> 0 . DP=33;DPR=31,1,0;I16=19,12,0,1,1173,45601,4,16,1775,103851,60,3600,589,12909,6,36;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.67982;MQBZ=0.321288;MQSBZ=0.341466;BQBZ=-1.68493;SCBZ=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255,51,255,255:17:0:0:10,7,0,0:17,0,0 0,15,158,15,158,158:5:0:0:4,1,0,0:5,0,0 0,20,224,27,227,224:10:1:0:5,4,0,1:9,1,0 17 466 . A <*> 0 . DP=34;DPR=33,0;I16=20,13,0,0,1268,49686,0,0,1895,111051,0,0,602,13102,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:11,7,0,0:18,0 0,15,173:5:0:0:4,1,0,0:5,0 0,30,255:10:0:0:5,5,0,0:10,0 17 467 . A <*> 0 . DP=34;DPR=33,0;I16=20,13,0,0,1246,48610,0,0,1895,111051,0,0,608,13194,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:11,7,0,0:18,0 0,15,177:5:0:0:4,1,0,0:5,0 0,30,251:10:0:0:5,5,0,0:10,0 17 468 . A <*> 0 . DP=35;DPR=34,0;I16=21,13,0,0,1253,48095,0,0,1955,114651,0,0,613,13273,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:12,7,0,0:19,0 0,15,174:5:0:0:4,1,0,0:5,0 0,30,251:10:0:0:5,5,0,0:10,0 17 469 . A <*> 0 . DP=35;DPR=34,0;I16=21,13,0,0,1260,49028,0,0,1955,114651,0,0,618,13340,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:12,7,0,0:19,0 0,15,165:5:0:0:4,1,0,0:5,0 0,30,255:10:0:0:5,5,0,0:10,0 17 470 . G <*> 0 . DP=35;DPR=34,0;I16=21,13,0,0,1265,48879,0,0,1955,114651,0,0,623,13445,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:12,7,0,0:19,0 0,15,167:5:0:0:4,1,0,0:5,0 0,30,238:10:0:0:5,5,0,0:10,0 -17 471 . T G,C,<*> 0 . DP=36;DPR=33,1,1,0;I16=21,12,0,2,1220,46380,18,162,1918,113282,97,4969,611,13281,16,256;QS=2.94529,0.0273556,0.0273556,0;VDB=0.96;SGB=0.346553;RPBZ=0.497712;MQBZ=-1.9761;MQSBZ=0.312094;BQBZ=-2.35032;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255,57,255,255,57,255,255,255:19:0:0:12,7,0,0:19,0,0,0 0,15,169,15,169,169,15,169,169,169:5:0:0:4,1,0,0:5,0,0,0 0,19,219,19,221,219,27,222,222,221:11:2:3:5,4,0,2:9,1,1,0 +17 471 . T G,C,<*> 0 . DP=36;DPR=33,1,1,0;I16=21,12,0,2,1220,46380,18,162,1918,113282,97,4969,611,13281,16,256;QS=2.94529,0.0273556,0.0273556,0;VDB=0.96;SGB=0.346553;RPBZ=0.497712;MQBZ=-1.9761;MQSBZ=0.312094;BQBZ=-2.35032;SCBZ=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255,57,255,255,57,255,255,255:19:0:0:12,7,0,0:19,0,0,0 0,15,169,15,169,169,15,169,169,169:5:0:0:4,1,0,0:5,0,0,0 0,19,219,19,221,219,27,222,222,221:11:2:3:5,4,0,2:9,1,1,0 17 472 . T <*> 0 . DP=35;DPR=34,0;I16=21,13,0,0,1234,46640,0,0,1955,114651,0,0,633,13665,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:12,7,0,0:19,0 0,15,172:5:0:0:4,1,0,0:5,0 0,30,241:10:0:0:5,5,0,0:10,0 17 473 . G <*> 0 . DP=35;DPR=34,0;I16=21,13,0,0,1303,51953,0,0,1955,114651,0,0,638,13780,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:12,7,0,0:19,0 0,15,159:5:0:0:4,1,0,0:5,0 0,30,250:10:0:0:5,5,0,0:10,0 17 474 . G <*> 0 . DP=36;DPR=35,0;I16=22,13,0,0,1279,49235,0,0,2015,118251,0,0,642,13884,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:12,7,0,0:19,0 0,15,146:5:0:0:4,1,0,0:5,0 0,33,255:11:0:0:6,5,0,0:11,0 @@ -414,7 +413,7 @@ 17 485 . G <*> 0 . DP=35;DPR=35,0;I16=23,12,0,0,1329,51411,0,0,2015,118251,0,0,669,14931,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:12,6,0,0:18,0 0,18,160:6:0:0:5,1,0,0:6,0 0,33,255:11:0:0:6,5,0,0:11,0 17 486 . A <*> 0 . DP=34;DPR=34,0;I16=22,12,0,0,1313,51667,0,0,1955,114651,0,0,671,14989,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:11,6,0,0:17,0 0,18,173:6:0:0:5,1,0,0:6,0 0,33,255:11:0:0:6,5,0,0:11,0 17 487 . G <*> 0 . DP=34;DPR=34,0;I16=22,12,0,0,1300,50304,0,0,1955,114651,0,0,672,15030,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:11,6,0,0:17,0 0,18,169:6:0:0:5,1,0,0:6,0 0,33,255:11:0:0:6,5,0,0:11,0 -17 488 . A G,<*> 0 . DP=35;DPR=34,1,0;I16=22,12,1,0,1278,48412,4,16,1986,117410,29,841,646,14380,25,625;QS=2.98947,0.0105263,0;SGB=-0.556633;RPBZ=0.594463;MQBZ=-3.36505;MQSBZ=0.10737;BQBZ=-1.69552;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255,54,255,255:18:0:0:12,6,0,0:18,0,0 0,18,177,18,177,177:6:0:0:5,1,0,0:6,0,0 0,23,255,30,255,255:11:1:0:5,5,1,0:10,1,0 +17 488 . A G,<*> 0 . DP=35;DPR=34,1,0;I16=22,12,1,0,1278,48412,4,16,1986,117410,29,841,646,14380,25,625;QS=2.98947,0.0105263,0;SGB=-0.556633;RPBZ=0.594463;MQBZ=-3.36505;MQSBZ=0.10737;BQBZ=-1.69552;SCBZ=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255,54,255,255:18:0:0:12,6,0,0:18,0,0 0,18,177,18,177,177:6:0:0:5,1,0,0:6,0,0 0,23,255,30,255,255:11:1:0:5,5,1,0:10,1,0 17 489 . A <*> 0 . DP=35;DPR=35,0;I16=23,12,0,0,1264,46916,0,0,2015,118251,0,0,671,15015,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:12,6,0,0:18,0 0,18,175:6:0:0:5,1,0,0:6,0 0,33,255:11:0:0:6,5,0,0:11,0 17 490 . A <*> 0 . DP=36;DPR=36,0;I16=24,12,0,0,1332,50280,0,0,2075,121851,0,0,671,15061,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:12,6,0,0:18,0 0,21,188:7:0:0:6,1,0,0:7,0 0,33,255:11:0:0:6,5,0,0:11,0 17 491 . T <*> 0 . DP=36;DPR=36,0;I16=24,12,0,0,1284,46802,0,0,2075,121851,0,0,671,15093,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:12,6,0,0:18,0 0,21,178:7:0:0:6,1,0,0:7,0 0,33,255:11:0:0:6,5,0,0:11,0 @@ -438,9 +437,9 @@ 17 509 . C <*> 0 . DP=34;DPR=34,0;I16=24,10,0,0,1272,48272,0,0,1986,117410,0,0,640,14430,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:13,5,0,0:18,0 0,21,186:7:0:0:6,1,0,0:7,0 0,27,241:9:0:0:5,4,0,0:9,0 17 510 . A <*> 0 . DP=34;DPR=34,0;I16=23,11,0,0,1211,44827,0,0,1986,117410,0,0,638,14398,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:13,6,0,0:19,0 0,21,187:7:0:0:6,1,0,0:7,0 0,24,221:8:0:0:4,4,0,0:8,0 17 511 . A <*> 0 . DP=34;DPR=34,0;I16=23,11,0,0,1238,46516,0,0,1986,117410,0,0,637,14395,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:13,6,0,0:19,0 0,21,195:7:0:0:6,1,0,0:7,0 0,24,233:8:0:0:4,4,0,0:8,0 -17 512 . A C,<*> 0 . DP=33;DPR=32,1,0;I16=22,10,0,1,1133,41513,13,169,1866,110210,60,3600,628,14340,9,81;QS=2.97766,0.0223368,0;SGB=-0.556633;RPBZ=-1.47079;MQBZ=0.253876;MQSBZ=-0.461593;BQBZ=-1.68442;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255,51,255,255:18:1:0:12,5,0,1:17,1,0 0,21,183,21,183,183:7:0:0:6,1,0,0:7,0,0 0,24,231,24,231,231:8:0:0:4,4,0,0:8,0,0 -17 513 . A T,<*> 0 . DP=32;DPR=31,1,0;I16=21,10,1,0,1125,42283,12,144,1806,106610,60,3600,623,14249,15,225;QS=2.97966,0.020339,0;SGB=-0.556633;RPBZ=-1.24609;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.57376;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,37,255,48,255,255:17:1:0:11,5,1,0:16,1,0 0,21,177,21,177,177:7:0:0:6,1,0,0:7,0,0 0,24,233,24,233,233:8:0:0:4,4,0,0:8,0,0 -17 514 . A T,<*> 0 . DP=32;DPR=31,1,0;I16=22,9,0,1,1086,40204,16,256,1806,106610,60,3600,627,14381,11,121;QS=2.97127,0.0287253,0;SGB=-0.556633;RPBZ=-1.4628;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.46657;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,34,255,48,255,255:17:1:0:12,4,0,1:16,1,0 0,21,172,21,172,172:7:0:0:6,1,0,0:7,0,0 0,24,235,24,235,235:8:0:0:4,4,0,0:8,0,0 +17 512 . A C,<*> 0 . DP=33;DPR=32,1,0;I16=22,10,0,1,1133,41513,13,169,1866,110210,60,3600,628,14340,9,81;QS=2.97766,0.0223368,0;SGB=-0.556633;RPBZ=-1.47079;MQBZ=0.253876;MQSBZ=-0.461593;BQBZ=-1.68442;SCBZ=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,39,255,51,255,255:18:1:0:12,5,0,1:17,1,0 0,21,183,21,183,183:7:0:0:6,1,0,0:7,0,0 0,24,231,24,231,231:8:0:0:4,4,0,0:8,0,0 +17 513 . A T,<*> 0 . DP=32;DPR=31,1,0;I16=21,10,1,0,1125,42283,12,144,1806,106610,60,3600,623,14249,15,225;QS=2.97966,0.020339,0;SGB=-0.556633;RPBZ=-1.24609;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.57376;SCBZ=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,37,255,48,255,255:17:1:0:11,5,1,0:16,1,0 0,21,177,21,177,177:7:0:0:6,1,0,0:7,0,0 0,24,233,24,233,233:8:0:0:4,4,0,0:8,0,0 +17 514 . A T,<*> 0 . DP=32;DPR=31,1,0;I16=22,9,0,1,1086,40204,16,256,1806,106610,60,3600,627,14381,11,121;QS=2.97127,0.0287253,0;SGB=-0.556633;RPBZ=-1.4628;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.46657;SCBZ=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,34,255,48,255,255:17:1:0:12,4,0,1:16,1,0 0,21,172,21,172,172:7:0:0:6,1,0,0:7,0,0 0,24,235,24,235,235:8:0:0:4,4,0,0:8,0,0 17 515 . C <*> 0 . DP=32;DPR=32,0;I16=22,10,0,0,1050,37704,0,0,1866,110210,0,0,638,14554,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:12,5,0,0:17,0 0,21,169:7:0:0:6,1,0,0:7,0 0,24,211:8:0:0:4,4,0,0:8,0 17 516 . C <*> 0 . DP=32;DPR=32,0;I16=22,10,0,0,1109,40651,0,0,1866,110210,0,0,637,14579,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:12,5,0,0:17,0 0,21,187:7:0:0:6,1,0,0:7,0 0,24,215:8:0:0:4,4,0,0:8,0 17 517 . T <*> 0 . DP=33;DPR=33,0;I16=23,10,0,0,1269,49995,0,0,1926,113810,0,0,636,14626,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:13,5,0,0:18,0 0,21,201:7:0:0:6,1,0,0:7,0 0,24,242:8:0:0:4,4,0,0:8,0 @@ -449,7 +448,7 @@ 17 520 . T <*> 0 . DP=36;DPR=36,0;I16=25,11,0,0,1243,45051,0,0,2106,124610,0,0,638,14818,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,63,255:21:0:0:15,6,0,0:21,0 0,21,180:7:0:0:6,1,0,0:7,0 0,24,223:8:0:0:4,4,0,0:8,0 17 521 . C <*> 0 . DP=34;DPR=34,0;I16=25,9,0,0,1281,49527,0,0,1986,117410,0,0,641,14875,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,60,255:20:0:0:15,5,0,0:20,0 0,21,191:7:0:0:6,1,0,0:7,0 0,21,204:7:0:0:4,3,0,0:7,0 17 522 . A <*> 0 . DP=32;DPR=32,0;I16=24,8,0,0,1158,43228,0,0,1897,112969,0,0,646,14960,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,60,255:20:0:0:15,5,0,0:20,0 0,21,185:7:0:0:6,1,0,0:7,0 0,15,170:5:0:0:3,2,0,0:5,0 -17 523 . T G,<*> 0 . DP=32;DPR=31,1,0;I16=23,8,1,0,1184,45708,15,225,1837,109369,60,3600,626,14446,25,625;QS=2.9794,0.0206044,0;SGB=-0.556633;RPBZ=1.13742;MQBZ=0.179605;MQSBZ=-1.73205;BQBZ=-1.68805;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,44,255,57,255,255:20:1:0:14,5,1,0:19,1,0 0,21,191,21,191,191:7:0:0:6,1,0,0:7,0,0 0,15,166,15,166,166:5:0:0:3,2,0,0:5,0,0 +17 523 . T G,<*> 0 . DP=32;DPR=31,1,0;I16=23,8,1,0,1184,45708,15,225,1837,109369,60,3600,626,14446,25,625;QS=2.9794,0.0206044,0;SGB=-0.556633;RPBZ=1.13742;MQBZ=0.179605;MQSBZ=-1.73205;BQBZ=-1.68805;SCBZ=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,44,255,57,255,255:20:1:0:14,5,1,0:19,1,0 0,21,191,21,191,191:7:0:0:6,1,0,0:7,0,0 0,15,166,15,166,166:5:0:0:3,2,0,0:5,0,0 17 524 . T <*> 0 . DP=32;DPR=32,0;I16=24,8,0,0,1096,39618,0,0,1897,112969,0,0,654,15108,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,60,255:20:0:0:15,5,0,0:20,0 0,21,194:7:0:0:6,1,0,0:7,0 0,15,150:5:0:0:3,2,0,0:5,0 17 525 . G <*> 0 . DP=32;DPR=32,0;I16=24,8,0,0,1188,45718,0,0,1897,112969,0,0,656,15120,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,60,255:20:0:0:15,5,0,0:20,0 0,21,188:7:0:0:6,1,0,0:7,0 0,15,133:5:0:0:3,2,0,0:5,0 17 526 . C <*> 0 . DP=32;DPR=32,0;I16=24,8,0,0,1154,44014,0,0,1897,112969,0,0,658,15156,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,60,255:20:0:0:15,5,0,0:20,0 0,21,185:7:0:0:6,1,0,0:7,0 0,15,137:5:0:0:3,2,0,0:5,0 @@ -461,7 +460,7 @@ 17 532 . T <*> 0 . DP=32;DPR=32,0;I16=25,7,0,0,1161,43607,0,0,1897,112969,0,0,649,14477,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:15,4,0,0:19,0 0,21,181:7:0:0:6,1,0,0:7,0 0,18,192:6:0:0:4,2,0,0:6,0 17 533 . C <*> 0 . DP=32;DPR=32,0;I16=25,7,0,0,1154,44084,0,0,1897,112969,0,0,644,14274,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:15,4,0,0:19,0 0,21,178:7:0:0:6,1,0,0:7,0 0,18,180:6:0:0:4,2,0,0:6,0 17 534 . T <*> 0 . DP=31;DPR=31,0;I16=24,7,0,0,1222,49526,0,0,1837,109369,0,0,640,14104,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:14,4,0,0:18,0 0,21,205:7:0:0:6,1,0,0:7,0 0,18,205:6:0:0:4,2,0,0:6,0 -17 535 . A G,<*> 0 . DP=31;DPR=30,1,0;I16=24,6,0,1,1080,39870,8,64,1777,105769,60,3600,611,13341,25,625;QS=2.98623,0.0137694,0;SGB=-0.556633;RPBZ=-0.894788;MQBZ=0.182574;MQSBZ=-1.85164;BQBZ=-1.6854;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,41,255,51,255,255:18:1:0:14,3,0,1:17,1,0 0,21,194,21,194,194:7:0:0:6,1,0,0:7,0,0 0,18,189,18,189,189:6:0:0:4,2,0,0:6,0,0 +17 535 . A G,<*> 0 . DP=31;DPR=30,1,0;I16=24,6,0,1,1080,39870,8,64,1777,105769,60,3600,611,13341,25,625;QS=2.98623,0.0137694,0;SGB=-0.556633;RPBZ=-0.894788;MQBZ=0.182574;MQSBZ=-1.85164;BQBZ=-1.6854;SCBZ=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,41,255,51,255,255:18:1:0:14,3,0,1:17,1,0 0,21,194,21,194,194:7:0:0:6,1,0,0:7,0,0 0,18,189,18,189,189:6:0:0:4,2,0,0:6,0,0 17 536 . C <*> 0 . DP=31;DPR=31,0;I16=24,7,0,0,1095,40551,0,0,1837,109369,0,0,631,13809,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:14,4,0,0:18,0 0,21,184:7:0:0:6,1,0,0:7,0 0,18,157:6:0:0:4,2,0,0:6,0 17 537 . C <*> 0 . DP=31;DPR=31,0;I16=24,7,0,0,1049,38677,0,0,1837,109369,0,0,626,13682,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:14,4,0,0:18,0 0,21,172:7:0:0:6,1,0,0:7,0 0,18,183:6:0:0:4,2,0,0:6,0 17 538 . A <*> 0 . DP=31;DPR=31,0;I16=24,7,0,0,1138,42478,0,0,1837,109369,0,0,620,13536,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:14,4,0,0:18,0 0,21,189:7:0:0:6,1,0,0:7,0 0,18,181:6:0:0:4,2,0,0:6,0 @@ -474,8 +473,8 @@ 17 545 . A <*> 0 . DP=33;DPR=33,0;I16=25,8,0,0,1197,44795,0,0,1926,113810,0,0,587,12951,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:14,5,0,0:19,0 0,24,196:8:0:0:7,1,0,0:8,0 0,18,184:6:0:0:4,2,0,0:6,0 17 546 . A <*> 0 . DP=32;DPR=32,0;I16=24,8,0,0,1136,41758,0,0,1866,110210,0,0,580,12802,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:14,5,0,0:19,0 0,21,166:7:0:0:6,1,0,0:7,0 0,18,193:6:0:0:4,2,0,0:6,0 17 547 . A <*> 0 . DP=32;DPR=32,0;I16=24,8,0,0,1159,43539,0,0,1866,110210,0,0,572,12634,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,57,255:19:0:0:14,5,0,0:19,0 0,21,180:7:0:0:6,1,0,0:7,0 0,18,195:6:0:0:4,2,0,0:6,0 -17 548 . A C,<*> 0 . DP=33;DPR=32,1,0;I16=23,9,1,0,1153,42673,9,81,1866,110210,60,3600,561,12489,3,9;QS=2.98607,0.0139319,0;SGB=-0.556633;RPBZ=1.57584;MQBZ=0.253876;MQSBZ=-2.34521;BQBZ=-1.68939;SCBZ=3.80814;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,44,255,54,255,255:19:1:0:13,5,1,0:18,1,0 0,21,181,21,181,181:7:0:0:6,1,0,0:7,0,0 0,21,211,21,211,211:7:0:0:4,3,0,0:7,0,0 -17 549 . T G,<*> 0 . DP=32;DPR=31,1,0;I16=23,8,0,1,1135,42143,20,400,1806,106610,60,3600,532,11720,25,625;QS=2.96918,0.0308166,0;SGB=-0.556633;RPBZ=-0.487556;MQBZ=0.258065;MQSBZ=-2.29695;BQBZ=-1.68602;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,34,255,51,255,255:18:1:0:13,4,0,1:17,1,0 0,21,168,21,168,168:7:0:0:6,1,0,0:7,0,0 0,21,208,21,208,208:7:0:0:4,3,0,0:7,0,0 +17 548 . A C,<*> 0 . DP=33;DPR=32,1,0;I16=23,9,1,0,1153,42673,9,81,1866,110210,60,3600,561,12489,3,9;QS=2.98607,0.0139319,0;SGB=-0.556633;RPBZ=1.57584;MQBZ=0.253876;MQSBZ=-2.34521;BQBZ=-1.68939;SCBZ=3.80814;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,44,255,54,255,255:19:1:0:13,5,1,0:18,1,0 0,21,181,21,181,181:7:0:0:6,1,0,0:7,0,0 0,21,211,21,211,211:7:0:0:4,3,0,0:7,0,0 +17 549 . T G,<*> 0 . DP=32;DPR=31,1,0;I16=23,8,0,1,1135,42143,20,400,1806,106610,60,3600,532,11720,25,625;QS=2.96918,0.0308166,0;SGB=-0.556633;RPBZ=-0.487556;MQBZ=0.258065;MQSBZ=-2.29695;BQBZ=-1.68602;SCBZ=-0.258065;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,34,255,51,255,255:18:1:0:13,4,0,1:17,1,0 0,21,168,21,168,168:7:0:0:6,1,0,0:7,0,0 0,21,208,21,208,208:7:0:0:4,3,0,0:7,0,0 17 550 . T <*> 0 . DP=32;DPR=32,0;I16=23,9,0,0,1056,37314,0,0,1866,110210,0,0,549,12177,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:13,5,0,0:18,0 0,21,150:7:0:0:6,1,0,0:7,0 0,21,220:7:0:0:4,3,0,0:7,0 17 551 . G <*> 0 . DP=31;DPR=31,0;I16=22,9,0,0,1121,41639,0,0,1806,106610,0,0,541,12045,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:12,5,0,0:17,0 0,21,172:7:0:0:6,1,0,0:7,0 0,21,208:7:0:0:4,3,0,0:7,0 17 552 . C <*> 0 . DP=30;DPR=30,0;I16=21,9,0,0,1093,41365,0,0,1746,103010,0,0,535,11947,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:11,5,0,0:16,0 0,21,167:7:0:0:6,1,0,0:7,0 0,21,208:7:0:0:4,3,0,0:7,0 @@ -485,14 +484,14 @@ 17 556 . C <*> 0 . DP=29;DPR=29,0;I16=20,9,0,0,1055,39195,0,0,1709,101641,0,0,509,11219,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:11,6,0,0:17,0 0,18,158:6:0:0:5,1,0,0:6,0 0,18,186:6:0:0:4,2,0,0:6,0 17 557 . A <*> 0 . DP=27;DPR=27,0;I16=18,9,0,0,987,36749,0,0,1589,94441,0,0,506,11074,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,45,255:15:0:0:9,6,0,0:15,0 0,18,157:6:0:0:5,1,0,0:6,0 0,18,186:6:0:0:4,2,0,0:6,0 17 558 . A <*> 0 . DP=27;DPR=27,0;I16=18,9,0,0,956,35872,0,0,1589,94441,0,0,502,10906,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,45,255:15:0:0:9,6,0,0:15,0 0,18,153:6:0:0:5,1,0,0:6,0 0,18,177:6:0:0:4,2,0,0:6,0 -17 559 . C A,<*> 0 . DP=27;DPR=26,1,0;I16=18,8,0,1,915,33775,14,196,1560,93600,29,841,473,10141,25,625;QS=2.92708,0.0729167,0;SGB=-0.556633;RPBZ=-1.02726;MQBZ=-5.09902;MQSBZ=-1.41421;BQBZ=-1.54776;SCBZ=5.09902;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,45,255,45,255,255:15:0:0:9,6,0,0:15,0,0 0,4,116,15,119,123:6:1:0:5,0,0,1:5,1,0 0,18,169,18,169,169:6:0:0:4,2,0,0:6,0,0 +17 559 . C A,<*> 0 . DP=27;DPR=26,1,0;I16=18,8,0,1,915,33775,14,196,1560,93600,29,841,473,10141,25,625;QS=2.92708,0.0729167,0;SGB=-0.556633;RPBZ=-1.02726;MQBZ=-5.09902;MQSBZ=-1.41421;BQBZ=-1.54776;SCBZ=5.09902;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,45,255,45,255,255:15:0:0:9,6,0,0:15,0,0 0,4,116,15,119,123:6:1:0:5,0,0,1:5,1,0 0,18,169,18,169,169:6:0:0:4,2,0,0:6,0,0 17 560 . C <*> 0 . DP=28;DPR=28,0;I16=19,9,0,0,992,36552,0,0,1649,98041,0,0,494,10654,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,45,255:15:0:0:9,6,0,0:15,0 0,18,160:6:0:0:5,1,0,0:6,0 0,21,181:7:0:0:5,2,0,0:7,0 17 561 . A <*> 0 . DP=28;DPR=28,0;I16=19,9,0,0,973,35555,0,0,1649,98041,0,0,491,10571,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,45,255:15:0:0:9,6,0,0:15,0 0,18,158:6:0:0:5,1,0,0:6,0 0,21,194:7:0:0:5,2,0,0:7,0 17 562 . C <*> 0 . DP=28;DPR=28,0;I16=19,9,0,0,1014,38392,0,0,1649,98041,0,0,488,10518,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,45,255:15:0:0:9,6,0,0:15,0 0,18,153:6:0:0:5,1,0,0:6,0 0,21,187:7:0:0:5,2,0,0:7,0 17 563 . A <*> 0 . DP=27;DPR=27,0;I16=18,9,0,0,903,32513,0,0,1589,94441,0,0,485,10445,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,45,255:15:0:0:9,6,0,0:15,0 0,15,149:5:0:0:4,1,0,0:5,0 0,21,179:7:0:0:5,2,0,0:7,0 17 564 . C <*> 0 . DP=27;DPR=27,0;I16=18,9,0,0,859,28747,0,0,1589,94441,0,0,482,10402,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,45,255:15:0:0:9,6,0,0:15,0 0,15,121:5:0:0:4,1,0,0:5,0 0,21,182:7:0:0:5,2,0,0:7,0 17 565 . G <*> 0 . DP=30;DPR=30,0;I16=18,12,0,0,842,27104,0,0,1769,105241,0,0,479,10389,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:9,8,0,0:17,0 0,18,100:6:0:0:4,2,0,0:6,0 0,21,154:7:0:0:5,2,0,0:7,0 -17 566 . C A,<*> 0 . DP=29;DPR=28,1,0;I16=16,12,1,0,920,33998,9,81,1649,98041,60,3600,454,9734,25,625;QS=2.98321,0.016791,0;SGB=-0.556633;RPBZ=0.239193;MQBZ=0.188982;MQSBZ=-1.19024;BQBZ=-1.43942;SCBZ=-0.188982;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,38,255,48,255,255:17:1:0:8,8,1,0:16,1,0 0,15,155,15,155,155:5:0:0:3,2,0,0:5,0,0 0,21,170,21,170,170:7:0:0:5,2,0,0:7,0,0 +17 566 . C A,<*> 0 . DP=29;DPR=28,1,0;I16=16,12,1,0,920,33998,9,81,1649,98041,60,3600,454,9734,25,625;QS=2.98321,0.016791,0;SGB=-0.556633;RPBZ=0.239193;MQBZ=0.188982;MQSBZ=-1.19024;BQBZ=-1.43942;SCBZ=-0.188982;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,38,255,48,255,255:17:1:0:8,8,1,0:16,1,0 0,15,155,15,155,155:5:0:0:3,2,0,0:5,0,0 0,21,170,21,170,170:7:0:0:5,2,0,0:7,0,0 17 567 . C <*> 0 . DP=30;DPR=30,0;I16=17,13,0,0,956,34312,0,0,1769,105241,0,0,496,10638,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:9,8,0,0:17,0 0,18,156:6:0:0:3,3,0,0:6,0 0,21,194:7:0:0:5,2,0,0:7,0 17 568 . C <*> 0 . DP=29;DPR=29,0;I16=16,13,0,0,1060,40304,0,0,1709,101641,0,0,497,10663,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:8,8,0,0:16,0 0,18,179:6:0:0:3,3,0,0:6,0 0,21,193:7:0:0:5,2,0,0:7,0 17 569 . T <*> 0 . DP=30;DPR=29,0;I16=16,13,0,0,1061,41321,0,0,1709,101641,0,0,497,10671,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:8,8,0,0:16,0 0,18,190:6:0:0:3,3,0,0:6,0 0,21,213:7:0:0:5,2,0,0:7,0 @@ -500,15 +499,15 @@ 17 571 . C <*> 0 . DP=31;DPR=30,0;I16=17,13,0,0,1069,40739,0,0,1769,105241,0,0,497,10783,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:9,8,0,0:17,0 0,18,159:6:0:0:3,3,0,0:6,0 0,21,193:7:0:0:5,2,0,0:7,0 17 572 . A <*> 0 . DP=31;DPR=30,0;I16=18,12,0,0,1092,41268,0,0,1769,105241,0,0,499,10887,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:9,8,0,0:17,0 0,21,204:7:0:0:4,3,0,0:7,0 0,18,175:6:0:0:5,1,0,0:6,0 17 573 . A <*> 0 . DP=31;DPR=30,0;I16=18,12,0,0,1060,38698,0,0,1769,105241,0,0,501,10975,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:9,8,0,0:17,0 0,21,201:7:0:0:4,3,0,0:7,0 0,18,178:6:0:0:5,1,0,0:6,0 -17 574 . C A,<*> 0 . DP=31;DPR=29,1,0;I16=18,11,0,1,1088,41328,15,225,1740,104400,29,841,478,10422,25,625;QS=2.94071,0.0592885,0;SGB=-0.556633;RPBZ=-0.173514;MQBZ=-5.38516;MQSBZ=-1.22474;BQBZ=-1.68578;SCBZ=3.60588;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255,48,255,255:16:0:0:8,8,0,0:16,0,0 0,9,170,21,173,177:8:1:0:5,2,0,1:7,1,0 0,18,173,18,173,173:6:0:0:5,1,0,0:6,0,0 -17 575 . T C,<*> 0 . DP=30;DPR=28,1,0;I16=17,11,0,1,1048,41548,9,81,1680,100800,29,841,480,10426,25,625;QS=2.96786,0.0321429,0;SGB=-0.556633;RPBZ=-0.119685;MQBZ=-5.2915;MQSBZ=-1.19024;BQBZ=-1.68121;SCBZ=3.53589;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255,48,255,255:16:0:0:8,8,0,0:16,0,0 0,13,200,21,203,202:8:1:0:5,2,0,1:7,1,0 0,15,163,15,163,163:5:0:0:4,1,0,0:5,0,0 +17 574 . C A,<*> 0 . DP=31;DPR=29,1,0;I16=18,11,0,1,1088,41328,15,225,1740,104400,29,841,478,10422,25,625;QS=2.94071,0.0592885,0;SGB=-0.556633;RPBZ=-0.173514;MQBZ=-5.38516;MQSBZ=-1.22474;BQBZ=-1.68578;SCBZ=3.60588;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255,48,255,255:16:0:0:8,8,0,0:16,0,0 0,9,170,21,173,177:8:1:0:5,2,0,1:7,1,0 0,18,173,18,173,173:6:0:0:5,1,0,0:6,0,0 +17 575 . T C,<*> 0 . DP=30;DPR=28,1,0;I16=17,11,0,1,1048,41548,9,81,1680,100800,29,841,480,10426,25,625;QS=2.96786,0.0321429,0;SGB=-0.556633;RPBZ=-0.119685;MQBZ=-5.2915;MQSBZ=-1.19024;BQBZ=-1.68121;SCBZ=3.53589;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255,48,255,255:16:0:0:8,8,0,0:16,0,0 0,13,200,21,203,202:8:1:0:5,2,0,1:7,1,0 0,15,163,15,163,163:5:0:0:4,1,0,0:5,0,0 17 576 . G <*> 0 . DP=30;DPR=29,0;I16=17,12,0,0,1043,39581,0,0,1709,101641,0,0,507,11087,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:8,8,0,0:16,0 0,24,208:8:0:0:5,3,0,0:8,0 0,15,151:5:0:0:4,1,0,0:5,0 17 577 . G <*> 0 . DP=30;DPR=29,0;I16=17,12,0,0,997,37255,0,0,1709,101641,0,0,509,11155,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:8,8,0,0:16,0 0,24,204:8:0:0:5,3,0,0:8,0 0,15,146:5:0:0:4,1,0,0:5,0 17 578 . G <*> 0 . DP=29;DPR=29,0;I16=16,13,0,0,975,34803,0,0,1709,101641,0,0,520,11286,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,48,255:16:0:0:7,9,0,0:16,0 0,24,198:8:0:0:5,3,0,0:8,0 0,15,151:5:0:0:4,1,0,0:5,0 17 579 . G <*> 0 . DP=30;DPR=30,0;I16=16,14,0,0,1038,38820,0,0,1769,105241,0,0,523,11335,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:8,9,0,0:17,0 0,24,224:8:0:0:4,4,0,0:8,0 0,15,144:5:0:0:4,1,0,0:5,0 -17 580 . A C,<*> 0 . DP=30;DPR=29,1,0;I16=15,14,1,0,1060,39178,16,256,1709,101641,60,3600,510,11078,17,289;QS=2.97338,0.0266223,0;SGB=-0.556633;RPBZ=1.32953;MQBZ=0.185695;MQSBZ=-1.06904;BQBZ=-1.69093;SCBZ=-0.267102;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,34,255,48,255,255:17:1:0:7,9,1,0:16,1,0 0,24,221,24,221,221:8:0:0:4,4,0,0:8,0,0 0,15,155,15,155,155:5:0:0:4,1,0,0:5,0,0 +17 580 . A C,<*> 0 . DP=30;DPR=29,1,0;I16=15,14,1,0,1060,39178,16,256,1709,101641,60,3600,510,11078,17,289;QS=2.97338,0.0266223,0;SGB=-0.556633;RPBZ=1.32953;MQBZ=0.185695;MQSBZ=-1.06904;BQBZ=-1.69093;SCBZ=-0.267102;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,34,255,48,255,255:17:1:0:7,9,1,0:16,1,0 0,24,221,24,221,221:8:0:0:4,4,0,0:8,0,0 0,15,155,15,155,155:5:0:0:4,1,0,0:5,0,0 17 581 . A <*> 0 . DP=31;DPR=31,0;I16=16,15,0,0,1083,39215,0,0,1829,108841,0,0,530,11384,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:8,10,0,0:18,0 0,24,223:8:0:0:4,4,0,0:8,0 0,15,153:5:0:0:4,1,0,0:5,0 -17 582 . C G,<*> 0 . DP=31;DPR=30,1,0;I16=15,15,1,0,1080,39870,8,64,1769,105241,60,3600,519,11211,15,225;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.34259;MQBZ=0.182574;MQSBZ=-1.0328;BQBZ=-1.68266;SCBZ=-0.262467;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,41,255,51,255,255:18:1:0:7,10,1,0:17,1,0 0,24,207,24,207,207:8:0:0:4,4,0,0:8,0,0 0,15,151,15,151,151:5:0:0:4,1,0,0:5,0,0 +17 582 . C G,<*> 0 . DP=31;DPR=30,1,0;I16=15,15,1,0,1080,39870,8,64,1769,105241,60,3600,519,11211,15,225;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.34259;MQBZ=0.182574;MQSBZ=-1.0328;BQBZ=-1.68266;SCBZ=-0.262467;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,41,255,51,255,255:18:1:0:7,10,1,0:17,1,0 0,24,207,24,207,207:8:0:0:4,4,0,0:8,0,0 0,15,151,15,151,151:5:0:0:4,1,0,0:5,0,0 17 583 . T <*> 0 . DP=30;DPR=30,0;I16=16,14,0,0,1135,43913,0,0,1769,105241,0,0,539,11523,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:8,9,0,0:17,0 0,24,238:8:0:0:4,4,0,0:8,0 0,15,163:5:0:0:4,1,0,0:5,0 17 584 . C <*> 0 . DP=31;DPR=31,0;I16=17,14,0,0,1069,39521,0,0,1798,106082,0,0,544,11644,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:9,9,0,0:18,0 0,24,209:8:0:0:4,4,0,0:8,0 0,15,157:5:0:0:4,1,0,0:5,0 17 585 . A <*> 0 . DP=31;DPR=31,0;I16=17,14,0,0,1096,39866,0,0,1798,106082,0,0,549,11751,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:9,9,0,0:18,0 0,24,211:8:0:0:4,4,0,0:8,0 0,15,157:5:0:0:4,1,0,0:5,0 @@ -519,10 +518,10 @@ 17 590 . C <*> 0 . DP=32;DPR=32,0;I16=17,15,0,0,1103,41355,0,0,1858,109682,0,0,574,12576,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:9,9,0,0:18,0 0,24,194:8:0:0:4,4,0,0:8,0 0,18,175:6:0:0:4,2,0,0:6,0 17 591 . A <*> 0 . DP=31;DPR=31,0;I16=16,15,0,0,1164,44088,0,0,1798,106082,0,0,579,12695,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:9,9,0,0:18,0 0,21,209:7:0:0:3,4,0,0:7,0 0,18,188:6:0:0:4,2,0,0:6,0 17 592 . A <*> 0 . DP=31;DPR=31,0;I16=16,15,0,0,1121,42193,0,0,1798,106082,0,0,583,12795,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:9,9,0,0:18,0 0,21,215:7:0:0:3,4,0,0:7,0 0,18,182:6:0:0:4,2,0,0:6,0 -17 593 . C A,<*> 0 . DP=31;DPR=30,1,0;I16=16,14,0,1,1071,39925,7,49,1769,105241,29,841,561,12253,25,625;QS=2.97021,0.0297872,0;SGB=-0.556633;RPBZ=0.559355;MQBZ=-3.80789;MQSBZ=-0.0464238;BQBZ=-1.57464;SCBZ=3.67454;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255,54,255,255:18:0:0:9,9,0,0:18,0,0 0,12,184,18,187,185:7:1:0:3,3,0,1:6,1,0 0,18,174,18,174,174:6:0:0:4,2,0,0:6,0,0 -17 594 . A G,<*> 0 . DP=33;DPR=32,1,0;I16=16,16,1,0,1161,42757,4,16,1858,109682,60,3600,572,12672,15,225;QS=2.99359,0.00641026,0;SGB=-0.556633;RPBZ=-0.998367;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68954;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,42,255,51,255,255:18:1:0:8,9,1,0:17,1,0 0,21,205,21,205,205:7:0:0:3,4,0,0:7,0,0 0,24,213,24,213,213:8:0:0:5,3,0,0:8,0,0 +17 593 . C A,<*> 0 . DP=31;DPR=30,1,0;I16=16,14,0,1,1071,39925,7,49,1769,105241,29,841,561,12253,25,625;QS=2.97021,0.0297872,0;SGB=-0.556633;RPBZ=0.559355;MQBZ=-3.80789;MQSBZ=-0.0464238;BQBZ=-1.57464;SCBZ=3.67454;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255,54,255,255:18:0:0:9,9,0,0:18,0,0 0,12,184,18,187,185:7:1:0:3,3,0,1:6,1,0 0,18,174,18,174,174:6:0:0:4,2,0,0:6,0,0 +17 594 . A G,<*> 0 . DP=33;DPR=32,1,0;I16=16,16,1,0,1161,42757,4,16,1858,109682,60,3600,572,12672,15,225;QS=2.99359,0.00641026,0;SGB=-0.556633;RPBZ=-0.998367;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68954;SCBZ=-0.253876;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,42,255,51,255,255:18:1:0:8,9,1,0:17,1,0 0,21,205,21,205,205:7:0:0:3,4,0,0:7,0,0 0,24,213,24,213,213:8:0:0:5,3,0,0:8,0,0 17 595 . A <*> 0 . DP=33;DPR=33,0;I16=17,16,0,0,1136,40412,0,0,1918,113282,0,0,589,12905,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:9,9,0,0:18,0 0,21,198:7:0:0:3,4,0,0:7,0 0,24,218:8:0:0:5,3,0,0:8,0 -17 596 . A G,<*> 0 . DP=33;DPR=32,1,0;I16=16,16,1,0,1061,37187,8,64,1858,109682,60,3600,590,12952,1,1;QS=2.98564,0.0143627,0;SGB=-0.556633;RPBZ=1.68146;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68357;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,41,255,51,255,255:18:1:0:8,9,1,0:17,1,0 0,21,169,21,169,169:7:0:0:3,4,0,0:7,0,0 0,24,231,24,231,231:8:0:0:5,3,0,0:8,0,0 +17 596 . A G,<*> 0 . DP=33;DPR=32,1,0;I16=16,16,1,0,1061,37187,8,64,1858,109682,60,3600,590,12952,1,1;QS=2.98564,0.0143627,0;SGB=-0.556633;RPBZ=1.68146;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68357;SCBZ=-0.253876;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,41,255,51,255,255:18:1:0:8,9,1,0:17,1,0 0,21,169,21,169,169:7:0:0:3,4,0,0:7,0,0 0,24,231,24,231,231:8:0:0:5,3,0,0:8,0,0 17 597 . C <*> 0 . DP=33;DPR=33,0;I16=17,16,0,0,1196,44890,0,0,1918,113282,0,0,592,12990,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,54,255:18:0:0:9,9,0,0:18,0 0,21,204:7:0:0:3,4,0,0:7,0 0,24,220:8:0:0:5,3,0,0:8,0 17 598 . T <*> 0 . DP=33;DPR=33,0;I16=16,17,0,0,1219,47333,0,0,1918,113282,0,0,597,13029,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:8,9,0,0:17,0 0,21,217:7:0:0:3,4,0,0:7,0 0,27,242:9:0:0:5,4,0,0:9,0 17 599 . T <*> 0 . DP=33;DPR=33,0;I16=16,17,0,0,1182,43598,0,0,1918,113282,0,0,599,13095,0,0;QS=3,0;MQ0F=0 PL:DP:DV:SP:DP4:DPR 0,51,255:17:0:0:8,9,0,0:17,0 0,21,197:7:0:0:3,4,0,0:7,0 0,27,247:9:0:0:5,4,0,0:9,0 diff --git a/test/mpileup/mpileup.5.out b/test/mpileup/mpileup.5.out index 5dcfa01ca..e23e8409f 100644 --- a/test/mpileup/mpileup.5.out +++ b/test/mpileup/mpileup.5.out @@ -12,7 +12,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -30,29 +29,29 @@ 17 100 . C <*> 0 . DP=18;ADF=16,0;ADR=1,0;AD=17,0;I16=16,1,0,0,672,27586,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,189:9:0:9,0:0,0:9,0 0,9,118:3:0:2,0:1,0:3,0 0,15,134:5:0:5,0:0,0:5,0 17 101 . C <*> 0 . DP=18;ADF=16,0;ADR=1,0;AD=17,0;I16=16,1,0,0,630,24730,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,182:9:0:9,0:0,0:9,0 0,9,108:3:0:2,0:1,0:3,0 0,15,132:5:0:5,0:0,0:5,0 17 102 . C <*> 0 . DP=18;ADF=16,0;ADR=1,0;AD=17,0;I16=16,1,0,0,676,27812,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,188:9:0:9,0:0,0:9,0 0,9,121:3:0:2,0:1,0:3,0 0,15,139:5:0:5,0:0,0:5,0 -17 103 . T C,<*> 0 . DP=18;ADF=15,1,0;ADR=1,0,0;AD=16,1,0;I16=15,1,1,0,668,28542,6,36,929,54841,29,841,323,7035,6,36;QS=2.98256,0.0174419,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64924;SCBZ=4;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,17,184,24,187,185:9:0:8,1,0:0,0,0:8,1,0 0,9,118,9,118,118:3:0:2,0,0:1,0,0:3,0,0 0,15,147,15,147,147:5:0:5,0,0:0,0,0:5,0,0 -17 104 . G C,<*> 0 . DP=18;ADF=15,1,0;ADR=1,0,0;AD=16,1,0;I16=15,1,1,0,601,24163,3,9,929,54841,29,841,320,6884,7,49;QS=2.98726,0.0127389,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64309;SCBZ=4;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,173,24,176,173:9:0:8,1,0:0,0,0:8,1,0 0,9,101,9,101,101:3:0:2,0,0:1,0,0:3,0,0 0,15,133,15,133,133:5:0:5,0,0:0,0,0:5,0,0 +17 103 . T C,<*> 0 . DP=18;ADF=15,1,0;ADR=1,0,0;AD=16,1,0;I16=15,1,1,0,668,28542,6,36,929,54841,29,841,323,7035,6,36;QS=2.98256,0.0174419,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64924;SCBZ=4;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,17,184,24,187,185:9:0:8,1,0:0,0,0:8,1,0 0,9,118,9,118,118:3:0:2,0,0:1,0,0:3,0,0 0,15,147,15,147,147:5:0:5,0,0:0,0,0:5,0,0 +17 104 . G C,<*> 0 . DP=18;ADF=15,1,0;ADR=1,0,0;AD=16,1,0;I16=15,1,1,0,601,24163,3,9,929,54841,29,841,320,6884,7,49;QS=2.98726,0.0127389,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64309;SCBZ=4;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,173,24,176,173:9:0:8,1,0:0,0,0:8,1,0 0,9,101,9,101,101:3:0:2,0,0:1,0,0:3,0,0 0,15,133,15,133,133:5:0:5,0,0:0,0,0:5,0,0 17 105 . G <*> 0 . DP=19;ADF=17,0;ADR=1,0;AD=18,0;I16=17,1,0,0,603,22351,0,0,1018,59282,0,0,325,6815,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,171:10:0:10,0:0,0:10,0 0,9,106:3:0:2,0:1,0:3,0 0,15,125:5:0:5,0:0,0:5,0 17 106 . G <*> 0 . DP=19;ADF=17,0;ADR=1,0;AD=18,0;I16=17,1,0,0,636,25058,0,0,1018,59282,0,0,324,6718,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,190:10:0:10,0:0,0:10,0 0,9,92:3:0:2,0:1,0:3,0 0,15,124:5:0:5,0:0,0:5,0 17 107 . C <*> 0 . DP=19;ADF=17,0;ADR=1,0;AD=18,0;I16=17,1,0,0,686,27952,0,0,1018,59282,0,0,323,6643,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,192:10:0:10,0:0,0:10,0 0,9,119:3:0:2,0:1,0:3,0 0,15,136:5:0:5,0:0,0:5,0 17 108 . C <*> 0 . DP=19;ADF=17,0;ADR=1,0;AD=18,0;I16=17,1,0,0,681,27429,0,0,1018,59282,0,0,322,6590,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,190:10:0:10,0:0,0:10,0 0,9,119:3:0:2,0:1,0:3,0 0,15,135:5:0:5,0:0,0:5,0 -17 109 . T C,<*> 0 . DP=19;ADF=16,1,0;ADR=1,0,0;AD=17,1,0;I16=16,1,1,0,716,30648,2,4,989,58441,29,841,309,6415,12,144;QS=2.98922,0.0107817,0;SGB=-0.556633;RPBZ=-0.674966;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.6661;SCBZ=3;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,20,191,27,194,191:10:0:9,1,0:0,0,0:9,1,0 0,9,120,9,120,120:3:0:2,0,0:1,0,0:3,0,0 0,15,150,15,150,150:5:0:5,0,0:0,0,0:5,0,0 +17 109 . T C,<*> 0 . DP=19;ADF=16,1,0;ADR=1,0,0;AD=17,1,0;I16=16,1,1,0,716,30648,2,4,989,58441,29,841,309,6415,12,144;QS=2.98922,0.0107817,0;SGB=-0.556633;RPBZ=-0.674966;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.6661;SCBZ=3;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,20,191,27,194,191:10:0:9,1,0:0,0,0:9,1,0 0,9,120,9,120,120:3:0:2,0,0:1,0,0:3,0,0 0,15,150,15,150,150:5:0:5,0,0:0,0,0:5,0,0 17 110 . G <*> 0 . DP=19;ADF=17,0;ADR=1,0;AD=18,0;I16=17,1,0,0,688,28036,0,0,1018,59282,0,0,320,6550,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,194:10:0:10,0:0,0:10,0 0,9,113:3:0:2,0:1,0:3,0 0,15,136:5:0:5,0:0,0:5,0 17 111 . G <*> 0 . DP=19;ADF=17,0;ADR=1,0;AD=18,0;I16=17,1,0,0,573,21453,0,0,1018,59282,0,0,318,6514,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,167:10:0:10,0:0,0:10,0 0,9,95:3:0:2,0:1,0:3,0 0,15,119:5:0:5,0:0,0:5,0 -17 112 . C G,<*> 0 . DP=19;ADF=16,1,0;ADR=1,0,0;AD=17,1,0;I16=16,1,1,0,657,26565,2,4,989,58441,29,841,301,6277,15,225;QS=2.98907,0.010929,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65292;SCBZ=3;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,20,187,27,190,187:10:0:9,1,0:0,0,0:9,1,0 0,9,103,9,103,103:3:0:2,0,0:1,0,0:3,0,0 0,15,135,15,135,135:5:0:5,0,0:0,0,0:5,0,0 -17 113 . A G,<*> 0 . DP=19;ADF=16,1,0;ADR=1,0,0;AD=17,1,0;I16=16,1,1,0,635,25055,4,16,989,58441,29,841,297,6207,16,256;QS=2.98817,0.0118343,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65205;SCBZ=3;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,20,172,27,175,172:10:0:9,1,0:0,0,0:9,1,0 0,9,102,9,102,102:3:0:2,0,0:1,0,0:3,0,0 0,15,139,15,139,139:5:0:5,0,0:0,0,0:5,0,0 +17 112 . C G,<*> 0 . DP=19;ADF=16,1,0;ADR=1,0,0;AD=17,1,0;I16=16,1,1,0,657,26565,2,4,989,58441,29,841,301,6277,15,225;QS=2.98907,0.010929,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65292;SCBZ=3;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,20,187,27,190,187:10:0:9,1,0:0,0,0:9,1,0 0,9,103,9,103,103:3:0:2,0,0:1,0,0:3,0,0 0,15,135,15,135,135:5:0:5,0,0:0,0,0:5,0,0 +17 113 . A G,<*> 0 . DP=19;ADF=16,1,0;ADR=1,0,0;AD=17,1,0;I16=16,1,1,0,635,25055,4,16,989,58441,29,841,297,6207,16,256;QS=2.98817,0.0118343,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65205;SCBZ=3;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,20,172,27,175,172:10:0:9,1,0:0,0,0:9,1,0 0,9,102,9,102,102:3:0:2,0,0:1,0,0:3,0,0 0,15,139,15,139,139:5:0:5,0,0:0,0,0:5,0,0 17 114 . C <*> 0 . DP=19;ADF=17,0;ADR=1,0;AD=18,0;I16=17,1,0,0,660,25876,0,0,1018,59282,0,0,310,6446,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,181:10:0:10,0:0,0:10,0 0,9,113:3:0:2,0:1,0:3,0 0,15,133:5:0:5,0:0,0:5,0 -17 115 . C A,<*> 0 . DP=21;ADF=17,1,0;ADR=2,0,0;AD=19,1,0;I16=17,2,1,0,688,27426,12,144,1078,62882,29,841,283,5827,25,625;QS=2.88785,0.11215,0;SGB=-0.556633;RPBZ=0.260329;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.47798;SCBZ=-0.418446;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,189,30,189,189:10:0:10,0,0:0,0,0:10,0,0 3,0,86,9,89,93:3:0:1,1,0:1,0,0:2,1,0 0,21,153,21,153,153:7:0:6,0,0:1,0,0:7,0,0 -17 116 . A C,<*> 0 . DP=21;ADF=17,1,0;ADR=2,0,0;AD=19,1,0;I16=17,2,1,0,705,27791,2,4,1078,62882,29,841,287,6073,19,361;QS=2.98873,0.0112676,0;SGB=-0.556633;RPBZ=0.0867763;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.65814;SCBZ=2.65016;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,20,179,27,182,179:10:0:9,1,0:0,0,0:9,1,0 0,9,102,9,102,102:3:0:2,0,0:1,0,0:3,0,0 0,21,175,21,175,175:7:0:6,0,0:1,0,0:7,0,0 +17 115 . C A,<*> 0 . DP=21;ADF=17,1,0;ADR=2,0,0;AD=19,1,0;I16=17,2,1,0,688,27426,12,144,1078,62882,29,841,283,5827,25,625;QS=2.88785,0.11215,0;SGB=-0.556633;RPBZ=0.260329;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.47798;SCBZ=-0.418446;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,189,30,189,189:10:0:10,0,0:0,0,0:10,0,0 3,0,86,9,89,93:3:0:1,1,0:1,0,0:2,1,0 0,21,153,21,153,153:7:0:6,0,0:1,0,0:7,0,0 +17 116 . A C,<*> 0 . DP=21;ADF=17,1,0;ADR=2,0,0;AD=19,1,0;I16=17,2,1,0,705,27791,2,4,1078,62882,29,841,287,6073,19,361;QS=2.98873,0.0112676,0;SGB=-0.556633;RPBZ=0.0867763;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.65814;SCBZ=2.65016;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,20,179,27,182,179:10:0:9,1,0:0,0,0:9,1,0 0,9,102,9,102,102:3:0:2,0,0:1,0,0:3,0,0 0,21,175,21,175,175:7:0:6,0,0:1,0,0:7,0,0 17 117 . G <*> 0 . DP=21;ADF=18,0;ADR=2,0;AD=20,0;I16=18,2,0,0,715,28045,0,0,1107,63723,0,0,304,6444,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,185:10:0:10,0:0,0:10,0 0,9,97:3:0:2,0:1,0:3,0 0,21,177:7:0:6,0:1,0:7,0 17 118 . G <*> 0 . DP=20;ADF=17,0;ADR=2,0;AD=19,0;I16=17,2,0,0,620,23470,0,0,1047,60123,0,0,303,6481,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,175:9:0:9,0:0,0:9,0 0,9,65:3:0:2,0:1,0:3,0 0,21,162:7:0:6,0:1,0:7,0 17 119 . G <*> 0 . DP=19;ADF=16,0;ADR=2,0;AD=18,0;I16=16,2,0,0,619,23459,0,0,987,56523,0,0,301,6493,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,176:9:0:9,0:0,0:9,0 0,6,76:2:0:1,0:1,0:2,0 0,21,160:7:0:6,0:1,0:7,0 -17 120 . A G,<*> 0 . DP=19;ADF=15,1,0;ADR=2,0,0;AD=17,1,0;I16=15,2,1,0,646,25392,4,16,958,55682,29,841,277,5999,23,529;QS=2.9873,0.0126984,0;SGB=-0.556633;RPBZ=0.28942;MQBZ=-2.23607;MQSBZ=-1.30384;BQBZ=-1.6486;SCBZ=3;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,171,24,174,171:9:0:8,1,0:0,0,0:8,1,0 0,6,88,6,88,88:2:0:1,0,0:1,0,0:2,0,0 0,21,171,21,171,171:7:0:6,0,0:1,0,0:7,0,0 +17 120 . A G,<*> 0 . DP=19;ADF=15,1,0;ADR=2,0,0;AD=17,1,0;I16=15,2,1,0,646,25392,4,16,958,55682,29,841,277,5999,23,529;QS=2.9873,0.0126984,0;SGB=-0.556633;RPBZ=0.28942;MQBZ=-2.23607;MQSBZ=-1.30384;BQBZ=-1.6486;SCBZ=3;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,171,24,174,171:9:0:8,1,0:0,0,0:8,1,0 0,6,88,6,88,88:2:0:1,0,0:1,0,0:2,0,0 0,21,171,21,171,171:7:0:6,0,0:1,0,0:7,0,0 17 121 . G <*> 0 . DP=19;ADF=16,0;ADR=2,0;AD=18,0;I16=16,2,0,0,650,25148,0,0,987,56523,0,0,298,6534,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,181:9:0:9,0:0,0:9,0 0,6,84:2:0:1,0:1,0:2,0 0,21,168:7:0:6,0:1,0:7,0 17 122 . C <*> 0 . DP=20;ADF=17,0;ADR=2,0;AD=19,0;I16=17,2,0,0,696,27784,0,0,1047,60123,0,0,296,6560,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,180:9:0:9,0:0,0:9,0 0,9,107:3:0:2,0:1,0:3,0 0,21,178:7:0:6,0:1,0:7,0 17 123 . T <*> 0 . DP=18;ADF=15,0;ADR=2,0;AD=17,0;I16=15,2,0,0,647,26145,0,0,927,52923,0,0,296,6554,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,24,170:8:0:8,0:0,0:8,0 0,9,123:3:0:2,0:1,0:3,0 0,18,166:6:0:5,0:1,0:6,0 17 124 . T <*> 0 . DP=19;ADF=16,0;ADR=2,0;AD=18,0;I16=16,2,0,0,606,22002,0,0,987,56523,0,0,296,6564,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,154:9:0:9,0:0,0:9,0 0,9,114:3:0:2,0:1,0:3,0 0,18,154:6:0:5,0:1,0:6,0 -17 125 . A T,<*> 0 . DP=18;ADF=14,1,0;ADR=2,0,0;AD=16,1,0;I16=14,2,1,0,589,22565,4,16,898,52082,29,841,272,5916,25,625;QS=2.98444,0.0155642,0;SGB=-0.556633;RPBZ=1.02125;MQBZ=-2.16025;MQSBZ=-1.23956;BQBZ=-1.64106;SCBZ=2.91548;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,15,149,21,152,149:8:0:7,1,0:0,0,0:7,1,0 0,9,114,9,114,114:3:0:2,0,0:1,0,0:3,0,0 0,18,162,18,162,162:6:0:5,0,0:1,0,0:6,0,0 +17 125 . A T,<*> 0 . DP=18;ADF=14,1,0;ADR=2,0,0;AD=16,1,0;I16=14,2,1,0,589,22565,4,16,898,52082,29,841,272,5916,25,625;QS=2.98444,0.0155642,0;SGB=-0.556633;RPBZ=1.02125;MQBZ=-2.16025;MQSBZ=-1.23956;BQBZ=-1.64106;SCBZ=2.91548;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,15,149,21,152,149:8:0:7,1,0:0,0,0:7,1,0 0,9,114,9,114,114:3:0:2,0,0:1,0,0:3,0,0 0,18,162,18,162,162:6:0:5,0,0:1,0,0:6,0,0 17 126 . A <*> 0 . DP=18;ADF=15,0;ADR=2,0;AD=17,0;I16=15,2,0,0,629,24725,0,0,927,52923,0,0,298,6536,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,24,162:8:0:8,0:0,0:8,0 0,9,117:3:0:2,0:1,0:3,0 0,18,174:6:0:5,0:1,0:6,0 17 127 . C <*> 0 . DP=18;ADF=15,0;ADR=2,0;AD=17,0;I16=15,2,0,0,627,24331,0,0,927,52923,0,0,299,6549,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,24,163:8:0:8,0:0,0:8,0 0,9,119:3:0:2,0:1,0:3,0 0,18,160:6:0:5,0:1,0:6,0 17 128 . A <*> 0 . DP=18;ADF=15,0;ADR=2,0;AD=17,0;I16=15,2,0,0,660,26364,0,0,927,52923,0,0,300,6580,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,24,169:8:0:8,0:0,0:8,0 0,9,121:3:0:2,0:1,0:3,0 0,18,168:6:0:5,0:1,0:6,0 @@ -86,7 +85,7 @@ 17 156 . C <*> 0 . DP=14;ADF=12,0;ADR=2,0;AD=14,0;I16=12,2,0,0,536,20884,0,0,809,47641,0,0,266,5934,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,163:7:0:7,0:0,0:7,0 0,6,84:2:0:1,0:1,0:2,0 0,15,150:5:0:4,0:1,0:5,0 17 157 . C <*> 0 . DP=14;ADF=12,0;ADR=2,0;AD=14,0;I16=12,2,0,0,555,22081,0,0,809,47641,0,0,264,5904,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,169:7:0:7,0:0,0:7,0 0,6,85:2:0:1,0:1,0:2,0 0,15,149:5:0:4,0:1,0:5,0 17 158 . T <*> 0 . DP=14;ADF=12,0;ADR=2,0;AD=14,0;I16=12,2,0,0,568,23154,0,0,809,47641,0,0,262,5886,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,170:7:0:7,0:0,0:7,0 0,6,84:2:0:1,0:1,0:2,0 0,15,159:5:0:4,0:1,0:5,0 -17 159 . A G,<*> 0 . DP=15;ADF=12,1,0;ADR=2,0,0;AD=14,1,0;I16=12,2,1,0,519,19467,5,25,809,47641,60,3600,260,5880,0,0;QS=2.97076,0.0292398,0;SGB=-0.556633;RPBZ=-1.62019;MQBZ=0.267261;MQSBZ=-2.54951;BQBZ=-1.63041;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,157,21,157,157:7:0:7,0,0:0,0,0:7,0,0 0,6,83,6,83,83:2:0:1,0,0:1,0,0:2,0,0 0,10,129,15,132,129:6:0:4,1,0:1,0,0:5,1,0 +17 159 . A G,<*> 0 . DP=15;ADF=12,1,0;ADR=2,0,0;AD=14,1,0;I16=12,2,1,0,519,19467,5,25,809,47641,60,3600,260,5880,0,0;QS=2.97076,0.0292398,0;SGB=-0.556633;RPBZ=-1.62019;MQBZ=0.267261;MQSBZ=-2.54951;BQBZ=-1.63041;SCBZ=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,157,21,157,157:7:0:7,0,0:0,0,0:7,0,0 0,6,83,6,83,83:2:0:1,0,0:1,0,0:2,0,0 0,10,129,15,132,129:6:0:4,1,0:1,0,0:5,1,0 17 160 . G <*> 0 . DP=15;ADF=13,0;ADR=2,0;AD=15,0;I16=13,2,0,0,547,20633,0,0,869,51241,0,0,259,5887,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,165:7:0:7,0:0,0:7,0 0,6,85:2:0:1,0:1,0:2,0 0,18,139:6:0:5,0:1,0:6,0 17 161 . A <*> 0 . DP=15;ADF=13,0;ADR=2,0;AD=15,0;I16=13,2,0,0,568,21610,0,0,869,51241,0,0,258,5908,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,157:7:0:7,0:0,0:7,0 0,6,83:2:0:1,0:1,0:2,0 0,18,162:6:0:5,0:1,0:6,0 17 162 . A <*> 0 . DP=15;ADF=13,0;ADR=2,0;AD=15,0;I16=13,2,0,0,558,21206,0,0,869,51241,0,0,255,5843,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,147:7:0:7,0:0,0:7,0 0,6,87:2:0:1,0:1,0:2,0 0,18,167:6:0:5,0:1,0:6,0 @@ -117,7 +116,7 @@ 17 187 . C <*> 0 . DP=14;ADF=13,0;ADR=1,0;AD=14,0;I16=13,1,0,0,511,18979,0,0,809,47641,0,0,266,5952,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,147:6:0:6,0:0,0:6,0 0,3,38:1:0:1,0:0,0:1,0 0,21,172:7:0:6,0:1,0:7,0 17 188 . C <*> 0 . DP=14;ADF=13,0;ADR=1,0;AD=14,0;I16=13,1,0,0,496,18042,0,0,809,47641,0,0,267,5989,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,147:6:0:6,0:0,0:6,0 0,3,37:1:0:1,0:0,0:1,0 0,21,162:7:0:6,0:1,0:7,0 17 189 . C <*> 0 . DP=15;ADF=13,0;ADR=2,0;AD=15,0;I16=13,2,0,0,552,20504,0,0,838,48482,0,0,268,6040,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,152:6:0:6,0:0,0:6,0 0,6,67:2:0:1,0:1,0:2,0 0,21,167:7:0:6,0:1,0:7,0 -17 190 . A C,<*> 0 . DP=15;ADF=12,1,0;ADR=2,0,0;AD=14,1,0;I16=12,2,1,0,500,18230,5,25,778,44882,60,3600,243,5381,25,625;QS=2.97664,0.0233645,0;SGB=-0.556633;RPBZ=0;MQBZ=0.392232;MQSBZ=-3.74166;BQBZ=-1.63041;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,138,18,138,138:6:0:6,0,0:0,0,0:6,0,0 0,6,68,6,68,68:2:0:1,0,0:1,0,0:2,0,0 0,12,153,18,156,153:7:0:5,1,0:1,0,0:6,1,0 +17 190 . A C,<*> 0 . DP=15;ADF=12,1,0;ADR=2,0,0;AD=14,1,0;I16=12,2,1,0,500,18230,5,25,778,44882,60,3600,243,5381,25,625;QS=2.97664,0.0233645,0;SGB=-0.556633;RPBZ=0;MQBZ=0.392232;MQSBZ=-3.74166;BQBZ=-1.63041;SCBZ=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,138,18,138,138:6:0:6,0,0:0,0,0:6,0,0 0,6,68,6,68,68:2:0:1,0,0:1,0,0:2,0,0 0,12,153,18,156,153:7:0:5,1,0:1,0,0:6,1,0 17 191 . T <*> 0 . DP=15;ADF=13,0;ADR=2,0;AD=15,0;I16=13,2,0,0,534,19276,0,0,838,48482,0,0,267,5939,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,143:6:0:6,0:0,0:6,0 0,6,67:2:0:1,0:1,0:2,0 0,21,169:7:0:6,0:1,0:7,0 17 192 . G <*> 0 . DP=15;ADF=13,0;ADR=2,0;AD=15,0;I16=13,2,0,0,499,17439,0,0,838,48482,0,0,266,5890,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,143:6:0:6,0:0,0:6,0 0,6,67:2:0:1,0:1,0:2,0 0,21,151:7:0:6,0:1,0:7,0 17 193 . T <*> 0 . DP=15;ADF=13,0;ADR=2,0;AD=15,0;I16=13,2,0,0,505,17811,0,0,838,48482,0,0,265,5859,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,140:6:0:6,0:0,0:6,0 0,6,63:2:0:1,0:1,0:2,0 0,21,157:7:0:6,0:1,0:7,0 @@ -150,10 +149,10 @@ 17 220 . G <*> 0 . DP=14;ADF=11,0;ADR=3,0;AD=14,0;I16=11,3,0,0,495,18407,0,0,747,42123,0,0,267,6079,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,188:7:0:6,0:1,0:7,0 0,9,88:3:0:1,0:2,0:3,0 0,12,84:4:0:4,0:0,0:4,0 17 221 . A <*> 0 . DP=14;ADF=11,0;ADR=3,0;AD=14,0;I16=11,3,0,0,488,17688,0,0,747,42123,0,0,267,6135,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,176:7:0:6,0:1,0:7,0 0,9,89:3:0:1,0:2,0:3,0 0,12,101:4:0:4,0:0,0:4,0 17 222 . A <*> 0 . DP=14;ADF=11,0;ADR=3,0;AD=14,0;I16=11,3,0,0,479,17747,0,0,747,42123,0,0,267,6203,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,186:7:0:6,0:1,0:7,0 0,9,89:3:0:1,0:2,0:3,0 0,12,73:4:0:4,0:0,0:4,0 -17 223 . G T,<*> 0 . DP=13;ADF=9,1,0;ADR=3,0,0;AD=12,1,0;I16=9,3,1,0,412,14782,8,64,627,34923,60,3600,243,5657,25,625;QS=2.96596,0.0340426,0;SGB=-0.556633;RPBZ=1.07052;MQBZ=0.547723;MQSBZ=-3.4641;BQBZ=-1.60577;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,11,166,18,169,167:7:0:5,1,0:1,0,0:6,1,0 0,6,53,6,53,53:2:0:0,0,0:2,0,0:2,0,0 0,12,81,12,81,81:4:0:4,0,0:0,0,0:4,0,0 +17 223 . G T,<*> 0 . DP=13;ADF=9,1,0;ADR=3,0,0;AD=12,1,0;I16=9,3,1,0,412,14782,8,64,627,34923,60,3600,243,5657,25,625;QS=2.96596,0.0340426,0;SGB=-0.556633;RPBZ=1.07052;MQBZ=0.547723;MQSBZ=-3.4641;BQBZ=-1.60577;SCBZ=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,11,166,18,169,167:7:0:5,1,0:1,0,0:6,1,0 0,6,53,6,53,53:2:0:0,0,0:2,0,0:2,0,0 0,12,81,12,81,81:4:0:4,0,0:0,0,0:4,0,0 17 224 . G <*> 0 . DP=12;ADF=9,0;ADR=3,0;AD=12,0;I16=9,3,0,0,379,12759,0,0,627,34923,0,0,270,6370,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,168:6:0:5,0:1,0:6,0 0,6,50:2:0:0,0:2,0:2,0 0,12,70:4:0:4,0:0,0:4,0 17 225 . C <*> 0 . DP=12;ADF=9,0;ADR=3,0;AD=12,0;I16=9,3,0,0,390,13960,0,0,627,34923,0,0,272,6466,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,165:6:0:5,0:1,0:6,0 0,6,48:2:0:0,0:2,0:2,0 0,12,86:4:0:4,0:0,0:4,0 -17 226 . A G,C,<*> 0 . DP=13;ADF=8,1,0,0;ADR=3,0,1,0;AD=11,1,1,0;I16=8,3,1,1,381,13669,6,18,567,31323,89,4441,248,5894,44,986;QS=2.94293,0.0392157,0.0178571,0;VDB=0.84;SGB=-2.62246;RPBZ=-0.592157;MQBZ=-0.615457;MQSBZ=-3.4641;BQBZ=-2.17723;SCBZ=2.34521;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,159,12,162,159,18,159,162,159:7:0:5,0,0,0:1,0,1,0:6,0,1,0 0,6,53,6,53,53,6,53,53,53:2:0:0,0,0,0:2,0,0,0:2,0,0,0 0,5,79,9,82,80,9,82,80,80:4:0:3,1,0,0:0,0,0,0:3,1,0,0 +17 226 . A G,C,<*> 0 . DP=13;ADF=8,1,0,0;ADR=3,0,1,0;AD=11,1,1,0;I16=8,3,1,1,381,13669,6,18,567,31323,89,4441,248,5894,44,986;QS=2.94293,0.0392157,0.0178571,0;VDB=0.84;SGB=-2.62246;RPBZ=-0.592157;MQBZ=-0.615457;MQSBZ=-3.4641;BQBZ=-2.17723;SCBZ=2.34521;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,18,159,12,162,159,18,159,162,159:7:0:5,0,0,0:1,0,1,0:6,0,1,0 0,6,53,6,53,53,6,53,53,53:2:0:0,0,0,0:2,0,0,0:2,0,0,0 0,5,79,9,82,80,9,82,80,80:4:0:3,1,0,0:0,0,0,0:3,1,0,0 17 227 . C <*> 0 . DP=13;ADF=9,0;ADR=4,0;AD=13,0;I16=9,4,0,0,412,14342,0,0,656,35764,0,0,292,6878,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,190:7:0:5,0:2,0:7,0 0,6,53:2:0:0,0:2,0:2,0 0,12,75:4:0:4,0:0,0:4,0 17 228 . C <*> 0 . DP=13;ADF=9,0;ADR=4,0;AD=13,0;I16=9,4,0,0,417,14381,0,0,656,35764,0,0,292,6884,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,187:7:0:5,0:2,0:7,0 0,6,45:2:0:0,0:2,0:2,0 0,12,96:4:0:4,0:0,0:4,0 17 229 . G <*> 0 . DP=13;ADF=9,0;ADR=4,0;AD=13,0;I16=9,4,0,0,368,11524,0,0,656,35764,0,0,292,6898,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,145:7:0:5,0:2,0:7,0 0,6,53:2:0:0,0:2,0:2,0 0,12,70:4:0:4,0:0,0:4,0 @@ -164,7 +163,7 @@ 17 234 . A <*> 0 . DP=14;ADF=10,0;ADR=4,0;AD=14,0;I16=10,4,0,0,502,18390,0,0,716,39364,0,0,292,6988,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,185:7:0:5,0:2,0:7,0 0,6,53:2:0:0,0:2,0:2,0 0,15,123:5:0:5,0:0,0:5,0 17 235 . A <*> 0 . DP=14;ADF=10,0;ADR=4,0;AD=14,0;I16=10,4,0,0,488,17796,0,0,716,39364,0,0,291,6951,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,21,186:7:0:5,0:2,0:7,0 0,6,53:2:0:0,0:2,0:2,0 0,15,115:5:0:5,0:0,0:5,0 17 236 . G <*> 0 . DP=15;ADF=11,0;ADR=4,0;AD=15,0;I16=11,4,0,0,501,17481,0,0,776,42964,0,0,290,6924,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,24,206:8:0:6,0:2,0:8,0 0,6,53:2:0:0,0:2,0:2,0 0,15,103:5:0:5,0:0,0:5,0 -17 237 . A C,<*> 0 . DP=14;ADF=9,1,0;ADR=4,0,0;AD=13,1,0;I16=9,4,1,0,465,16877,8,64,656,35764,60,3600,266,6282,25,625;QS=2.93162,0.0683761,0;SGB=-0.556633;RPBZ=1.11754;MQBZ=0.632456;MQSBZ=-3.60555;BQBZ=-1.61959;SCBZ=-0.27735;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,24,206,24,206,206:8:0:6,0,0:2,0,0:8,0,0 0,6,53,6,53,53:2:0:0,0,0:2,0,0:2,0,0 0,3,84,9,87,87:4:0:3,1,0:0,0,0:3,1,0 +17 237 . A C,<*> 0 . DP=14;ADF=9,1,0;ADR=4,0,0;AD=13,1,0;I16=9,4,1,0,465,16877,8,64,656,35764,60,3600,266,6282,25,625;QS=2.93162,0.0683761,0;SGB=-0.556633;RPBZ=1.11754;MQBZ=0.632456;MQSBZ=-3.60555;BQBZ=-1.61959;SCBZ=-0.27735;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,24,206,24,206,206:8:0:6,0,0:2,0,0:8,0,0 0,6,53,6,53,53:2:0:0,0,0:2,0,0:2,0,0 0,3,84,9,87,87:4:0:3,1,0:0,0,0:3,1,0 17 238 . C <*> 0 . DP=14;ADF=10,0;ADR=4,0;AD=14,0;I16=10,4,0,0,482,17238,0,0,716,39364,0,0,292,6900,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,24,211:8:0:6,0:2,0:8,0 0,6,53:2:0:0,0:2,0:2,0 0,12,82:4:0:4,0:0,0:4,0 17 239 . A <*> 0 . DP=15;ADF=10,0;ADR=5,0;AD=15,0;I16=10,5,0,0,525,19155,0,0,776,42964,0,0,292,6852,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,223:9:0:6,0:3,0:9,0 0,6,50:2:0:0,0:2,0:2,0 0,12,108:4:0:4,0:0,0:4,0 17 240 . C <*> 0 . DP=15;ADF=10,0;ADR=5,0;AD=15,0;I16=10,5,0,0,512,17930,0,0,776,42964,0,0,292,6764,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,220:9:0:6,0:3,0:9,0 0,6,53:2:0:0,0:2,0:2,0 0,12,106:4:0:4,0:0,0:4,0 @@ -194,18 +193,18 @@ 17 264 . C <*> 0 . DP=22;ADF=10,0;ADR=12,0;AD=22,0;I16=10,12,0,0,821,31325,0,0,1049,54897,0,0,386,8326,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:7,0:4,0:11,0 0,15,104:5:0:0,0:5,0:5,0 0,18,172:6:0:3,0:3,0:6,0 17 265 . A <*> 0 . DP=21;ADF=9,0;ADR=12,0;AD=21,0;I16=9,12,0,0,800,31906,0,0,989,51297,0,0,390,8380,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:7,0:4,0:11,0 0,15,114:5:0:0,0:5,0:5,0 0,15,129:5:0:2,0:3,0:5,0 17 266 . G <*> 0 . DP=21;ADF=9,0;ADR=12,0;AD=21,0;I16=9,12,0,0,754,28204,0,0,989,51297,0,0,394,8458,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:7,0:4,0:11,0 0,15,99:5:0:0,0:5,0:5,0 0,15,138:5:0:2,0:3,0:5,0 -17 267 . T G,<*> 0 . DP=21;ADF=9,0,0;ADR=11,1,0;AD=20,1,0;I16=9,11,0,1,739,27465,8,64,960,50456,29,841,373,7935,25,625;QS=2.94203,0.057971,0;SGB=-0.556633;RPBZ=-0.330396;MQBZ=-1.23153;MQSBZ=-3.3021;BQBZ=-1.66282;SCBZ=2.91633;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,254,33,254,254:11:0:7,0,0:4,0,0:11,0,0 0,6,93,12,96,96:5:0:0,0,0:4,1,0:4,1,0 0,15,149,15,149,149:5:0:2,0,0:3,0,0:5,0,0 +17 267 . T G,<*> 0 . DP=21;ADF=9,0,0;ADR=11,1,0;AD=20,1,0;I16=9,11,0,1,739,27465,8,64,960,50456,29,841,373,7935,25,625;QS=2.94203,0.057971,0;SGB=-0.556633;RPBZ=-0.330396;MQBZ=-1.23153;MQSBZ=-3.3021;BQBZ=-1.66282;SCBZ=2.91633;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,254,33,254,254:11:0:7,0,0:4,0,0:11,0,0 0,6,93,12,96,96:5:0:0,0,0:4,1,0:4,1,0 0,15,149,15,149,149:5:0:2,0,0:3,0,0:5,0,0 17 268 . T <*> 0 . DP=21;ADF=9,0;ADR=12,0;AD=21,0;I16=9,12,0,0,748,27708,0,0,989,51297,0,0,402,8686,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,238:11:0:7,0:4,0:11,0 0,15,110:5:0:0,0:5,0:5,0 0,15,156:5:0:2,0:3,0:5,0 17 269 . C <*> 0 . DP=22;ADF=9,0;ADR=13,0;AD=22,0;I16=9,13,0,0,767,28641,0,0,1018,52138,0,0,406,8836,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:7,0:5,0:12,0 0,15,91:5:0:0,0:5,0:5,0 0,15,154:5:0:2,0:3,0:5,0 17 270 . C <*> 0 . DP=22;ADF=9,0;ADR=13,0;AD=22,0;I16=9,13,0,0,766,28210,0,0,1018,52138,0,0,410,8962,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:7,0:5,0:12,0 0,15,98:5:0:0,0:5,0:5,0 0,15,143:5:0:2,0:3,0:5,0 17 271 . T <*> 0 . DP=22;ADF=9,0;ADR=13,0;AD=22,0;I16=9,13,0,0,847,32935,0,0,1018,52138,0,0,413,9065,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:7,0:5,0:12,0 0,15,113:5:0:0,0:5,0:5,0 0,15,152:5:0:2,0:3,0:5,0 17 272 . C <*> 0 . DP=22;ADF=9,0;ADR=13,0;AD=22,0;I16=9,13,0,0,815,31449,0,0,1018,52138,0,0,415,9143,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:7,0:5,0:12,0 0,15,97:5:0:0,0:5,0:5,0 0,15,149:5:0:2,0:3,0:5,0 -17 273 . T C,<*> 0 . DP=22;ADF=9,0,0;ADR=12,1,0;AD=21,1,0;I16=9,12,0,1,798,30664,5,25,989,51297,29,841,392,8620,25,625;QS=2.96094,0.0390625,0;SGB=-0.556633;RPBZ=-0.236567;MQBZ=-1.16701;MQSBZ=-3.42286;BQBZ=-1.66779;SCBZ=3.00076;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255,36,255,255:12:0:7,0,0:5,0,0:12,0,0 0,7,89,12,92,90:5:0:0,0,0:4,1,0:4,1,0 0,15,161,15,161,161:5:0:2,0,0:3,0,0:5,0,0 +17 273 . T C,<*> 0 . DP=22;ADF=9,0,0;ADR=12,1,0;AD=21,1,0;I16=9,12,0,1,798,30664,5,25,989,51297,29,841,392,8620,25,625;QS=2.96094,0.0390625,0;SGB=-0.556633;RPBZ=-0.236567;MQBZ=-1.16701;MQSBZ=-3.42286;BQBZ=-1.66779;SCBZ=3.00076;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255,36,255,255:12:0:7,0,0:5,0,0:12,0,0 0,7,89,12,92,90:5:0:0,0,0:4,1,0:4,1,0 0,15,161,15,161,161:5:0:2,0,0:3,0,0:5,0,0 17 274 . C <*> 0 . DP=22;ADF=9,0;ADR=13,0;AD=22,0;I16=9,13,0,0,767,28193,0,0,1018,52138,0,0,419,9371,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:7,0:5,0:12,0 0,15,101:5:0:0,0:5,0:5,0 0,15,144:5:0:2,0:3,0:5,0 17 275 . C <*> 0 . DP=20;ADF=7,0;ADR=13,0;AD=20,0;I16=7,13,0,0,768,29994,0,0,898,44938,0,0,423,9519,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,15,114:5:0:0,0:5,0:5,0 0,12,122:4:0:1,0:3,0:4,0 17 276 . A <*> 0 . DP=20;ADF=7,0;ADR=13,0;AD=20,0;I16=7,13,0,0,805,32931,0,0,898,44938,0,0,424,9538,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,253:11:0:6,0:5,0:11,0 0,15,122:5:0:0,0:5,0:5,0 0,12,124:4:0:1,0:3,0:4,0 17 277 . G <*> 0 . DP=20;ADF=7,0;ADR=13,0;AD=20,0;I16=7,13,0,0,764,29732,0,0,898,44938,0,0,425,9579,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,15,114:5:0:0,0:5,0:5,0 0,12,121:4:0:1,0:3,0:4,0 -17 278 . A C,<*> 0 . DP=21;ADF=6,1,0;ADR=14,0,0;AD=20,1,0;I16=6,14,1,0,722,26452,7,49,867,42179,60,3600,415,9521,11,121;QS=2.97935,0.020649,0;SGB=-0.556633;RPBZ=1.65198;MQBZ=1.0247;MQSBZ=-3.24037;BQBZ=-1.66667;SCBZ=-0.324037;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,22,231,30,234,231:11:0:5,1,0:5,0,0:10,1,0 0,18,123,18,123,123:6:0:0,0,0:6,0,0:6,0,0 0,12,121,12,121,121:4:0:1,0,0:3,0,0:4,0,0 +17 278 . A C,<*> 0 . DP=21;ADF=6,1,0;ADR=14,0,0;AD=20,1,0;I16=6,14,1,0,722,26452,7,49,867,42179,60,3600,415,9521,11,121;QS=2.97935,0.020649,0;SGB=-0.556633;RPBZ=1.65198;MQBZ=1.0247;MQSBZ=-3.24037;BQBZ=-1.66667;SCBZ=-0.324037;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,22,231,30,234,231:11:0:5,1,0:5,0,0:10,1,0 0,18,123,18,123,123:6:0:0,0,0:6,0,0:6,0,0 0,12,121,12,121,121:4:0:1,0,0:3,0,0:4,0,0 17 279 . A <*> 0 . DP=22;ADF=7,0;ADR=15,0;AD=22,0;I16=7,15,0,0,786,28694,0,0,956,46620,0,0,427,9677,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:6,0:6,0:12,0 0,18,123:6:0:0,0:6,0:6,0 0,12,122:4:0:1,0:3,0:4,0 17 280 . A <*> 0 . DP=22;ADF=7,0;ADR=15,0;AD=22,0;I16=7,15,0,0,815,31561,0,0,956,46620,0,0,428,9684,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,253:12:0:6,0:6,0:12,0 0,18,130:6:0:0,0:6,0:6,0 0,12,129:4:0:1,0:3,0:4,0 17 281 . G <*> 0 . DP=22;ADF=7,0;ADR=15,0;AD=22,0;I16=7,15,0,0,820,31416,0,0,956,46620,0,0,428,9662,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:6,0:6,0:12,0 0,18,122:6:0:0,0:6,0:6,0 0,12,123:4:0:1,0:3,0:4,0 @@ -224,13 +223,13 @@ 17 294 . A <*> 0 . DP=26;ADF=10,0;ADR=16,0;AD=26,0;I16=10,16,0,0,931,33937,0,0,1227,63779,0,0,443,9785,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,252:12:0:6,0:6,0:12,0 0,24,201:8:0:3,0:5,0:8,0 0,18,161:6:0:1,0:5,0:6,0 17 295 . C <*> 0 . DP=25;ADF=10,0;ADR=15,0;AD=25,0;I16=10,15,0,0,909,34117,0,0,1198,62938,0,0,447,9833,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,183:8:0:3,0:5,0:8,0 0,18,159:6:0:1,0:5,0:6,0 17 296 . A <*> 0 . DP=25;ADF=10,0;ADR=15,0;AD=25,0;I16=10,15,0,0,874,31846,0,0,1198,62938,0,0,451,9905,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,169:8:0:3,0:5,0:8,0 0,18,169:6:0:1,0:5,0:6,0 -17 297 . C G,<*> 0 . DP=25;ADF=9,1,0;ADR=15,0,0;AD=24,1,0;I16=9,15,1,0,901,34305,4,16,1138,59338,60,3600,445,9901,10,100;QS=2.98261,0.0173913,0;SGB=-0.556633;RPBZ=-1.24856;MQBZ=0.806872;MQSBZ=-3.22749;BQBZ=-1.67542;SCBZ=-0.368383;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255,33,255,255:11:0:6,0,0:5,0,0:11,0,0 0,15,168,21,171,168:8:0:2,1,0:5,0,0:7,1,0 0,18,161,18,161,161:6:0:1,0,0:5,0,0:6,0,0 +17 297 . C G,<*> 0 . DP=25;ADF=9,1,0;ADR=15,0,0;AD=24,1,0;I16=9,15,1,0,901,34305,4,16,1138,59338,60,3600,445,9901,10,100;QS=2.98261,0.0173913,0;SGB=-0.556633;RPBZ=-1.24856;MQBZ=0.806872;MQSBZ=-3.22749;BQBZ=-1.67542;SCBZ=-0.368383;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255,33,255,255:11:0:6,0,0:5,0,0:11,0,0 0,15,168,21,171,168:8:0:2,1,0:5,0,0:7,1,0 0,18,161,18,161,161:6:0:1,0,0:5,0,0:6,0,0 17 298 . A <*> 0 . DP=26;ADF=11,0;ADR=15,0;AD=26,0;I16=11,15,0,0,936,34652,0,0,1258,66538,0,0,459,10121,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,184:8:0:3,0:5,0:8,0 0,21,191:7:0:2,0:5,0:7,0 17 299 . C <*> 0 . DP=27;ADF=11,0;ADR=15,0;AD=26,0;I16=11,15,0,0,971,36863,0,0,1258,66538,0,0,464,10266,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,193:8:0:3,0:5,0:8,0 0,21,189:7:0:2,0:5,0:7,0 17 300 . A <*> 0 . DP=27;ADF=11,0;ADR=15,0;AD=26,0;I16=11,15,0,0,1001,39455,0,0,1258,66538,0,0,469,10437,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,204:8:0:3,0:5,0:8,0 0,21,210:7:0:2,0:5,0:7,0 17 301 . G <*> 0 . DP=25;ADF=10,0;ADR=14,0;AD=24,0;I16=10,14,0,0,928,36116,0,0,1169,62097,0,0,476,10632,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,255:10:0:5,0:5,0:10,0 0,21,195:7:0:3,0:4,0:7,0 0,21,196:7:0:2,0:5,0:7,0 17 302 . T <*> 0 . DP=25;ADF=10,0;ADR=14,0;AD=24,0;I16=10,14,0,0,879,32885,0,0,1169,62097,0,0,483,10849,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,231:10:0:5,0:5,0:10,0 0,21,172:7:0:3,0:4,0:7,0 0,21,202:7:0:2,0:5,0:7,0 -17 302 . T TA 0 . INDEL;IDV=7;IMF=1;DP=25;ADF=2,8;ADR=4,11;AD=6,19;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.539485,2.46052;VDB=0.241622;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.22749;BQBZ=-1.67542;SCBZ=-0.268121;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 161,0,99:11:6:1,4:4,2:5,6 158,0,14:7:0:1,2:0,4:1,6 201,21,0:7:0:0,2:0,5:0,7 +17 302 . T TA 0 . INDEL;IDV=7;IMF=1;DP=25;ADF=2,8;ADR=4,11;AD=6,19;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.539485,2.46052;VDB=0.241622;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.22749;BQBZ=-1.67542;SCBZ=-0.268121;MQ0F=0 PL:DP:SP:ADF:ADR:AD 161,0,99:11:6:1,4:4,2:5,6 158,0,14:7:0:1,2:0,4:1,6 201,21,0:7:0:0,2:0,5:0,7 17 303 . G <*> 0 . DP=25;ADF=10,0;ADR=15,0;AD=25,0;I16=10,15,0,0,968,37972,0,0,1229,65697,0,0,497,11181,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:5,0:6,0:11,0 0,21,197:7:0:3,0:4,0:7,0 0,21,195:7:0:2,0:5,0:7,0 17 304 . C <*> 0 . DP=27;ADF=11,0;ADR=16,0;AD=27,0;I16=11,16,0,0,991,37005,0,0,1318,70138,0,0,503,11359,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:5,0:6,0:11,0 0,24,206:8:0:4,0:4,0:8,0 0,24,200:8:0:2,0:6,0:8,0 17 305 . C <*> 0 . DP=27;ADF=11,0;ADR=16,0;AD=27,0;I16=11,16,0,0,1057,41761,0,0,1318,70138,0,0,510,11508,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:5,0:6,0:11,0 0,24,213:8:0:4,0:4,0:8,0 0,24,211:8:0:2,0:6,0:8,0 @@ -263,9 +262,9 @@ 17 332 . A <*> 0 . DP=32;ADF=14,0;ADR=18,0;AD=32,0;I16=14,18,0,0,1156,42666,0,0,1649,90897,0,0,560,12178,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:6,0:6,0:12,0 0,27,214:9:0:4,0:5,0:9,0 0,33,255:11:0:4,0:7,0:11,0 17 333 . A <*> 0 . DP=32;ADF=14,0;ADR=18,0;AD=32,0;I16=14,18,0,0,1141,41987,0,0,1649,90897,0,0,558,12064,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:6,0:6,0:12,0 0,27,223:9:0:4,0:5,0:9,0 0,33,255:11:0:4,0:7,0:11,0 17 334 . A <*> 0 . DP=32;ADF=14,0;ADR=18,0;AD=32,0;I16=14,18,0,0,1162,43328,0,0,1649,90897,0,0,556,11986,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:6,0:6,0:12,0 0,27,221:9:0:4,0:5,0:9,0 0,33,255:11:0:4,0:7,0:11,0 -17 335 . A G,<*> 0 . DP=32;ADF=13,1,0;ADR=18,0,0;AD=31,1,0;I16=13,18,1,0,1084,40336,4,16,1589,87297,60,3600,555,11943,0,0;QS=2.98919,0.0108108,0;SGB=-0.556633;RPBZ=-1.67936;MQBZ=0.622171;MQSBZ=-2.25492;BQBZ=-1.68602;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,252,33,252,252:11:0:5,0,0:6,0,0:11,0,0 0,27,219,27,219,219:9:0:4,0,0:5,0,0:9,0,0 0,25,245,33,248,245:12:0:4,1,0:7,0,0:11,1,0 +17 335 . A G,<*> 0 . DP=32;ADF=13,1,0;ADR=18,0,0;AD=31,1,0;I16=13,18,1,0,1084,40336,4,16,1589,87297,60,3600,555,11943,0,0;QS=2.98919,0.0108108,0;SGB=-0.556633;RPBZ=-1.67936;MQBZ=0.622171;MQSBZ=-2.25492;BQBZ=-1.68602;SCBZ=-0.258065;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,252,33,252,252:11:0:5,0,0:6,0,0:11,0,0 0,27,219,27,219,219:9:0:4,0,0:5,0,0:9,0,0 0,25,245,33,248,245:12:0:4,1,0:7,0,0:11,1,0 17 336 . A <*> 0 . DP=32;ADF=14,0;ADR=18,0;AD=32,0;I16=14,18,0,0,1094,39794,0,0,1649,90897,0,0,555,11935,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:5,0:6,0:11,0 0,27,212:9:0:4,0:5,0:9,0 0,36,255:12:0:5,0:7,0:12,0 -17 337 . C A,<*> 0 . DP=32;ADF=14,0,0;ADR=17,1,0;AD=31,1,0;I16=14,17,0,1,1125,42481,5,25,1612,89528,37,1369,536,11590,18,324;QS=2.98113,0.0188679,0;SGB=-0.556633;RPBZ=0.812593;MQBZ=-1.03695;MQSBZ=-2.25492;BQBZ=-1.68353;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255,33,255,255:11:0:5,0,0:6,0,0:11,0,0 0,17,195,24,198,195:9:0:4,0,0:4,1,0:8,1,0 0,36,255,36,255,255:12:0:5,0,0:7,0,0:12,0,0 +17 337 . C A,<*> 0 . DP=32;ADF=14,0,0;ADR=17,1,0;AD=31,1,0;I16=14,17,0,1,1125,42481,5,25,1612,89528,37,1369,536,11590,18,324;QS=2.98113,0.0188679,0;SGB=-0.556633;RPBZ=0.812593;MQBZ=-1.03695;MQSBZ=-2.25492;BQBZ=-1.68353;SCBZ=-0.258065;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255,33,255,255:11:0:5,0,0:6,0,0:11,0,0 0,17,195,24,198,195:9:0:4,0,0:4,1,0:8,1,0 0,36,255,36,255,255:12:0:5,0,0:7,0,0:12,0,0 17 338 . T <*> 0 . DP=30;ADF=14,0;ADR=16,0;AD=30,0;I16=14,16,0,0,1190,47898,0,0,1560,86456,0,0,554,11878,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,255:10:0:5,0:5,0:10,0 0,24,226:8:0:4,0:4,0:8,0 0,36,255:12:0:5,0:7,0:12,0 17 339 . C <*> 0 . DP=31;ADF=14,0;ADR=17,0;AD=31,0;I16=14,17,0,0,1130,43210,0,0,1589,87297,0,0,554,11874,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:5,0:6,0:11,0 0,24,185:8:0:4,0:4,0:8,0 0,36,255:12:0:5,0:7,0:12,0 17 340 . C <*> 0 . DP=31;ADF=14,0;ADR=17,0;AD=31,0;I16=14,17,0,0,1196,47044,0,0,1589,87297,0,0,554,11852,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:5,0:6,0:11,0 0,24,221:8:0:4,0:4,0:8,0 0,36,255:12:0:5,0:7,0:12,0 @@ -283,11 +282,11 @@ 17 352 . A <*> 0 . DP=31;ADF=16,0;ADR=15,0;AD=31,0;I16=16,15,0,0,1162,45664,0,0,1651,92815,0,0,569,13029,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,27,230:9:0:5,0:4,0:9,0 0,33,255:11:0:5,0:6,0:11,0 17 353 . G <*> 0 . DP=29;ADF=15,0;ADR=14,0;AD=29,0;I16=15,14,0,0,1109,43095,0,0,1562,88374,0,0,570,13064,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,255:10:0:5,0:5,0:10,0 0,27,231:9:0:5,0:4,0:9,0 0,30,255:10:0:5,0:5,0:10,0 17 354 . A <*> 0 . DP=28;ADF=14,0;ADR=14,0;AD=28,0;I16=14,14,0,0,1078,42938,0,0,1502,84774,0,0,571,13075,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,225:9:0:4,0:5,0:9,0 0,27,244:9:0:5,0:4,0:9,0 0,30,255:10:0:5,0:5,0:10,0 -17 355 . G T,<*> 0 . DP=28;ADF=14,0,0;ADR=13,1,0;AD=27,1,0;I16=14,13,0,1,1001,37907,41,1681,1442,81174,60,3600,547,12487,25,625;QS=2.875,0.125,0;SGB=-0.556633;RPBZ=0.185772;MQBZ=0.520126;MQSBZ=-1.7696;BQBZ=0.683978;SCBZ=-0.27735;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 14,0,200,38,203,231:9:0:4,0,0:4,1,0:8,1,0 0,27,222,27,222,222:9:0:5,0,0:4,0,0:9,0,0 0,30,255,30,255,255:10:0:5,0,0:5,0,0:10,0,0 +17 355 . G T,<*> 0 . DP=28;ADF=14,0,0;ADR=13,1,0;AD=27,1,0;I16=14,13,0,1,1001,37907,41,1681,1442,81174,60,3600,547,12487,25,625;QS=2.875,0.125,0;SGB=-0.556633;RPBZ=0.185772;MQBZ=0.520126;MQSBZ=-1.7696;BQBZ=0.683978;SCBZ=-0.27735;MQ0F=0 PL:DP:SP:ADF:ADR:AD 14,0,200,38,203,231:9:0:4,0,0:4,1,0:8,1,0 0,27,222,27,222,222:9:0:5,0,0:4,0,0:9,0,0 0,30,255,30,255,255:10:0:5,0,0:5,0,0:10,0,0 17 356 . G <*> 0 . DP=27;ADF=14,0;ADR=13,0;AD=27,0;I16=14,13,0,0,993,37481,0,0,1465,83405,0,0,574,13174,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,27,228:9:0:4,0:5,0:9,0 0,24,201:8:0:5,0:3,0:8,0 0,30,255:10:0:5,0:5,0:10,0 17 357 . C <*> 0 . DP=28;ADF=15,0;ADR=13,0;AD=28,0;I16=15,13,0,0,1026,39496,0,0,1525,87005,0,0,575,13209,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,255:10:0:5,0:5,0:10,0 0,24,205:8:0:5,0:3,0:8,0 0,30,252:10:0:5,0:5,0:10,0 17 358 . A <*> 0 . DP=28;ADF=15,0;ADR=13,0;AD=28,0;I16=15,13,0,0,1050,40518,0,0,1525,87005,0,0,576,13216,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,254:10:0:5,0:5,0:10,0 0,24,197:8:0:5,0:3,0:8,0 0,30,255:10:0:5,0:5,0:10,0 -17 359 . G T,<*> 0 . DP=29;ADF=15,0,0;ADR=13,1,0;AD=28,1,0;I16=15,13,0,1,1085,42761,10,100,1525,87005,60,3600,552,12620,25,625;QS=2.96032,0.0396825,0;SGB=-0.556633;RPBZ=-0.119611;MQBZ=0.456435;MQSBZ=-1.53333;BQBZ=-1.68246;SCBZ=5.2915;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,255,30,255,255:10:0:5,0,0:5,0,0:10,0,0 0,13,178,21,181,180:8:0:5,0,0:2,1,0:7,1,0 0,33,255,33,255,255:11:0:5,0,0:6,0,0:11,0,0 +17 359 . G T,<*> 0 . DP=29;ADF=15,0,0;ADR=13,1,0;AD=28,1,0;I16=15,13,0,1,1085,42761,10,100,1525,87005,60,3600,552,12620,25,625;QS=2.96032,0.0396825,0;SGB=-0.556633;RPBZ=-0.119611;MQBZ=0.456435;MQSBZ=-1.53333;BQBZ=-1.68246;SCBZ=5.2915;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,255,30,255,255:10:0:5,0,0:5,0,0:10,0,0 0,13,178,21,181,180:8:0:5,0,0:2,1,0:7,1,0 0,33,255,33,255,255:11:0:5,0,0:6,0,0:11,0,0 17 360 . A <*> 0 . DP=29;ADF=15,0;ADR=14,0;AD=29,0;I16=15,14,0,0,1111,43259,0,0,1585,90605,0,0,579,13297,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,252:10:0:5,0:5,0:10,0 0,24,220:8:0:5,0:3,0:8,0 0,33,255:11:0:5,0:6,0:11,0 17 361 . A <*> 0 . DP=29;ADF=15,0;ADR=14,0;AD=29,0;I16=15,14,0,0,1116,43442,0,0,1585,90605,0,0,579,13273,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,252:10:0:5,0:5,0:10,0 0,24,219:8:0:5,0:3,0:8,0 0,33,255:11:0:5,0:6,0:11,0 17 362 . A <*> 0 . DP=29;ADF=16,0;ADR=13,0;AD=29,0;I16=16,13,0,0,1104,42700,0,0,1585,90605,0,0,580,13272,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,218:8:0:5,0:3,0:8,0 0,30,255:10:0:5,0:5,0:10,0 @@ -297,13 +296,13 @@ 17 366 . A <*> 0 . DP=29;ADF=16,0;ADR=13,0;AD=29,0;I16=16,13,0,0,1090,41562,0,0,1585,90605,0,0,581,13167,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,211:8:0:5,0:3,0:8,0 0,30,255:10:0:5,0:5,0:10,0 17 367 . T <*> 0 . DP=29;ADF=16,0;ADR=13,0;AD=29,0;I16=16,13,0,0,1055,39149,0,0,1585,90605,0,0,579,13093,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,204:8:0:5,0:3,0:8,0 0,30,255:10:0:5,0:5,0:10,0 17 368 . A <*> 0 . DP=29;ADF=16,0;ADR=13,0;AD=29,0;I16=16,13,0,0,1054,39632,0,0,1585,90605,0,0,576,12998,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,208:8:0:5,0:3,0:8,0 0,30,255:10:0:5,0:5,0:10,0 -17 369 . T G,<*> 0 . DP=28;ADF=16,0,0;ADR=11,1,0;AD=27,1,0;I16=16,11,0,1,1037,40275,6,36,1496,86164,60,3600,548,12256,25,625;QS=2.97683,0.023166,0;SGB=-0.556633;RPBZ=0.12395;MQBZ=0.408248;MQSBZ=-1.37784;BQBZ=-1.68703;SCBZ=5.19615;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,250,30,250,250:10:0:6,0,0:4,0,0:10,0,0 0,15,189,21,192,190:8:0:5,0,0:2,1,0:7,1,0 0,30,255,30,255,255:10:0:5,0,0:5,0,0:10,0,0 +17 369 . T G,<*> 0 . DP=28;ADF=16,0,0;ADR=11,1,0;AD=27,1,0;I16=16,11,0,1,1037,40275,6,36,1496,86164,60,3600,548,12256,25,625;QS=2.97683,0.023166,0;SGB=-0.556633;RPBZ=0.12395;MQBZ=0.408248;MQSBZ=-1.37784;BQBZ=-1.68703;SCBZ=5.19615;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,250,30,250,250:10:0:6,0,0:4,0,0:10,0,0 0,15,189,21,192,190:8:0:5,0,0:2,1,0:7,1,0 0,30,255,30,255,255:10:0:5,0,0:5,0,0:10,0,0 17 370 . C <*> 0 . DP=28;ADF=16,0;ADR=12,0;AD=28,0;I16=16,12,0,0,1045,40219,0,0,1556,89764,0,0,570,12790,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,255:10:0:6,0:4,0:10,0 0,24,201:8:0:5,0:3,0:8,0 0,30,255:10:0:5,0:5,0:10,0 17 371 . T <*> 0 . DP=29;ADF=16,0;ADR=13,0;AD=29,0;I16=16,13,0,0,1155,46591,0,0,1616,93364,0,0,567,12725,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,255:10:0:6,0:4,0:10,0 0,24,227:8:0:5,0:3,0:8,0 0,33,255:11:0:5,0:6,0:11,0 17 372 . C <*> 0 . DP=30;ADF=16,0;ADR=14,0;AD=30,0;I16=16,14,0,0,1139,44019,0,0,1676,96964,0,0,564,12636,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,215:8:0:5,0:3,0:8,0 0,33,255:11:0:5,0:6,0:11,0 17 373 . A <*> 0 . DP=30;ADF=16,0;ADR=14,0;AD=30,0;I16=16,14,0,0,1142,44118,0,0,1676,96964,0,0,561,12525,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,220:8:0:5,0:3,0:8,0 0,33,255:11:0:5,0:6,0:11,0 17 374 . T <*> 0 . DP=30;ADF=16,0;ADR=14,0;AD=30,0;I16=16,14,0,0,1098,41180,0,0,1676,96964,0,0,556,12344,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,33,255:11:0:6,0:5,0:11,0 0,24,221:8:0:5,0:3,0:8,0 0,33,255:11:0:5,0:6,0:11,0 -17 375 . A T,<*> 0 . DP=31;ADF=17,0,0;ADR=13,1,0;AD=30,1,0;I16=17,13,0,1,1138,43798,14,196,1676,96964,60,3600,547,12177,4,16;QS=2.9661,0.0338983,0;SGB=-0.556633;RPBZ=-1.45432;MQBZ=0.3849;MQSBZ=-1.26404;BQBZ=-1.68488;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255,36,255,255:12:0:7,0,0:5,0,0:12,0,0 0,24,218,24,218,218:8:0:5,0,0:3,0,0:8,0,0 0,18,255,30,255,255:11:0:5,0,0:5,1,0:10,1,0 +17 375 . A T,<*> 0 . DP=31;ADF=17,0,0;ADR=13,1,0;AD=30,1,0;I16=17,13,0,1,1138,43798,14,196,1676,96964,60,3600,547,12177,4,16;QS=2.9661,0.0338983,0;SGB=-0.556633;RPBZ=-1.45432;MQBZ=0.3849;MQSBZ=-1.26404;BQBZ=-1.68488;SCBZ=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255,36,255,255:12:0:7,0,0:5,0,0:12,0,0 0,24,218,24,218,218:8:0:5,0,0:3,0,0:8,0,0 0,18,255,30,255,255:11:0:5,0,0:5,1,0:10,1,0 17 376 . G <*> 0 . DP=31;ADF=17,0;ADR=14,0;AD=31,0;I16=17,14,0,0,1131,42581,0,0,1736,100564,0,0,547,12073,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:7,0:5,0:12,0 0,24,220:8:0:5,0:3,0:8,0 0,33,255:11:0:5,0:6,0:11,0 17 377 . T <*> 0 . DP=31;ADF=17,0;ADR=14,0;AD=31,0;I16=17,14,0,0,1116,41750,0,0,1736,100564,0,0,543,11985,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:7,0:5,0:12,0 0,24,211:8:0:5,0:3,0:8,0 0,33,255:11:0:5,0:6,0:11,0 17 378 . T <*> 0 . DP=30;ADF=18,0;ADR=12,0;AD=30,0;I16=18,12,0,0,1098,41066,0,0,1707,99723,0,0,541,11927,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255:13:0:8,0:5,0:13,0 0,21,186:7:0:5,0:2,0:7,0 0,30,255:10:0:5,0:5,0:10,0 @@ -312,7 +311,7 @@ 17 381 . T <*> 0 . DP=29;ADF=18,0;ADR=11,0;AD=29,0;I16=18,11,0,0,1167,47337,0,0,1678,98882,0,0,537,11729,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:8,0:4,0:12,0 0,21,211:7:0:5,0:2,0:7,0 0,30,255:10:0:5,0:5,0:10,0 17 382 . T <*> 0 . DP=29;ADF=18,0;ADR=11,0;AD=29,0;I16=18,11,0,0,1062,40514,0,0,1678,98882,0,0,535,11693,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:8,0:4,0:12,0 0,21,182:7:0:5,0:2,0:7,0 0,30,255:10:0:5,0:5,0:10,0 17 383 . T <*> 0 . DP=29;ADF=18,0;ADR=11,0;AD=29,0;I16=18,11,0,0,1059,39847,0,0,1678,98882,0,0,532,11638,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,36,255:12:0:8,0:4,0:12,0 0,21,172:7:0:5,0:2,0:7,0 0,30,255:10:0:5,0:5,0:10,0 -17 384 . A C,<*> 0 . DP=31;ADF=19,0,0;ADR=11,1,0;AD=30,1,0;I16=19,11,0,1,1077,39885,4,16,1738,102482,60,3600,504,10988,25,625;QS=2.98419,0.0158103,0;SGB=-0.556633;RPBZ=0.615229;MQBZ=0.262613;MQSBZ=-0.333409;BQBZ=-1.68746;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255,39,255,255:13:0:8,0,0:5,0,0:13,0,0 0,15,171,21,174,171:8:0:6,0,0:1,1,0:7,1,0 0,30,255,30,255,255:10:0:5,0,0:5,0,0:10,0,0 +17 384 . A C,<*> 0 . DP=31;ADF=19,0,0;ADR=11,1,0;AD=30,1,0;I16=19,11,0,1,1077,39885,4,16,1738,102482,60,3600,504,10988,25,625;QS=2.98419,0.0158103,0;SGB=-0.556633;RPBZ=0.615229;MQBZ=0.262613;MQSBZ=-0.333409;BQBZ=-1.68746;SCBZ=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255,39,255,255:13:0:8,0,0:5,0,0:13,0,0 0,15,171,21,174,171:8:0:6,0,0:1,1,0:7,1,0 0,30,255,30,255,255:10:0:5,0,0:5,0,0:10,0,0 17 385 . C <*> 0 . DP=31;ADF=19,0;ADR=12,0;AD=31,0;I16=19,12,0,0,1118,41180,0,0,1798,106082,0,0,527,11569,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255:13:0:8,0:5,0:13,0 0,24,186:8:0:6,0:2,0:8,0 0,30,255:10:0:5,0:5,0:10,0 17 386 . T <*> 0 . DP=30;ADF=18,0;ADR=12,0;AD=30,0;I16=18,12,0,0,1158,45592,0,0,1738,102482,0,0,526,11556,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255:13:0:8,0:5,0:13,0 0,21,191:7:0:5,0:2,0:7,0 0,30,255:10:0:5,0:5,0:10,0 17 387 . T <*> 0 . DP=30;ADF=18,0;ADR=12,0;AD=30,0;I16=18,12,0,0,1105,41821,0,0,1738,102482,0,0,525,11573,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255:13:0:8,0:5,0:13,0 0,21,187:7:0:5,0:2,0:7,0 0,30,255:10:0:5,0:5,0:10,0 @@ -329,7 +328,7 @@ 17 398 . A <*> 0 . DP=28;ADF=17,0;ADR=11,0;AD=28,0;I16=17,11,0,0,1025,38361,0,0,1587,92523,0,0,524,11850,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255:13:0:8,0:5,0:13,0 0,15,144:5:0:3,0:2,0:5,0 0,30,255:10:0:6,0:4,0:10,0 17 399 . A <*> 0 . DP=28;ADF=17,0;ADR=11,0;AD=28,0;I16=17,11,0,0,1023,38949,0,0,1587,92523,0,0,526,11900,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255:13:0:8,0:5,0:13,0 0,15,140:5:0:3,0:2,0:5,0 0,30,255:10:0:6,0:4,0:10,0 17 400 . A <*> 0 . DP=29;ADF=17,0;ADR=12,0;AD=29,0;I16=17,12,0,0,1070,40554,0,0,1647,96123,0,0,526,11828,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255:13:0:8,0:5,0:13,0 0,15,159:5:0:3,0:2,0:5,0 0,33,255:11:0:6,0:5,0:11,0 -17 401 . A C,<*> 0 . DP=29;ADF=17,0,0;ADR=11,1,0;AD=28,1,0;I16=17,11,0,1,1063,41001,8,64,1587,92523,60,3600,501,11113,25,625;QS=2.97985,0.0201511,0;SGB=-0.556633;RPBZ=-0.478622;MQBZ=0.339683;MQSBZ=0.29364;BQBZ=-1.68267;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255,39,255,255:13:0:8,0,0:5,0,0:13,0,0 0,15,160,15,160,160:5:0:3,0,0:2,0,0:5,0,0 0,22,255,30,255,255:11:0:6,0,0:4,1,0:10,1,0 +17 401 . A C,<*> 0 . DP=29;ADF=17,0,0;ADR=11,1,0;AD=28,1,0;I16=17,11,0,1,1063,41001,8,64,1587,92523,60,3600,501,11113,25,625;QS=2.97985,0.0201511,0;SGB=-0.556633;RPBZ=-0.478622;MQBZ=0.339683;MQSBZ=0.29364;BQBZ=-1.68267;SCBZ=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255,39,255,255:13:0:8,0,0:5,0,0:13,0,0 0,15,160,15,160,160:5:0:3,0,0:2,0,0:5,0,0 0,22,255,30,255,255:11:0:6,0,0:4,1,0:10,1,0 17 402 . T <*> 0 . DP=29;ADF=17,0;ADR=12,0;AD=29,0;I16=17,12,0,0,1076,40740,0,0,1647,96123,0,0,526,11680,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255:13:0:8,0:5,0:13,0 0,15,149:5:0:3,0:2,0:5,0 0,33,255:11:0:6,0:5,0:11,0 17 403 . T <*> 0 . DP=29;ADF=17,0;ADR=12,0;AD=29,0;I16=17,12,0,0,1085,40985,0,0,1647,96123,0,0,526,11654,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255:13:0:8,0:5,0:13,0 0,15,148:5:0:3,0:2,0:5,0 0,33,255:11:0:6,0:5,0:11,0 17 404 . G <*> 0 . DP=29;ADF=17,0;ADR=12,0;AD=29,0;I16=17,12,0,0,1074,40524,0,0,1647,96123,0,0,525,11609,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255:13:0:8,0:5,0:13,0 0,15,131:5:0:3,0:2,0:5,0 0,33,255:11:0:6,0:5,0:11,0 @@ -340,7 +339,7 @@ 17 409 . T <*> 0 . DP=29;ADF=17,0;ADR=12,0;AD=29,0;I16=17,12,0,0,1100,42734,0,0,1678,98882,0,0,525,11503,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,42,255:14:0:8,0:6,0:14,0 0,12,131:4:0:2,0:2,0:4,0 0,33,255:11:0:7,0:4,0:11,0 17 410 . T <*> 0 . DP=29;ADF=17,0;ADR=12,0;AD=29,0;I16=17,12,0,0,1035,38325,0,0,1678,98882,0,0,524,11432,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,42,255:14:0:8,0:6,0:14,0 0,12,125:4:0:2,0:2,0:4,0 0,33,255:11:0:7,0:4,0:11,0 17 411 . T <*> 0 . DP=29;ADF=17,0;ADR=12,0;AD=29,0;I16=17,12,0,0,1022,37928,0,0,1678,98882,0,0,522,11342,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,42,255:14:0:8,0:6,0:14,0 0,12,111:4:0:2,0:2,0:4,0 0,33,255:11:0:7,0:4,0:11,0 -17 412 . C T,<*> 0 . DP=30;ADF=17,1,0;ADR=12,0,0;AD=29,1,0;I16=17,12,1,0,1094,42458,14,196,1678,98882,60,3600,495,10659,25,625;QS=2.97455,0.0254545,0;SGB=-0.556633;RPBZ=-0.40473;MQBZ=0.267261;MQSBZ=-0.293785;BQBZ=-1.6942;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,255,42,255,255:15:0:8,1,0:6,0,0:14,1,0 0,12,124,12,124,124:4:0:2,0,0:2,0,0:4,0,0 0,33,255,33,255,255:11:0:7,0,0:4,0,0:11,0,0 +17 412 . C T,<*> 0 . DP=30;ADF=17,1,0;ADR=12,0,0;AD=29,1,0;I16=17,12,1,0,1094,42458,14,196,1678,98882,60,3600,495,10659,25,625;QS=2.97455,0.0254545,0;SGB=-0.556633;RPBZ=-0.40473;MQBZ=0.267261;MQSBZ=-0.293785;BQBZ=-1.6942;SCBZ=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,30,255,42,255,255:15:0:8,1,0:6,0,0:14,1,0 0,12,124,12,124,124:4:0:2,0,0:2,0,0:4,0,0 0,33,255,33,255,255:11:0:7,0,0:4,0,0:11,0,0 17 413 . A <*> 0 . DP=31;ADF=18,0;ADR=13,0;AD=31,0;I16=18,13,0,0,1189,45985,0,0,1798,106082,0,0,520,11258,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:9,0:8,0:17,0 0,9,102:3:0:2,0:1,0:3,0 0,33,255:11:0:7,0:4,0:11,0 17 414 . T <*> 0 . DP=30;ADF=18,0;ADR=12,0;AD=30,0;I16=18,12,0,0,1151,44355,0,0,1738,102482,0,0,523,11265,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:9,0:7,0:16,0 0,9,109:3:0:2,0:1,0:3,0 0,33,255:11:0:7,0:4,0:11,0 17 415 . G <*> 0 . DP=30;ADF=18,0;ADR=12,0;AD=30,0;I16=18,12,0,0,1131,43175,0,0,1738,102482,0,0,526,11306,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:9,0:7,0:16,0 0,9,110:3:0:2,0:1,0:3,0 0,33,255:11:0:7,0:4,0:11,0 @@ -365,7 +364,7 @@ 17 434 . T <*> 0 . DP=29;ADF=15,0;ADR=14,0;AD=29,0;I16=15,14,0,0,1036,37654,0,0,1647,96123,0,0,561,12567,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:8,0:8,0:16,0 0,9,98:3:0:2,0:1,0:3,0 0,30,243:10:0:5,0:5,0:10,0 17 435 . A <*> 0 . DP=29;ADF=15,0;ADR=14,0;AD=29,0;I16=15,14,0,0,1035,38091,0,0,1647,96123,0,0,562,12596,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:8,0:8,0:16,0 0,9,103:3:0:2,0:1,0:3,0 0,30,237:10:0:5,0:5,0:10,0 17 436 . T <*> 0 . DP=28;ADF=14,0;ADR=14,0;AD=28,0;I16=14,14,0,0,998,36220,0,0,1587,92523,0,0,564,12654,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:8,0:8,0:16,0 0,9,110:3:0:2,0:1,0:3,0 0,27,223:9:0:4,0:5,0:9,0 -17 437 . T G,<*> 0 . DP=28;ADF=13,1,0;ADR=14,0,0;AD=27,1,0;I16=13,14,1,0,990,36832,6,36,1558,91682,29,841,549,12435,16,256;QS=2.9781,0.0218978,0;SGB=-0.556633;RPBZ=-1.36214;MQBZ=-2.88675;MQSBZ=0.6;BQBZ=-1.67909;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255,48,255,255:16:0:8,0,0:8,0,0:16,0,0 0,9,109,9,109,109:3:0:2,0,0:1,0,0:3,0,0 0,17,200,24,203,201:9:0:3,1,0:5,0,0:8,1,0 +17 437 . T G,<*> 0 . DP=28;ADF=13,1,0;ADR=14,0,0;AD=27,1,0;I16=13,14,1,0,990,36832,6,36,1558,91682,29,841,549,12435,16,256;QS=2.9781,0.0218978,0;SGB=-0.556633;RPBZ=-1.36214;MQBZ=-2.88675;MQSBZ=0.6;BQBZ=-1.67909;SCBZ=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255,48,255,255:16:0:8,0,0:8,0,0:16,0,0 0,9,109,9,109,109:3:0:2,0,0:1,0,0:3,0,0 0,17,200,24,203,201:9:0:3,1,0:5,0,0:8,1,0 17 438 . A <*> 0 . DP=28;ADF=14,0;ADR=14,0;AD=28,0;I16=14,14,0,0,984,35784,0,0,1587,92523,0,0,565,12707,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:8,0:8,0:16,0 0,9,107:3:0:2,0:1,0:3,0 0,27,220:9:0:4,0:5,0:9,0 17 439 . C <*> 0 . DP=28;ADF=14,0;ADR=14,0;AD=28,0;I16=14,14,0,0,1055,40273,0,0,1587,92523,0,0,563,12649,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:8,0:8,0:16,0 0,9,107:3:0:2,0:1,0:3,0 0,27,224:9:0:4,0:5,0:9,0 17 440 . A <*> 0 . DP=28;ADF=14,0;ADR=14,0;AD=28,0;I16=14,14,0,0,1095,43251,0,0,1587,92523,0,0,561,12615,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:8,0:8,0:16,0 0,9,115:3:0:2,0:1,0:3,0 0,27,247:9:0:4,0:5,0:9,0 @@ -393,13 +392,13 @@ 17 462 . G <*> 0 . DP=32;ADF=18,0;ADR=13,0;AD=31,0;I16=18,13,0,0,1169,46001,0,0,1775,103851,0,0,577,12669,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:10,0:7,0:17,0 0,12,131:4:0:3,0:1,0:4,0 0,30,241:10:0:5,0:5,0:10,0 17 463 . G <*> 0 . DP=32;ADF=18,0;ADR=13,0;AD=31,0;I16=18,13,0,0,1095,41573,0,0,1775,103851,0,0,583,12729,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:10,0:7,0:17,0 0,12,126:4:0:3,0:1,0:4,0 0,30,221:10:0:5,0:5,0:10,0 17 464 . A <*> 0 . DP=32;ADF=18,0;ADR=13,0;AD=31,0;I16=18,13,0,0,1100,41724,0,0,1775,103851,0,0,589,12821,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:10,0:7,0:17,0 0,12,148:4:0:3,0:1,0:4,0 0,30,217:10:0:5,0:5,0:10,0 -17 465 . C T,<*> 0 . DP=33;ADF=19,0,0;ADR=12,1,0;AD=31,1,0;I16=19,12,0,1,1173,45601,4,16,1775,103851,60,3600,589,12909,6,36;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.67982;MQBZ=0.321288;MQSBZ=0.341466;BQBZ=-1.68493;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255,51,255,255:17:0:10,0,0:7,0,0:17,0,0 0,15,158,15,158,158:5:0:4,0,0:1,0,0:5,0,0 0,20,224,27,227,224:10:0:5,0,0:4,1,0:9,1,0 +17 465 . C T,<*> 0 . DP=33;ADF=19,0,0;ADR=12,1,0;AD=31,1,0;I16=19,12,0,1,1173,45601,4,16,1775,103851,60,3600,589,12909,6,36;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.67982;MQBZ=0.321288;MQSBZ=0.341466;BQBZ=-1.68493;SCBZ=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255,51,255,255:17:0:10,0,0:7,0,0:17,0,0 0,15,158,15,158,158:5:0:4,0,0:1,0,0:5,0,0 0,20,224,27,227,224:10:0:5,0,0:4,1,0:9,1,0 17 466 . A <*> 0 . DP=34;ADF=20,0;ADR=13,0;AD=33,0;I16=20,13,0,0,1268,49686,0,0,1895,111051,0,0,602,13102,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:11,0:7,0:18,0 0,15,173:5:0:4,0:1,0:5,0 0,30,255:10:0:5,0:5,0:10,0 17 467 . A <*> 0 . DP=34;ADF=20,0;ADR=13,0;AD=33,0;I16=20,13,0,0,1246,48610,0,0,1895,111051,0,0,608,13194,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:11,0:7,0:18,0 0,15,177:5:0:4,0:1,0:5,0 0,30,251:10:0:5,0:5,0:10,0 17 468 . A <*> 0 . DP=35;ADF=21,0;ADR=13,0;AD=34,0;I16=21,13,0,0,1253,48095,0,0,1955,114651,0,0,613,13273,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:12,0:7,0:19,0 0,15,174:5:0:4,0:1,0:5,0 0,30,251:10:0:5,0:5,0:10,0 17 469 . A <*> 0 . DP=35;ADF=21,0;ADR=13,0;AD=34,0;I16=21,13,0,0,1260,49028,0,0,1955,114651,0,0,618,13340,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:12,0:7,0:19,0 0,15,165:5:0:4,0:1,0:5,0 0,30,255:10:0:5,0:5,0:10,0 17 470 . G <*> 0 . DP=35;ADF=21,0;ADR=13,0;AD=34,0;I16=21,13,0,0,1265,48879,0,0,1955,114651,0,0,623,13445,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:12,0:7,0:19,0 0,15,167:5:0:4,0:1,0:5,0 0,30,238:10:0:5,0:5,0:10,0 -17 471 . T G,C,<*> 0 . DP=36;ADF=21,0,0,0;ADR=12,1,1,0;AD=33,1,1,0;I16=21,12,0,2,1220,46380,18,162,1918,113282,97,4969,611,13281,16,256;QS=2.94529,0.0273556,0.0273556,0;VDB=0.96;SGB=0.346553;RPBZ=0.497712;MQBZ=-1.9761;MQSBZ=0.312094;BQBZ=-2.35032;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255,57,255,255,57,255,255,255:19:0:12,0,0,0:7,0,0,0:19,0,0,0 0,15,169,15,169,169,15,169,169,169:5:0:4,0,0,0:1,0,0,0:5,0,0,0 0,19,219,19,221,219,27,222,222,221:11:3:5,0,0,0:4,1,1,0:9,1,1,0 +17 471 . T G,C,<*> 0 . DP=36;ADF=21,0,0,0;ADR=12,1,1,0;AD=33,1,1,0;I16=21,12,0,2,1220,46380,18,162,1918,113282,97,4969,611,13281,16,256;QS=2.94529,0.0273556,0.0273556,0;VDB=0.96;SGB=0.346553;RPBZ=0.497712;MQBZ=-1.9761;MQSBZ=0.312094;BQBZ=-2.35032;SCBZ=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255,57,255,255,57,255,255,255:19:0:12,0,0,0:7,0,0,0:19,0,0,0 0,15,169,15,169,169,15,169,169,169:5:0:4,0,0,0:1,0,0,0:5,0,0,0 0,19,219,19,221,219,27,222,222,221:11:3:5,0,0,0:4,1,1,0:9,1,1,0 17 472 . T <*> 0 . DP=35;ADF=21,0;ADR=13,0;AD=34,0;I16=21,13,0,0,1234,46640,0,0,1955,114651,0,0,633,13665,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:12,0:7,0:19,0 0,15,172:5:0:4,0:1,0:5,0 0,30,241:10:0:5,0:5,0:10,0 17 473 . G <*> 0 . DP=35;ADF=21,0;ADR=13,0;AD=34,0;I16=21,13,0,0,1303,51953,0,0,1955,114651,0,0,638,13780,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:12,0:7,0:19,0 0,15,159:5:0:4,0:1,0:5,0 0,30,250:10:0:5,0:5,0:10,0 17 474 . G <*> 0 . DP=36;ADF=22,0;ADR=13,0;AD=35,0;I16=22,13,0,0,1279,49235,0,0,2015,118251,0,0,642,13884,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:12,0:7,0:19,0 0,15,146:5:0:4,0:1,0:5,0 0,33,255:11:0:6,0:5,0:11,0 @@ -416,7 +415,7 @@ 17 485 . G <*> 0 . DP=35;ADF=23,0;ADR=12,0;AD=35,0;I16=23,12,0,0,1329,51411,0,0,2015,118251,0,0,669,14931,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:12,0:6,0:18,0 0,18,160:6:0:5,0:1,0:6,0 0,33,255:11:0:6,0:5,0:11,0 17 486 . A <*> 0 . DP=34;ADF=22,0;ADR=12,0;AD=34,0;I16=22,12,0,0,1313,51667,0,0,1955,114651,0,0,671,14989,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:11,0:6,0:17,0 0,18,173:6:0:5,0:1,0:6,0 0,33,255:11:0:6,0:5,0:11,0 17 487 . G <*> 0 . DP=34;ADF=22,0;ADR=12,0;AD=34,0;I16=22,12,0,0,1300,50304,0,0,1955,114651,0,0,672,15030,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:11,0:6,0:17,0 0,18,169:6:0:5,0:1,0:6,0 0,33,255:11:0:6,0:5,0:11,0 -17 488 . A G,<*> 0 . DP=35;ADF=22,1,0;ADR=12,0,0;AD=34,1,0;I16=22,12,1,0,1278,48412,4,16,1986,117410,29,841,646,14380,25,625;QS=2.98947,0.0105263,0;SGB=-0.556633;RPBZ=0.594463;MQBZ=-3.36505;MQSBZ=0.10737;BQBZ=-1.69552;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255,54,255,255:18:0:12,0,0:6,0,0:18,0,0 0,18,177,18,177,177:6:0:5,0,0:1,0,0:6,0,0 0,23,255,30,255,255:11:0:5,1,0:5,0,0:10,1,0 +17 488 . A G,<*> 0 . DP=35;ADF=22,1,0;ADR=12,0,0;AD=34,1,0;I16=22,12,1,0,1278,48412,4,16,1986,117410,29,841,646,14380,25,625;QS=2.98947,0.0105263,0;SGB=-0.556633;RPBZ=0.594463;MQBZ=-3.36505;MQSBZ=0.10737;BQBZ=-1.69552;SCBZ=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255,54,255,255:18:0:12,0,0:6,0,0:18,0,0 0,18,177,18,177,177:6:0:5,0,0:1,0,0:6,0,0 0,23,255,30,255,255:11:0:5,1,0:5,0,0:10,1,0 17 489 . A <*> 0 . DP=35;ADF=23,0;ADR=12,0;AD=35,0;I16=23,12,0,0,1264,46916,0,0,2015,118251,0,0,671,15015,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:12,0:6,0:18,0 0,18,175:6:0:5,0:1,0:6,0 0,33,255:11:0:6,0:5,0:11,0 17 490 . A <*> 0 . DP=36;ADF=24,0;ADR=12,0;AD=36,0;I16=24,12,0,0,1332,50280,0,0,2075,121851,0,0,671,15061,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:12,0:6,0:18,0 0,21,188:7:0:6,0:1,0:7,0 0,33,255:11:0:6,0:5,0:11,0 17 491 . T <*> 0 . DP=36;ADF=24,0;ADR=12,0;AD=36,0;I16=24,12,0,0,1284,46802,0,0,2075,121851,0,0,671,15093,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:12,0:6,0:18,0 0,21,178:7:0:6,0:1,0:7,0 0,33,255:11:0:6,0:5,0:11,0 @@ -440,9 +439,9 @@ 17 509 . C <*> 0 . DP=34;ADF=24,0;ADR=10,0;AD=34,0;I16=24,10,0,0,1272,48272,0,0,1986,117410,0,0,640,14430,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:13,0:5,0:18,0 0,21,186:7:0:6,0:1,0:7,0 0,27,241:9:0:5,0:4,0:9,0 17 510 . A <*> 0 . DP=34;ADF=23,0;ADR=11,0;AD=34,0;I16=23,11,0,0,1211,44827,0,0,1986,117410,0,0,638,14398,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:13,0:6,0:19,0 0,21,187:7:0:6,0:1,0:7,0 0,24,221:8:0:4,0:4,0:8,0 17 511 . A <*> 0 . DP=34;ADF=23,0;ADR=11,0;AD=34,0;I16=23,11,0,0,1238,46516,0,0,1986,117410,0,0,637,14395,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:13,0:6,0:19,0 0,21,195:7:0:6,0:1,0:7,0 0,24,233:8:0:4,0:4,0:8,0 -17 512 . A C,<*> 0 . DP=33;ADF=22,0,0;ADR=10,1,0;AD=32,1,0;I16=22,10,0,1,1133,41513,13,169,1866,110210,60,3600,628,14340,9,81;QS=2.97766,0.0223368,0;SGB=-0.556633;RPBZ=-1.47079;MQBZ=0.253876;MQSBZ=-0.461593;BQBZ=-1.68442;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255,51,255,255:18:0:12,0,0:5,1,0:17,1,0 0,21,183,21,183,183:7:0:6,0,0:1,0,0:7,0,0 0,24,231,24,231,231:8:0:4,0,0:4,0,0:8,0,0 -17 513 . A T,<*> 0 . DP=32;ADF=21,1,0;ADR=10,0,0;AD=31,1,0;I16=21,10,1,0,1125,42283,12,144,1806,106610,60,3600,623,14249,15,225;QS=2.97966,0.020339,0;SGB=-0.556633;RPBZ=-1.24609;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.57376;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,37,255,48,255,255:17:0:11,1,0:5,0,0:16,1,0 0,21,177,21,177,177:7:0:6,0,0:1,0,0:7,0,0 0,24,233,24,233,233:8:0:4,0,0:4,0,0:8,0,0 -17 514 . A T,<*> 0 . DP=32;ADF=22,0,0;ADR=9,1,0;AD=31,1,0;I16=22,9,0,1,1086,40204,16,256,1806,106610,60,3600,627,14381,11,121;QS=2.97127,0.0287253,0;SGB=-0.556633;RPBZ=-1.4628;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.46657;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,34,255,48,255,255:17:0:12,0,0:4,1,0:16,1,0 0,21,172,21,172,172:7:0:6,0,0:1,0,0:7,0,0 0,24,235,24,235,235:8:0:4,0,0:4,0,0:8,0,0 +17 512 . A C,<*> 0 . DP=33;ADF=22,0,0;ADR=10,1,0;AD=32,1,0;I16=22,10,0,1,1133,41513,13,169,1866,110210,60,3600,628,14340,9,81;QS=2.97766,0.0223368,0;SGB=-0.556633;RPBZ=-1.47079;MQBZ=0.253876;MQSBZ=-0.461593;BQBZ=-1.68442;SCBZ=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,39,255,51,255,255:18:0:12,0,0:5,1,0:17,1,0 0,21,183,21,183,183:7:0:6,0,0:1,0,0:7,0,0 0,24,231,24,231,231:8:0:4,0,0:4,0,0:8,0,0 +17 513 . A T,<*> 0 . DP=32;ADF=21,1,0;ADR=10,0,0;AD=31,1,0;I16=21,10,1,0,1125,42283,12,144,1806,106610,60,3600,623,14249,15,225;QS=2.97966,0.020339,0;SGB=-0.556633;RPBZ=-1.24609;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.57376;SCBZ=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,37,255,48,255,255:17:0:11,1,0:5,0,0:16,1,0 0,21,177,21,177,177:7:0:6,0,0:1,0,0:7,0,0 0,24,233,24,233,233:8:0:4,0,0:4,0,0:8,0,0 +17 514 . A T,<*> 0 . DP=32;ADF=22,0,0;ADR=9,1,0;AD=31,1,0;I16=22,9,0,1,1086,40204,16,256,1806,106610,60,3600,627,14381,11,121;QS=2.97127,0.0287253,0;SGB=-0.556633;RPBZ=-1.4628;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.46657;SCBZ=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,34,255,48,255,255:17:0:12,0,0:4,1,0:16,1,0 0,21,172,21,172,172:7:0:6,0,0:1,0,0:7,0,0 0,24,235,24,235,235:8:0:4,0,0:4,0,0:8,0,0 17 515 . C <*> 0 . DP=32;ADF=22,0;ADR=10,0;AD=32,0;I16=22,10,0,0,1050,37704,0,0,1866,110210,0,0,638,14554,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:12,0:5,0:17,0 0,21,169:7:0:6,0:1,0:7,0 0,24,211:8:0:4,0:4,0:8,0 17 516 . C <*> 0 . DP=32;ADF=22,0;ADR=10,0;AD=32,0;I16=22,10,0,0,1109,40651,0,0,1866,110210,0,0,637,14579,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:12,0:5,0:17,0 0,21,187:7:0:6,0:1,0:7,0 0,24,215:8:0:4,0:4,0:8,0 17 517 . T <*> 0 . DP=33;ADF=23,0;ADR=10,0;AD=33,0;I16=23,10,0,0,1269,49995,0,0,1926,113810,0,0,636,14626,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:13,0:5,0:18,0 0,21,201:7:0:6,0:1,0:7,0 0,24,242:8:0:4,0:4,0:8,0 @@ -451,7 +450,7 @@ 17 520 . T <*> 0 . DP=36;ADF=25,0;ADR=11,0;AD=36,0;I16=25,11,0,0,1243,45051,0,0,2106,124610,0,0,638,14818,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,63,255:21:0:15,0:6,0:21,0 0,21,180:7:0:6,0:1,0:7,0 0,24,223:8:0:4,0:4,0:8,0 17 521 . C <*> 0 . DP=34;ADF=25,0;ADR=9,0;AD=34,0;I16=25,9,0,0,1281,49527,0,0,1986,117410,0,0,641,14875,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,60,255:20:0:15,0:5,0:20,0 0,21,191:7:0:6,0:1,0:7,0 0,21,204:7:0:4,0:3,0:7,0 17 522 . A <*> 0 . DP=32;ADF=24,0;ADR=8,0;AD=32,0;I16=24,8,0,0,1158,43228,0,0,1897,112969,0,0,646,14960,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,60,255:20:0:15,0:5,0:20,0 0,21,185:7:0:6,0:1,0:7,0 0,15,170:5:0:3,0:2,0:5,0 -17 523 . T G,<*> 0 . DP=32;ADF=23,1,0;ADR=8,0,0;AD=31,1,0;I16=23,8,1,0,1184,45708,15,225,1837,109369,60,3600,626,14446,25,625;QS=2.9794,0.0206044,0;SGB=-0.556633;RPBZ=1.13742;MQBZ=0.179605;MQSBZ=-1.73205;BQBZ=-1.68805;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,44,255,57,255,255:20:0:14,1,0:5,0,0:19,1,0 0,21,191,21,191,191:7:0:6,0,0:1,0,0:7,0,0 0,15,166,15,166,166:5:0:3,0,0:2,0,0:5,0,0 +17 523 . T G,<*> 0 . DP=32;ADF=23,1,0;ADR=8,0,0;AD=31,1,0;I16=23,8,1,0,1184,45708,15,225,1837,109369,60,3600,626,14446,25,625;QS=2.9794,0.0206044,0;SGB=-0.556633;RPBZ=1.13742;MQBZ=0.179605;MQSBZ=-1.73205;BQBZ=-1.68805;SCBZ=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,44,255,57,255,255:20:0:14,1,0:5,0,0:19,1,0 0,21,191,21,191,191:7:0:6,0,0:1,0,0:7,0,0 0,15,166,15,166,166:5:0:3,0,0:2,0,0:5,0,0 17 524 . T <*> 0 . DP=32;ADF=24,0;ADR=8,0;AD=32,0;I16=24,8,0,0,1096,39618,0,0,1897,112969,0,0,654,15108,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,60,255:20:0:15,0:5,0:20,0 0,21,194:7:0:6,0:1,0:7,0 0,15,150:5:0:3,0:2,0:5,0 17 525 . G <*> 0 . DP=32;ADF=24,0;ADR=8,0;AD=32,0;I16=24,8,0,0,1188,45718,0,0,1897,112969,0,0,656,15120,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,60,255:20:0:15,0:5,0:20,0 0,21,188:7:0:6,0:1,0:7,0 0,15,133:5:0:3,0:2,0:5,0 17 526 . C <*> 0 . DP=32;ADF=24,0;ADR=8,0;AD=32,0;I16=24,8,0,0,1154,44014,0,0,1897,112969,0,0,658,15156,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,60,255:20:0:15,0:5,0:20,0 0,21,185:7:0:6,0:1,0:7,0 0,15,137:5:0:3,0:2,0:5,0 @@ -463,7 +462,7 @@ 17 532 . T <*> 0 . DP=32;ADF=25,0;ADR=7,0;AD=32,0;I16=25,7,0,0,1161,43607,0,0,1897,112969,0,0,649,14477,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:15,0:4,0:19,0 0,21,181:7:0:6,0:1,0:7,0 0,18,192:6:0:4,0:2,0:6,0 17 533 . C <*> 0 . DP=32;ADF=25,0;ADR=7,0;AD=32,0;I16=25,7,0,0,1154,44084,0,0,1897,112969,0,0,644,14274,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:15,0:4,0:19,0 0,21,178:7:0:6,0:1,0:7,0 0,18,180:6:0:4,0:2,0:6,0 17 534 . T <*> 0 . DP=31;ADF=24,0;ADR=7,0;AD=31,0;I16=24,7,0,0,1222,49526,0,0,1837,109369,0,0,640,14104,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:14,0:4,0:18,0 0,21,205:7:0:6,0:1,0:7,0 0,18,205:6:0:4,0:2,0:6,0 -17 535 . A G,<*> 0 . DP=31;ADF=24,0,0;ADR=6,1,0;AD=30,1,0;I16=24,6,0,1,1080,39870,8,64,1777,105769,60,3600,611,13341,25,625;QS=2.98623,0.0137694,0;SGB=-0.556633;RPBZ=-0.894788;MQBZ=0.182574;MQSBZ=-1.85164;BQBZ=-1.6854;SCBZ=0;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,41,255,51,255,255:18:0:14,0,0:3,1,0:17,1,0 0,21,194,21,194,194:7:0:6,0,0:1,0,0:7,0,0 0,18,189,18,189,189:6:0:4,0,0:2,0,0:6,0,0 +17 535 . A G,<*> 0 . DP=31;ADF=24,0,0;ADR=6,1,0;AD=30,1,0;I16=24,6,0,1,1080,39870,8,64,1777,105769,60,3600,611,13341,25,625;QS=2.98623,0.0137694,0;SGB=-0.556633;RPBZ=-0.894788;MQBZ=0.182574;MQSBZ=-1.85164;BQBZ=-1.6854;SCBZ=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,41,255,51,255,255:18:0:14,0,0:3,1,0:17,1,0 0,21,194,21,194,194:7:0:6,0,0:1,0,0:7,0,0 0,18,189,18,189,189:6:0:4,0,0:2,0,0:6,0,0 17 536 . C <*> 0 . DP=31;ADF=24,0;ADR=7,0;AD=31,0;I16=24,7,0,0,1095,40551,0,0,1837,109369,0,0,631,13809,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:14,0:4,0:18,0 0,21,184:7:0:6,0:1,0:7,0 0,18,157:6:0:4,0:2,0:6,0 17 537 . C <*> 0 . DP=31;ADF=24,0;ADR=7,0;AD=31,0;I16=24,7,0,0,1049,38677,0,0,1837,109369,0,0,626,13682,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:14,0:4,0:18,0 0,21,172:7:0:6,0:1,0:7,0 0,18,183:6:0:4,0:2,0:6,0 17 538 . A <*> 0 . DP=31;ADF=24,0;ADR=7,0;AD=31,0;I16=24,7,0,0,1138,42478,0,0,1837,109369,0,0,620,13536,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:14,0:4,0:18,0 0,21,189:7:0:6,0:1,0:7,0 0,18,181:6:0:4,0:2,0:6,0 @@ -476,8 +475,8 @@ 17 545 . A <*> 0 . DP=33;ADF=25,0;ADR=8,0;AD=33,0;I16=25,8,0,0,1197,44795,0,0,1926,113810,0,0,587,12951,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:14,0:5,0:19,0 0,24,196:8:0:7,0:1,0:8,0 0,18,184:6:0:4,0:2,0:6,0 17 546 . A <*> 0 . DP=32;ADF=24,0;ADR=8,0;AD=32,0;I16=24,8,0,0,1136,41758,0,0,1866,110210,0,0,580,12802,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:14,0:5,0:19,0 0,21,166:7:0:6,0:1,0:7,0 0,18,193:6:0:4,0:2,0:6,0 17 547 . A <*> 0 . DP=32;ADF=24,0;ADR=8,0;AD=32,0;I16=24,8,0,0,1159,43539,0,0,1866,110210,0,0,572,12634,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,57,255:19:0:14,0:5,0:19,0 0,21,180:7:0:6,0:1,0:7,0 0,18,195:6:0:4,0:2,0:6,0 -17 548 . A C,<*> 0 . DP=33;ADF=23,1,0;ADR=9,0,0;AD=32,1,0;I16=23,9,1,0,1153,42673,9,81,1866,110210,60,3600,561,12489,3,9;QS=2.98607,0.0139319,0;SGB=-0.556633;RPBZ=1.57584;MQBZ=0.253876;MQSBZ=-2.34521;BQBZ=-1.68939;SCBZ=3.80814;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,44,255,54,255,255:19:0:13,1,0:5,0,0:18,1,0 0,21,181,21,181,181:7:0:6,0,0:1,0,0:7,0,0 0,21,211,21,211,211:7:0:4,0,0:3,0,0:7,0,0 -17 549 . T G,<*> 0 . DP=32;ADF=23,0,0;ADR=8,1,0;AD=31,1,0;I16=23,8,0,1,1135,42143,20,400,1806,106610,60,3600,532,11720,25,625;QS=2.96918,0.0308166,0;SGB=-0.556633;RPBZ=-0.487556;MQBZ=0.258065;MQSBZ=-2.29695;BQBZ=-1.68602;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,34,255,51,255,255:18:0:13,0,0:4,1,0:17,1,0 0,21,168,21,168,168:7:0:6,0,0:1,0,0:7,0,0 0,21,208,21,208,208:7:0:4,0,0:3,0,0:7,0,0 +17 548 . A C,<*> 0 . DP=33;ADF=23,1,0;ADR=9,0,0;AD=32,1,0;I16=23,9,1,0,1153,42673,9,81,1866,110210,60,3600,561,12489,3,9;QS=2.98607,0.0139319,0;SGB=-0.556633;RPBZ=1.57584;MQBZ=0.253876;MQSBZ=-2.34521;BQBZ=-1.68939;SCBZ=3.80814;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,44,255,54,255,255:19:0:13,1,0:5,0,0:18,1,0 0,21,181,21,181,181:7:0:6,0,0:1,0,0:7,0,0 0,21,211,21,211,211:7:0:4,0,0:3,0,0:7,0,0 +17 549 . T G,<*> 0 . DP=32;ADF=23,0,0;ADR=8,1,0;AD=31,1,0;I16=23,8,0,1,1135,42143,20,400,1806,106610,60,3600,532,11720,25,625;QS=2.96918,0.0308166,0;SGB=-0.556633;RPBZ=-0.487556;MQBZ=0.258065;MQSBZ=-2.29695;BQBZ=-1.68602;SCBZ=-0.258065;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,34,255,51,255,255:18:0:13,0,0:4,1,0:17,1,0 0,21,168,21,168,168:7:0:6,0,0:1,0,0:7,0,0 0,21,208,21,208,208:7:0:4,0,0:3,0,0:7,0,0 17 550 . T <*> 0 . DP=32;ADF=23,0;ADR=9,0;AD=32,0;I16=23,9,0,0,1056,37314,0,0,1866,110210,0,0,549,12177,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:13,0:5,0:18,0 0,21,150:7:0:6,0:1,0:7,0 0,21,220:7:0:4,0:3,0:7,0 17 551 . G <*> 0 . DP=31;ADF=22,0;ADR=9,0;AD=31,0;I16=22,9,0,0,1121,41639,0,0,1806,106610,0,0,541,12045,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:12,0:5,0:17,0 0,21,172:7:0:6,0:1,0:7,0 0,21,208:7:0:4,0:3,0:7,0 17 552 . C <*> 0 . DP=30;ADF=21,0;ADR=9,0;AD=30,0;I16=21,9,0,0,1093,41365,0,0,1746,103010,0,0,535,11947,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:11,0:5,0:16,0 0,21,167:7:0:6,0:1,0:7,0 0,21,208:7:0:4,0:3,0:7,0 @@ -487,14 +486,14 @@ 17 556 . C <*> 0 . DP=29;ADF=20,0;ADR=9,0;AD=29,0;I16=20,9,0,0,1055,39195,0,0,1709,101641,0,0,509,11219,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:11,0:6,0:17,0 0,18,158:6:0:5,0:1,0:6,0 0,18,186:6:0:4,0:2,0:6,0 17 557 . A <*> 0 . DP=27;ADF=18,0;ADR=9,0;AD=27,0;I16=18,9,0,0,987,36749,0,0,1589,94441,0,0,506,11074,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,45,255:15:0:9,0:6,0:15,0 0,18,157:6:0:5,0:1,0:6,0 0,18,186:6:0:4,0:2,0:6,0 17 558 . A <*> 0 . DP=27;ADF=18,0;ADR=9,0;AD=27,0;I16=18,9,0,0,956,35872,0,0,1589,94441,0,0,502,10906,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,45,255:15:0:9,0:6,0:15,0 0,18,153:6:0:5,0:1,0:6,0 0,18,177:6:0:4,0:2,0:6,0 -17 559 . C A,<*> 0 . DP=27;ADF=18,0,0;ADR=8,1,0;AD=26,1,0;I16=18,8,0,1,915,33775,14,196,1560,93600,29,841,473,10141,25,625;QS=2.92708,0.0729167,0;SGB=-0.556633;RPBZ=-1.02726;MQBZ=-5.09902;MQSBZ=-1.41421;BQBZ=-1.54776;SCBZ=5.09902;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,45,255,45,255,255:15:0:9,0,0:6,0,0:15,0,0 0,4,116,15,119,123:6:0:5,0,0:0,1,0:5,1,0 0,18,169,18,169,169:6:0:4,0,0:2,0,0:6,0,0 +17 559 . C A,<*> 0 . DP=27;ADF=18,0,0;ADR=8,1,0;AD=26,1,0;I16=18,8,0,1,915,33775,14,196,1560,93600,29,841,473,10141,25,625;QS=2.92708,0.0729167,0;SGB=-0.556633;RPBZ=-1.02726;MQBZ=-5.09902;MQSBZ=-1.41421;BQBZ=-1.54776;SCBZ=5.09902;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,45,255,45,255,255:15:0:9,0,0:6,0,0:15,0,0 0,4,116,15,119,123:6:0:5,0,0:0,1,0:5,1,0 0,18,169,18,169,169:6:0:4,0,0:2,0,0:6,0,0 17 560 . C <*> 0 . DP=28;ADF=19,0;ADR=9,0;AD=28,0;I16=19,9,0,0,992,36552,0,0,1649,98041,0,0,494,10654,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,45,255:15:0:9,0:6,0:15,0 0,18,160:6:0:5,0:1,0:6,0 0,21,181:7:0:5,0:2,0:7,0 17 561 . A <*> 0 . DP=28;ADF=19,0;ADR=9,0;AD=28,0;I16=19,9,0,0,973,35555,0,0,1649,98041,0,0,491,10571,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,45,255:15:0:9,0:6,0:15,0 0,18,158:6:0:5,0:1,0:6,0 0,21,194:7:0:5,0:2,0:7,0 17 562 . C <*> 0 . DP=28;ADF=19,0;ADR=9,0;AD=28,0;I16=19,9,0,0,1014,38392,0,0,1649,98041,0,0,488,10518,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,45,255:15:0:9,0:6,0:15,0 0,18,153:6:0:5,0:1,0:6,0 0,21,187:7:0:5,0:2,0:7,0 17 563 . A <*> 0 . DP=27;ADF=18,0;ADR=9,0;AD=27,0;I16=18,9,0,0,903,32513,0,0,1589,94441,0,0,485,10445,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,45,255:15:0:9,0:6,0:15,0 0,15,149:5:0:4,0:1,0:5,0 0,21,179:7:0:5,0:2,0:7,0 17 564 . C <*> 0 . DP=27;ADF=18,0;ADR=9,0;AD=27,0;I16=18,9,0,0,859,28747,0,0,1589,94441,0,0,482,10402,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,45,255:15:0:9,0:6,0:15,0 0,15,121:5:0:4,0:1,0:5,0 0,21,182:7:0:5,0:2,0:7,0 17 565 . G <*> 0 . DP=30;ADF=18,0;ADR=12,0;AD=30,0;I16=18,12,0,0,842,27104,0,0,1769,105241,0,0,479,10389,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:9,0:8,0:17,0 0,18,100:6:0:4,0:2,0:6,0 0,21,154:7:0:5,0:2,0:7,0 -17 566 . C A,<*> 0 . DP=29;ADF=16,1,0;ADR=12,0,0;AD=28,1,0;I16=16,12,1,0,920,33998,9,81,1649,98041,60,3600,454,9734,25,625;QS=2.98321,0.016791,0;SGB=-0.556633;RPBZ=0.239193;MQBZ=0.188982;MQSBZ=-1.19024;BQBZ=-1.43942;SCBZ=-0.188982;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,38,255,48,255,255:17:0:8,1,0:8,0,0:16,1,0 0,15,155,15,155,155:5:0:3,0,0:2,0,0:5,0,0 0,21,170,21,170,170:7:0:5,0,0:2,0,0:7,0,0 +17 566 . C A,<*> 0 . DP=29;ADF=16,1,0;ADR=12,0,0;AD=28,1,0;I16=16,12,1,0,920,33998,9,81,1649,98041,60,3600,454,9734,25,625;QS=2.98321,0.016791,0;SGB=-0.556633;RPBZ=0.239193;MQBZ=0.188982;MQSBZ=-1.19024;BQBZ=-1.43942;SCBZ=-0.188982;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,38,255,48,255,255:17:0:8,1,0:8,0,0:16,1,0 0,15,155,15,155,155:5:0:3,0,0:2,0,0:5,0,0 0,21,170,21,170,170:7:0:5,0,0:2,0,0:7,0,0 17 567 . C <*> 0 . DP=30;ADF=17,0;ADR=13,0;AD=30,0;I16=17,13,0,0,956,34312,0,0,1769,105241,0,0,496,10638,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:9,0:8,0:17,0 0,18,156:6:0:3,0:3,0:6,0 0,21,194:7:0:5,0:2,0:7,0 17 568 . C <*> 0 . DP=29;ADF=16,0;ADR=13,0;AD=29,0;I16=16,13,0,0,1060,40304,0,0,1709,101641,0,0,497,10663,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:8,0:8,0:16,0 0,18,179:6:0:3,0:3,0:6,0 0,21,193:7:0:5,0:2,0:7,0 17 569 . T <*> 0 . DP=30;ADF=16,0;ADR=13,0;AD=29,0;I16=16,13,0,0,1061,41321,0,0,1709,101641,0,0,497,10671,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:8,0:8,0:16,0 0,18,190:6:0:3,0:3,0:6,0 0,21,213:7:0:5,0:2,0:7,0 @@ -502,15 +501,15 @@ 17 571 . C <*> 0 . DP=31;ADF=17,0;ADR=13,0;AD=30,0;I16=17,13,0,0,1069,40739,0,0,1769,105241,0,0,497,10783,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:9,0:8,0:17,0 0,18,159:6:0:3,0:3,0:6,0 0,21,193:7:0:5,0:2,0:7,0 17 572 . A <*> 0 . DP=31;ADF=18,0;ADR=12,0;AD=30,0;I16=18,12,0,0,1092,41268,0,0,1769,105241,0,0,499,10887,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:9,0:8,0:17,0 0,21,204:7:0:4,0:3,0:7,0 0,18,175:6:0:5,0:1,0:6,0 17 573 . A <*> 0 . DP=31;ADF=18,0;ADR=12,0;AD=30,0;I16=18,12,0,0,1060,38698,0,0,1769,105241,0,0,501,10975,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:9,0:8,0:17,0 0,21,201:7:0:4,0:3,0:7,0 0,18,178:6:0:5,0:1,0:6,0 -17 574 . C A,<*> 0 . DP=31;ADF=18,0,0;ADR=11,1,0;AD=29,1,0;I16=18,11,0,1,1088,41328,15,225,1740,104400,29,841,478,10422,25,625;QS=2.94071,0.0592885,0;SGB=-0.556633;RPBZ=-0.173514;MQBZ=-5.38516;MQSBZ=-1.22474;BQBZ=-1.68578;SCBZ=3.60588;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255,48,255,255:16:0:8,0,0:8,0,0:16,0,0 0,9,170,21,173,177:8:0:5,0,0:2,1,0:7,1,0 0,18,173,18,173,173:6:0:5,0,0:1,0,0:6,0,0 -17 575 . T C,<*> 0 . DP=30;ADF=17,0,0;ADR=11,1,0;AD=28,1,0;I16=17,11,0,1,1048,41548,9,81,1680,100800,29,841,480,10426,25,625;QS=2.96786,0.0321429,0;SGB=-0.556633;RPBZ=-0.119685;MQBZ=-5.2915;MQSBZ=-1.19024;BQBZ=-1.68121;SCBZ=3.53589;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255,48,255,255:16:0:8,0,0:8,0,0:16,0,0 0,13,200,21,203,202:8:0:5,0,0:2,1,0:7,1,0 0,15,163,15,163,163:5:0:4,0,0:1,0,0:5,0,0 +17 574 . C A,<*> 0 . DP=31;ADF=18,0,0;ADR=11,1,0;AD=29,1,0;I16=18,11,0,1,1088,41328,15,225,1740,104400,29,841,478,10422,25,625;QS=2.94071,0.0592885,0;SGB=-0.556633;RPBZ=-0.173514;MQBZ=-5.38516;MQSBZ=-1.22474;BQBZ=-1.68578;SCBZ=3.60588;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255,48,255,255:16:0:8,0,0:8,0,0:16,0,0 0,9,170,21,173,177:8:0:5,0,0:2,1,0:7,1,0 0,18,173,18,173,173:6:0:5,0,0:1,0,0:6,0,0 +17 575 . T C,<*> 0 . DP=30;ADF=17,0,0;ADR=11,1,0;AD=28,1,0;I16=17,11,0,1,1048,41548,9,81,1680,100800,29,841,480,10426,25,625;QS=2.96786,0.0321429,0;SGB=-0.556633;RPBZ=-0.119685;MQBZ=-5.2915;MQSBZ=-1.19024;BQBZ=-1.68121;SCBZ=3.53589;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255,48,255,255:16:0:8,0,0:8,0,0:16,0,0 0,13,200,21,203,202:8:0:5,0,0:2,1,0:7,1,0 0,15,163,15,163,163:5:0:4,0,0:1,0,0:5,0,0 17 576 . G <*> 0 . DP=30;ADF=17,0;ADR=12,0;AD=29,0;I16=17,12,0,0,1043,39581,0,0,1709,101641,0,0,507,11087,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:8,0:8,0:16,0 0,24,208:8:0:5,0:3,0:8,0 0,15,151:5:0:4,0:1,0:5,0 17 577 . G <*> 0 . DP=30;ADF=17,0;ADR=12,0;AD=29,0;I16=17,12,0,0,997,37255,0,0,1709,101641,0,0,509,11155,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:8,0:8,0:16,0 0,24,204:8:0:5,0:3,0:8,0 0,15,146:5:0:4,0:1,0:5,0 17 578 . G <*> 0 . DP=29;ADF=16,0;ADR=13,0;AD=29,0;I16=16,13,0,0,975,34803,0,0,1709,101641,0,0,520,11286,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,48,255:16:0:7,0:9,0:16,0 0,24,198:8:0:5,0:3,0:8,0 0,15,151:5:0:4,0:1,0:5,0 17 579 . G <*> 0 . DP=30;ADF=16,0;ADR=14,0;AD=30,0;I16=16,14,0,0,1038,38820,0,0,1769,105241,0,0,523,11335,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:8,0:9,0:17,0 0,24,224:8:0:4,0:4,0:8,0 0,15,144:5:0:4,0:1,0:5,0 -17 580 . A C,<*> 0 . DP=30;ADF=15,1,0;ADR=14,0,0;AD=29,1,0;I16=15,14,1,0,1060,39178,16,256,1709,101641,60,3600,510,11078,17,289;QS=2.97338,0.0266223,0;SGB=-0.556633;RPBZ=1.32953;MQBZ=0.185695;MQSBZ=-1.06904;BQBZ=-1.69093;SCBZ=-0.267102;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,34,255,48,255,255:17:0:7,1,0:9,0,0:16,1,0 0,24,221,24,221,221:8:0:4,0,0:4,0,0:8,0,0 0,15,155,15,155,155:5:0:4,0,0:1,0,0:5,0,0 +17 580 . A C,<*> 0 . DP=30;ADF=15,1,0;ADR=14,0,0;AD=29,1,0;I16=15,14,1,0,1060,39178,16,256,1709,101641,60,3600,510,11078,17,289;QS=2.97338,0.0266223,0;SGB=-0.556633;RPBZ=1.32953;MQBZ=0.185695;MQSBZ=-1.06904;BQBZ=-1.69093;SCBZ=-0.267102;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,34,255,48,255,255:17:0:7,1,0:9,0,0:16,1,0 0,24,221,24,221,221:8:0:4,0,0:4,0,0:8,0,0 0,15,155,15,155,155:5:0:4,0,0:1,0,0:5,0,0 17 581 . A <*> 0 . DP=31;ADF=16,0;ADR=15,0;AD=31,0;I16=16,15,0,0,1083,39215,0,0,1829,108841,0,0,530,11384,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:8,0:10,0:18,0 0,24,223:8:0:4,0:4,0:8,0 0,15,153:5:0:4,0:1,0:5,0 -17 582 . C G,<*> 0 . DP=31;ADF=15,1,0;ADR=15,0,0;AD=30,1,0;I16=15,15,1,0,1080,39870,8,64,1769,105241,60,3600,519,11211,15,225;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.34259;MQBZ=0.182574;MQSBZ=-1.0328;BQBZ=-1.68266;SCBZ=-0.262467;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,41,255,51,255,255:18:0:7,1,0:10,0,0:17,1,0 0,24,207,24,207,207:8:0:4,0,0:4,0,0:8,0,0 0,15,151,15,151,151:5:0:4,0,0:1,0,0:5,0,0 +17 582 . C G,<*> 0 . DP=31;ADF=15,1,0;ADR=15,0,0;AD=30,1,0;I16=15,15,1,0,1080,39870,8,64,1769,105241,60,3600,519,11211,15,225;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.34259;MQBZ=0.182574;MQSBZ=-1.0328;BQBZ=-1.68266;SCBZ=-0.262467;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,41,255,51,255,255:18:0:7,1,0:10,0,0:17,1,0 0,24,207,24,207,207:8:0:4,0,0:4,0,0:8,0,0 0,15,151,15,151,151:5:0:4,0,0:1,0,0:5,0,0 17 583 . T <*> 0 . DP=30;ADF=16,0;ADR=14,0;AD=30,0;I16=16,14,0,0,1135,43913,0,0,1769,105241,0,0,539,11523,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:8,0:9,0:17,0 0,24,238:8:0:4,0:4,0:8,0 0,15,163:5:0:4,0:1,0:5,0 17 584 . C <*> 0 . DP=31;ADF=17,0;ADR=14,0;AD=31,0;I16=17,14,0,0,1069,39521,0,0,1798,106082,0,0,544,11644,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:9,0:9,0:18,0 0,24,209:8:0:4,0:4,0:8,0 0,15,157:5:0:4,0:1,0:5,0 17 585 . A <*> 0 . DP=31;ADF=17,0;ADR=14,0;AD=31,0;I16=17,14,0,0,1096,39866,0,0,1798,106082,0,0,549,11751,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:9,0:9,0:18,0 0,24,211:8:0:4,0:4,0:8,0 0,15,157:5:0:4,0:1,0:5,0 @@ -521,10 +520,10 @@ 17 590 . C <*> 0 . DP=32;ADF=17,0;ADR=15,0;AD=32,0;I16=17,15,0,0,1103,41355,0,0,1858,109682,0,0,574,12576,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:9,0:9,0:18,0 0,24,194:8:0:4,0:4,0:8,0 0,18,175:6:0:4,0:2,0:6,0 17 591 . A <*> 0 . DP=31;ADF=16,0;ADR=15,0;AD=31,0;I16=16,15,0,0,1164,44088,0,0,1798,106082,0,0,579,12695,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:9,0:9,0:18,0 0,21,209:7:0:3,0:4,0:7,0 0,18,188:6:0:4,0:2,0:6,0 17 592 . A <*> 0 . DP=31;ADF=16,0;ADR=15,0;AD=31,0;I16=16,15,0,0,1121,42193,0,0,1798,106082,0,0,583,12795,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:9,0:9,0:18,0 0,21,215:7:0:3,0:4,0:7,0 0,18,182:6:0:4,0:2,0:6,0 -17 593 . C A,<*> 0 . DP=31;ADF=16,0,0;ADR=14,1,0;AD=30,1,0;I16=16,14,0,1,1071,39925,7,49,1769,105241,29,841,561,12253,25,625;QS=2.97021,0.0297872,0;SGB=-0.556633;RPBZ=0.559355;MQBZ=-3.80789;MQSBZ=-0.0464238;BQBZ=-1.57464;SCBZ=3.67454;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255,54,255,255:18:0:9,0,0:9,0,0:18,0,0 0,12,184,18,187,185:7:0:3,0,0:3,1,0:6,1,0 0,18,174,18,174,174:6:0:4,0,0:2,0,0:6,0,0 -17 594 . A G,<*> 0 . DP=33;ADF=16,1,0;ADR=16,0,0;AD=32,1,0;I16=16,16,1,0,1161,42757,4,16,1858,109682,60,3600,572,12672,15,225;QS=2.99359,0.00641026,0;SGB=-0.556633;RPBZ=-0.998367;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68954;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,42,255,51,255,255:18:0:8,1,0:9,0,0:17,1,0 0,21,205,21,205,205:7:0:3,0,0:4,0,0:7,0,0 0,24,213,24,213,213:8:0:5,0,0:3,0,0:8,0,0 +17 593 . C A,<*> 0 . DP=31;ADF=16,0,0;ADR=14,1,0;AD=30,1,0;I16=16,14,0,1,1071,39925,7,49,1769,105241,29,841,561,12253,25,625;QS=2.97021,0.0297872,0;SGB=-0.556633;RPBZ=0.559355;MQBZ=-3.80789;MQSBZ=-0.0464238;BQBZ=-1.57464;SCBZ=3.67454;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255,54,255,255:18:0:9,0,0:9,0,0:18,0,0 0,12,184,18,187,185:7:0:3,0,0:3,1,0:6,1,0 0,18,174,18,174,174:6:0:4,0,0:2,0,0:6,0,0 +17 594 . A G,<*> 0 . DP=33;ADF=16,1,0;ADR=16,0,0;AD=32,1,0;I16=16,16,1,0,1161,42757,4,16,1858,109682,60,3600,572,12672,15,225;QS=2.99359,0.00641026,0;SGB=-0.556633;RPBZ=-0.998367;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68954;SCBZ=-0.253876;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,42,255,51,255,255:18:0:8,1,0:9,0,0:17,1,0 0,21,205,21,205,205:7:0:3,0,0:4,0,0:7,0,0 0,24,213,24,213,213:8:0:5,0,0:3,0,0:8,0,0 17 595 . A <*> 0 . DP=33;ADF=17,0;ADR=16,0;AD=33,0;I16=17,16,0,0,1136,40412,0,0,1918,113282,0,0,589,12905,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:9,0:9,0:18,0 0,21,198:7:0:3,0:4,0:7,0 0,24,218:8:0:5,0:3,0:8,0 -17 596 . A G,<*> 0 . DP=33;ADF=16,1,0;ADR=16,0,0;AD=32,1,0;I16=16,16,1,0,1061,37187,8,64,1858,109682,60,3600,590,12952,1,1;QS=2.98564,0.0143627,0;SGB=-0.556633;RPBZ=1.68146;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68357;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,41,255,51,255,255:18:0:8,1,0:9,0,0:17,1,0 0,21,169,21,169,169:7:0:3,0,0:4,0,0:7,0,0 0,24,231,24,231,231:8:0:5,0,0:3,0,0:8,0,0 +17 596 . A G,<*> 0 . DP=33;ADF=16,1,0;ADR=16,0,0;AD=32,1,0;I16=16,16,1,0,1061,37187,8,64,1858,109682,60,3600,590,12952,1,1;QS=2.98564,0.0143627,0;SGB=-0.556633;RPBZ=1.68146;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68357;SCBZ=-0.253876;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,41,255,51,255,255:18:0:8,1,0:9,0,0:17,1,0 0,21,169,21,169,169:7:0:3,0,0:4,0,0:7,0,0 0,24,231,24,231,231:8:0:5,0,0:3,0,0:8,0,0 17 597 . C <*> 0 . DP=33;ADF=17,0;ADR=16,0;AD=33,0;I16=17,16,0,0,1196,44890,0,0,1918,113282,0,0,592,12990,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,54,255:18:0:9,0:9,0:18,0 0,21,204:7:0:3,0:4,0:7,0 0,24,220:8:0:5,0:3,0:8,0 17 598 . T <*> 0 . DP=33;ADF=16,0;ADR=17,0;AD=33,0;I16=16,17,0,0,1219,47333,0,0,1918,113282,0,0,597,13029,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:8,0:9,0:17,0 0,21,217:7:0:3,0:4,0:7,0 0,27,242:9:0:5,0:4,0:9,0 17 599 . T <*> 0 . DP=33;ADF=16,0;ADR=17,0;AD=33,0;I16=16,17,0,0,1182,43598,0,0,1918,113282,0,0,599,13095,0,0;QS=3,0;MQ0F=0 PL:DP:SP:ADF:ADR:AD 0,51,255:17:0:8,0:9,0:17,0 0,21,197:7:0:3,0:4,0:7,0 0,27,247:9:0:5,0:4,0:9,0 diff --git a/test/mpileup/mpileup.6.out b/test/mpileup/mpileup.6.out index 51c080cb0..5bb6f8220 100644 --- a/test/mpileup/mpileup.6.out +++ b/test/mpileup/mpileup.6.out @@ -12,7 +12,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -24,97 +23,97 @@ ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00100 HG00101 HG00102 17 100 . C <*> . . END=102;MinDP=3;QS=3,0 PL:DP 0,27,182:9 0,9,108:3 0,15,132:5 -17 103 . T C,<*> 0 . DP=18;I16=15,1,1,0,668,28542,6,36,929,54841,29,841,323,7035,6,36;QS=2.98256,0.0174419,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64924;SCBZ=4;FS=0;MQ0F=0 PL:DP:DV 0,17,184,24,187,185:9:1 0,9,118,9,118,118:3:0 0,15,147,15,147,147:5:0 -17 104 . G C,<*> 0 . DP=18;I16=15,1,1,0,601,24163,3,9,929,54841,29,841,320,6884,7,49;QS=2.98726,0.0127389,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64309;SCBZ=4;FS=0;MQ0F=0 PL:DP:DV 0,18,173,24,176,173:9:1 0,9,101,9,101,101:3:0 0,15,133,15,133,133:5:0 +17 103 . T C,<*> 0 . DP=18;I16=15,1,1,0,668,28542,6,36,929,54841,29,841,323,7035,6,36;QS=2.98256,0.0174419,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64924;SCBZ=4;MQ0F=0 PL:DP:DV 0,17,184,24,187,185:9:1 0,9,118,9,118,118:3:0 0,15,147,15,147,147:5:0 +17 104 . G C,<*> 0 . DP=18;I16=15,1,1,0,601,24163,3,9,929,54841,29,841,320,6884,7,49;QS=2.98726,0.0127389,0;SGB=-0.556633;RPBZ=-1.02125;MQBZ=-2.73861;MQSBZ=0.365148;BQBZ=-1.64309;SCBZ=4;MQ0F=0 PL:DP:DV 0,18,173,24,176,173:9:1 0,9,101,9,101,101:3:0 0,15,133,15,133,133:5:0 17 105 . G <*> . . END=108;MinDP=3;QS=3,0 PL:DP 0,30,171:10 0,9,92:3 0,15,124:5 -17 109 . T C,<*> 0 . DP=19;I16=16,1,1,0,716,30648,2,4,989,58441,29,841,309,6415,12,144;QS=2.98922,0.0107817,0;SGB=-0.556633;RPBZ=-0.674966;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.6661;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV 0,20,191,27,194,191:10:1 0,9,120,9,120,120:3:0 0,15,150,15,150,150:5:0 +17 109 . T C,<*> 0 . DP=19;I16=16,1,1,0,716,30648,2,4,989,58441,29,841,309,6415,12,144;QS=2.98922,0.0107817,0;SGB=-0.556633;RPBZ=-0.674966;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.6661;SCBZ=3;MQ0F=0 PL:DP:DV 0,20,191,27,194,191:10:1 0,9,120,9,120,120:3:0 0,15,150,15,150,150:5:0 17 110 . G <*> . . END=111;MinDP=3;QS=3,0 PL:DP 0,30,167:10 0,9,95:3 0,15,119:5 -17 112 . C G,<*> 0 . DP=19;I16=16,1,1,0,657,26565,2,4,989,58441,29,841,301,6277,15,225;QS=2.98907,0.010929,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65292;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV 0,20,187,27,190,187:10:1 0,9,103,9,103,103:3:0 0,15,135,15,135,135:5:0 -17 113 . A G,<*> 0 . DP=19;I16=16,1,1,0,635,25055,4,16,989,58441,29,841,297,6207,16,256;QS=2.98817,0.0118343,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65205;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV 0,20,172,27,175,172:10:1 0,9,102,9,102,102:3:0 0,15,139,15,139,139:5:0 +17 112 . C G,<*> 0 . DP=19;I16=16,1,1,0,657,26565,2,4,989,58441,29,841,301,6277,15,225;QS=2.98907,0.010929,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65292;SCBZ=3;MQ0F=0 PL:DP:DV 0,20,187,27,190,187:10:1 0,9,103,9,103,103:3:0 0,15,135,15,135,135:5:0 +17 113 . A G,<*> 0 . DP=19;I16=16,1,1,0,635,25055,4,16,989,58441,29,841,297,6207,16,256;QS=2.98817,0.0118343,0;SGB=-0.556633;RPBZ=-0.482118;MQBZ=-2.82843;MQSBZ=0.353553;BQBZ=-1.65205;SCBZ=3;MQ0F=0 PL:DP:DV 0,20,172,27,175,172:10:1 0,9,102,9,102,102:3:0 0,15,139,15,139,139:5:0 17 114 . C <*> . . MinDP=3;QS=3,0 PL:DP 0,30,181:10 0,9,113:3 0,15,133:5 -17 115 . C A,<*> 0 . DP=21;I16=17,2,1,0,688,27426,12,144,1078,62882,29,841,283,5827,25,625;QS=2.88785,0.11215,0;SGB=-0.556633;RPBZ=0.260329;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.47798;SCBZ=-0.418446;FS=0;MQ0F=0 PL:DP:DV 0,30,189,30,189,189:10:0 3,0,86,9,89,93:3:1 0,21,153,21,153,153:7:0 -17 116 . A C,<*> 0 . DP=21;I16=17,2,1,0,705,27791,2,4,1078,62882,29,841,287,6073,19,361;QS=2.98873,0.0112676,0;SGB=-0.556633;RPBZ=0.0867763;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.65814;SCBZ=2.65016;FS=0;MQ0F=0 PL:DP:DV 0,20,179,27,182,179:10:1 0,9,102,9,102,102:3:0 0,21,175,21,175,175:7:0 +17 115 . C A,<*> 0 . DP=21;I16=17,2,1,0,688,27426,12,144,1078,62882,29,841,283,5827,25,625;QS=2.88785,0.11215,0;SGB=-0.556633;RPBZ=0.260329;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.47798;SCBZ=-0.418446;MQ0F=0 PL:DP:DV 0,30,189,30,189,189:10:0 3,0,86,9,89,93:3:1 0,21,153,21,153,153:7:0 +17 116 . A C,<*> 0 . DP=21;I16=17,2,1,0,705,27791,2,4,1078,62882,29,841,287,6073,19,361;QS=2.98873,0.0112676,0;SGB=-0.556633;RPBZ=0.0867763;MQBZ=-2.38048;MQSBZ=-1.42419;BQBZ=-1.65814;SCBZ=2.65016;MQ0F=0 PL:DP:DV 0,20,179,27,182,179:10:1 0,9,102,9,102,102:3:0 0,21,175,21,175,175:7:0 17 117 . G <*> . . END=119;MinDP=2;QS=3,0 PL:DP 0,27,175:9 0,6,76:2 0,21,160:7 -17 120 . A G,<*> 0 . DP=19;I16=15,2,1,0,646,25392,4,16,958,55682,29,841,277,5999,23,529;QS=2.9873,0.0126984,0;SGB=-0.556633;RPBZ=0.28942;MQBZ=-2.23607;MQSBZ=-1.30384;BQBZ=-1.6486;SCBZ=3;FS=0;MQ0F=0 PL:DP:DV 0,18,171,24,174,171:9:1 0,6,88,6,88,88:2:0 0,21,171,21,171,171:7:0 +17 120 . A G,<*> 0 . DP=19;I16=15,2,1,0,646,25392,4,16,958,55682,29,841,277,5999,23,529;QS=2.9873,0.0126984,0;SGB=-0.556633;RPBZ=0.28942;MQBZ=-2.23607;MQSBZ=-1.30384;BQBZ=-1.6486;SCBZ=3;MQ0F=0 PL:DP:DV 0,18,171,24,174,171:9:1 0,6,88,6,88,88:2:0 0,21,171,21,171,171:7:0 17 121 . G <*> . . END=124;MinDP=2;QS=3,0 PL:DP 0,24,170:8 0,6,84:2 0,18,154:6 -17 125 . A T,<*> 0 . DP=18;I16=14,2,1,0,589,22565,4,16,898,52082,29,841,272,5916,25,625;QS=2.98444,0.0155642,0;SGB=-0.556633;RPBZ=1.02125;MQBZ=-2.16025;MQSBZ=-1.23956;BQBZ=-1.64106;SCBZ=2.91548;FS=0;MQ0F=0 PL:DP:DV 0,15,149,21,152,149:8:1 0,9,114,9,114,114:3:0 0,18,162,18,162,162:6:0 +17 125 . A T,<*> 0 . DP=18;I16=14,2,1,0,589,22565,4,16,898,52082,29,841,272,5916,25,625;QS=2.98444,0.0155642,0;SGB=-0.556633;RPBZ=1.02125;MQBZ=-2.16025;MQSBZ=-1.23956;BQBZ=-1.64106;SCBZ=2.91548;MQ0F=0 PL:DP:DV 0,15,149,21,152,149:8:1 0,9,114,9,114,114:3:0 0,18,162,18,162,162:6:0 17 126 . A <*> . . END=158;MinDP=2;QS=3,0 PL:DP 0,18,128:6 0,6,81:2 0,15,102:5 -17 159 . A G,<*> 0 . DP=15;I16=12,2,1,0,519,19467,5,25,809,47641,60,3600,260,5880,0,0;QS=2.97076,0.0292398,0;SGB=-0.556633;RPBZ=-1.62019;MQBZ=0.267261;MQSBZ=-2.54951;BQBZ=-1.63041;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,21,157,21,157,157:7:0 0,6,83,6,83,83:2:0 0,10,129,15,132,129:6:1 +17 159 . A G,<*> 0 . DP=15;I16=12,2,1,0,519,19467,5,25,809,47641,60,3600,260,5880,0,0;QS=2.97076,0.0292398,0;SGB=-0.556633;RPBZ=-1.62019;MQBZ=0.267261;MQSBZ=-2.54951;BQBZ=-1.63041;SCBZ=0;MQ0F=0 PL:DP:DV 0,21,157,21,157,157:7:0 0,6,83,6,83,83:2:0 0,10,129,15,132,129:6:1 17 160 . G <*> . . END=173;MinDP=2;QS=3,0 PL:DP 0,15,106:5 0,6,75:2 0,15,138:5 17 174 . G <*> . . END=188;MinDP=1;QS=3,0 PL:DP 0,15,111:5 0,3,27:1 0,21,116:7 17 189 . C <*> . . MinDP=2;QS=3,0 PL:DP 0,18,152:6 0,6,67:2 0,21,167:7 -17 190 . A C,<*> 0 . DP=15;I16=12,2,1,0,500,18230,5,25,778,44882,60,3600,243,5381,25,625;QS=2.97664,0.0233645,0;SGB=-0.556633;RPBZ=0;MQBZ=0.392232;MQSBZ=-3.74166;BQBZ=-1.63041;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,18,138,18,138,138:6:0 0,6,68,6,68,68:2:0 0,12,153,18,156,153:7:1 +17 190 . A C,<*> 0 . DP=15;I16=12,2,1,0,500,18230,5,25,778,44882,60,3600,243,5381,25,625;QS=2.97664,0.0233645,0;SGB=-0.556633;RPBZ=0;MQBZ=0.392232;MQSBZ=-3.74166;BQBZ=-1.63041;SCBZ=0;MQ0F=0 PL:DP:DV 0,18,138,18,138,138:6:0 0,6,68,6,68,68:2:0 0,12,153,18,156,153:7:1 17 191 . T <*> . . END=222;MinDP=2;QS=3,0 PL:DP 0,18,140:6 0,6,63:2 0,12,73:4 -17 223 . G T,<*> 0 . DP=13;I16=9,3,1,0,412,14782,8,64,627,34923,60,3600,243,5657,25,625;QS=2.96596,0.0340426,0;SGB=-0.556633;RPBZ=1.07052;MQBZ=0.547723;MQSBZ=-3.4641;BQBZ=-1.60577;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,11,166,18,169,167:7:1 0,6,53,6,53,53:2:0 0,12,81,12,81,81:4:0 +17 223 . G T,<*> 0 . DP=13;I16=9,3,1,0,412,14782,8,64,627,34923,60,3600,243,5657,25,625;QS=2.96596,0.0340426,0;SGB=-0.556633;RPBZ=1.07052;MQBZ=0.547723;MQSBZ=-3.4641;BQBZ=-1.60577;SCBZ=0;MQ0F=0 PL:DP:DV 0,11,166,18,169,167:7:1 0,6,53,6,53,53:2:0 0,12,81,12,81,81:4:0 17 224 . G <*> . . END=225;MinDP=2;QS=3,0 PL:DP 0,18,165:6 0,6,48:2 0,12,70:4 -17 226 . A G,C,<*> 0 . DP=13;I16=8,3,1,1,381,13669,6,18,567,31323,89,4441,248,5894,44,986;QS=2.94293,0.0392157,0.0178571,0;VDB=0.84;SGB=-2.62246;RPBZ=-0.592157;MQBZ=-0.615457;MQSBZ=-3.4641;BQBZ=-2.17723;SCBZ=2.34521;FS=0;MQ0F=0 PL:DP:DV 0,18,159,12,162,159,18,159,162,159:7:1 0,6,53,6,53,53,6,53,53,53:2:0 0,5,79,9,82,80,9,82,80,80:4:1 +17 226 . A G,C,<*> 0 . DP=13;I16=8,3,1,1,381,13669,6,18,567,31323,89,4441,248,5894,44,986;QS=2.94293,0.0392157,0.0178571,0;VDB=0.84;SGB=-2.62246;RPBZ=-0.592157;MQBZ=-0.615457;MQSBZ=-3.4641;BQBZ=-2.17723;SCBZ=2.34521;MQ0F=0 PL:DP:DV 0,18,159,12,162,159,18,159,162,159:7:1 0,6,53,6,53,53,6,53,53,53:2:0 0,5,79,9,82,80,9,82,80,80:4:1 17 227 . C <*> . . END=236;MinDP=2;QS=3,0 PL:DP 0,21,145:7 0,6,45:2 0,12,70:4 -17 237 . A C,<*> 0 . DP=14;I16=9,4,1,0,465,16877,8,64,656,35764,60,3600,266,6282,25,625;QS=2.93162,0.0683761,0;SGB=-0.556633;RPBZ=1.11754;MQBZ=0.632456;MQSBZ=-3.60555;BQBZ=-1.61959;SCBZ=-0.27735;FS=0;MQ0F=0 PL:DP:DV 0,24,206,24,206,206:8:0 0,6,53,6,53,53:2:0 0,3,84,9,87,87:4:1 +17 237 . A C,<*> 0 . DP=14;I16=9,4,1,0,465,16877,8,64,656,35764,60,3600,266,6282,25,625;QS=2.93162,0.0683761,0;SGB=-0.556633;RPBZ=1.11754;MQBZ=0.632456;MQSBZ=-3.60555;BQBZ=-1.61959;SCBZ=-0.27735;MQ0F=0 PL:DP:DV 0,24,206,24,206,206:8:0 0,6,53,6,53,53:2:0 0,3,84,9,87,87:4:1 17 238 . C <*> . . END=255;MinDP=2;QS=3,0 PL:DP 0,24,211:8 0,6,50:2 0,12,64:4 17 256 . A <*> . . END=266;MinDP=5;QS=3,0 PL:DP 0,33,247:11 0,15,92:5 0,15,122:5 -17 267 . T G,<*> 0 . DP=21;I16=9,11,0,1,739,27465,8,64,960,50456,29,841,373,7935,25,625;QS=2.94203,0.057971,0;SGB=-0.556633;RPBZ=-0.330396;MQBZ=-1.23153;MQSBZ=-3.3021;BQBZ=-1.66282;SCBZ=2.91633;FS=0;MQ0F=0 PL:DP:DV 0,33,254,33,254,254:11:0 0,6,93,12,96,96:5:1 0,15,149,15,149,149:5:0 +17 267 . T G,<*> 0 . DP=21;I16=9,11,0,1,739,27465,8,64,960,50456,29,841,373,7935,25,625;QS=2.94203,0.057971,0;SGB=-0.556633;RPBZ=-0.330396;MQBZ=-1.23153;MQSBZ=-3.3021;BQBZ=-1.66282;SCBZ=2.91633;MQ0F=0 PL:DP:DV 0,33,254,33,254,254:11:0 0,6,93,12,96,96:5:1 0,15,149,15,149,149:5:0 17 268 . T <*> . . END=272;MinDP=5;QS=3,0 PL:DP 0,33,238:11 0,15,91:5 0,15,143:5 -17 273 . T C,<*> 0 . DP=22;I16=9,12,0,1,798,30664,5,25,989,51297,29,841,392,8620,25,625;QS=2.96094,0.0390625,0;SGB=-0.556633;RPBZ=-0.236567;MQBZ=-1.16701;MQSBZ=-3.42286;BQBZ=-1.66779;SCBZ=3.00076;FS=0;MQ0F=0 PL:DP:DV 0,36,255,36,255,255:12:0 0,7,89,12,92,90:5:1 0,15,161,15,161,161:5:0 +17 273 . T C,<*> 0 . DP=22;I16=9,12,0,1,798,30664,5,25,989,51297,29,841,392,8620,25,625;QS=2.96094,0.0390625,0;SGB=-0.556633;RPBZ=-0.236567;MQBZ=-1.16701;MQSBZ=-3.42286;BQBZ=-1.66779;SCBZ=3.00076;MQ0F=0 PL:DP:DV 0,36,255,36,255,255:12:0 0,7,89,12,92,90:5:1 0,15,161,15,161,161:5:0 17 274 . C <*> . . MinDP=5;QS=3,0 PL:DP 0,36,255:12 0,15,101:5 0,15,144:5 17 275 . C <*> . . END=277;MinDP=4;QS=3,0 PL:DP 0,33,253:11 0,15,114:5 0,12,121:4 -17 278 . A C,<*> 0 . DP=21;I16=6,14,1,0,722,26452,7,49,867,42179,60,3600,415,9521,11,121;QS=2.97935,0.020649,0;SGB=-0.556633;RPBZ=1.65198;MQBZ=1.0247;MQSBZ=-3.24037;BQBZ=-1.66667;SCBZ=-0.324037;FS=0;MQ0F=0 PL:DP:DV 0,22,231,30,234,231:11:1 0,18,123,18,123,123:6:0 0,12,121,12,121,121:4:0 +17 278 . A C,<*> 0 . DP=21;I16=6,14,1,0,722,26452,7,49,867,42179,60,3600,415,9521,11,121;QS=2.97935,0.020649,0;SGB=-0.556633;RPBZ=1.65198;MQBZ=1.0247;MQSBZ=-3.24037;BQBZ=-1.66667;SCBZ=-0.324037;MQ0F=0 PL:DP:DV 0,22,231,30,234,231:11:1 0,18,123,18,123,123:6:0 0,12,121,12,121,121:4:0 17 279 . A <*> . . END=282;MinDP=4;QS=3,0 PL:DP 0,36,253:12 0,18,122:6 0,12,119:4 17 283 . C <*> . . END=296;MinDP=5;QS=3,0 PL:DP 0,33,240:11 0,18,119:6 0,15,122:5 -17 297 . C G,<*> 0 . DP=25;I16=9,15,1,0,901,34305,4,16,1138,59338,60,3600,445,9901,10,100;QS=2.98261,0.0173913,0;SGB=-0.556633;RPBZ=-1.24856;MQBZ=0.806872;MQSBZ=-3.22749;BQBZ=-1.67542;SCBZ=-0.368383;FS=0;MQ0F=0 PL:DP:DV 0,33,255,33,255,255:11:0 0,15,168,21,171,168:8:1 0,18,161,18,161,161:6:0 +17 297 . C G,<*> 0 . DP=25;I16=9,15,1,0,901,34305,4,16,1138,59338,60,3600,445,9901,10,100;QS=2.98261,0.0173913,0;SGB=-0.556633;RPBZ=-1.24856;MQBZ=0.806872;MQSBZ=-3.22749;BQBZ=-1.67542;SCBZ=-0.368383;MQ0F=0 PL:DP:DV 0,33,255,33,255,255:11:0 0,15,168,21,171,168:8:1 0,18,161,18,161,161:6:0 17 298 . A <*> . . END=301;MinDP=7;QS=3,0 PL:DP 0,30,231:10 0,21,172:7 0,21,189:7 -17 302 . T TA 0 . INDEL;IDV=7;IMF=1;DP=25;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.539485,2.46052;VDB=0.241622;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.22749;BQBZ=-1.67542;SCBZ=-0.268121;FS=0;MQ0F=0 PL:DP:DV 161,0,99:11:6 158,0,14:7:6 201,21,0:7:7 +17 302 . T TA 0 . INDEL;IDV=7;IMF=1;DP=25;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.539485,2.46052;VDB=0.241622;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.22749;BQBZ=-1.67542;SCBZ=-0.268121;MQ0F=0 PL:DP:DV 161,0,99:11:6 158,0,14:7:6 201,21,0:7:7 17 303 . G <*> . . END=334;MinDP=7;QS=3,0 PL:DP 0,30,235:10 0,21,197:7 0,21,195:7 -17 335 . A G,<*> 0 . DP=32;I16=13,18,1,0,1084,40336,4,16,1589,87297,60,3600,555,11943,0,0;QS=2.98919,0.0108108,0;SGB=-0.556633;RPBZ=-1.67936;MQBZ=0.622171;MQSBZ=-2.25492;BQBZ=-1.68602;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV 0,33,252,33,252,252:11:0 0,27,219,27,219,219:9:0 0,25,245,33,248,245:12:1 +17 335 . A G,<*> 0 . DP=32;I16=13,18,1,0,1084,40336,4,16,1589,87297,60,3600,555,11943,0,0;QS=2.98919,0.0108108,0;SGB=-0.556633;RPBZ=-1.67936;MQBZ=0.622171;MQSBZ=-2.25492;BQBZ=-1.68602;SCBZ=-0.258065;MQ0F=0 PL:DP:DV 0,33,252,33,252,252:11:0 0,27,219,27,219,219:9:0 0,25,245,33,248,245:12:1 17 336 . A <*> . . MinDP=9;QS=3,0 PL:DP 0,33,255:11 0,27,212:9 0,36,255:12 -17 337 . C A,<*> 0 . DP=32;I16=14,17,0,1,1125,42481,5,25,1612,89528,37,1369,536,11590,18,324;QS=2.98113,0.0188679,0;SGB=-0.556633;RPBZ=0.812593;MQBZ=-1.03695;MQSBZ=-2.25492;BQBZ=-1.68353;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV 0,33,255,33,255,255:11:0 0,17,195,24,198,195:9:1 0,36,255,36,255,255:12:0 +17 337 . C A,<*> 0 . DP=32;I16=14,17,0,1,1125,42481,5,25,1612,89528,37,1369,536,11590,18,324;QS=2.98113,0.0188679,0;SGB=-0.556633;RPBZ=0.812593;MQBZ=-1.03695;MQSBZ=-2.25492;BQBZ=-1.68353;SCBZ=-0.258065;MQ0F=0 PL:DP:DV 0,33,255,33,255,255:11:0 0,17,195,24,198,195:9:1 0,36,255,36,255,255:12:0 17 338 . T <*> . . END=354;MinDP=8;QS=3,0 PL:DP 0,27,225:9 0,24,185:8 0,30,255:10 -17 355 . G T,<*> 0 . DP=28;I16=14,13,0,1,1001,37907,41,1681,1442,81174,60,3600,547,12487,25,625;QS=2.875,0.125,0;SGB=-0.556633;RPBZ=0.185772;MQBZ=0.520126;MQSBZ=-1.7696;BQBZ=0.683978;SCBZ=-0.27735;FS=0;MQ0F=0 PL:DP:DV 14,0,200,38,203,231:9:1 0,27,222,27,222,222:9:0 0,30,255,30,255,255:10:0 +17 355 . G T,<*> 0 . DP=28;I16=14,13,0,1,1001,37907,41,1681,1442,81174,60,3600,547,12487,25,625;QS=2.875,0.125,0;SGB=-0.556633;RPBZ=0.185772;MQBZ=0.520126;MQSBZ=-1.7696;BQBZ=0.683978;SCBZ=-0.27735;MQ0F=0 PL:DP:DV 14,0,200,38,203,231:9:1 0,27,222,27,222,222:9:0 0,30,255,30,255,255:10:0 17 356 . G <*> . . END=358;MinDP=8;QS=3,0 PL:DP 0,27,228:9 0,24,197:8 0,30,252:10 -17 359 . G T,<*> 0 . DP=29;I16=15,13,0,1,1085,42761,10,100,1525,87005,60,3600,552,12620,25,625;QS=2.96032,0.0396825,0;SGB=-0.556633;RPBZ=-0.119611;MQBZ=0.456435;MQSBZ=-1.53333;BQBZ=-1.68246;SCBZ=5.2915;FS=0;MQ0F=0 PL:DP:DV 0,30,255,30,255,255:10:0 0,13,178,21,181,180:8:1 0,33,255,33,255,255:11:0 +17 359 . G T,<*> 0 . DP=29;I16=15,13,0,1,1085,42761,10,100,1525,87005,60,3600,552,12620,25,625;QS=2.96032,0.0396825,0;SGB=-0.556633;RPBZ=-0.119611;MQBZ=0.456435;MQSBZ=-1.53333;BQBZ=-1.68246;SCBZ=5.2915;MQ0F=0 PL:DP:DV 0,30,255,30,255,255:10:0 0,13,178,21,181,180:8:1 0,33,255,33,255,255:11:0 17 360 . A <*> . . END=368;MinDP=8;QS=3,0 PL:DP 0,30,252:10 0,24,204:8 0,30,255:10 -17 369 . T G,<*> 0 . DP=28;I16=16,11,0,1,1037,40275,6,36,1496,86164,60,3600,548,12256,25,625;QS=2.97683,0.023166,0;SGB=-0.556633;RPBZ=0.12395;MQBZ=0.408248;MQSBZ=-1.37784;BQBZ=-1.68703;SCBZ=5.19615;FS=0;MQ0F=0 PL:DP:DV 0,30,250,30,250,250:10:0 0,15,189,21,192,190:8:1 0,30,255,30,255,255:10:0 +17 369 . T G,<*> 0 . DP=28;I16=16,11,0,1,1037,40275,6,36,1496,86164,60,3600,548,12256,25,625;QS=2.97683,0.023166,0;SGB=-0.556633;RPBZ=0.12395;MQBZ=0.408248;MQSBZ=-1.37784;BQBZ=-1.68703;SCBZ=5.19615;MQ0F=0 PL:DP:DV 0,30,250,30,250,250:10:0 0,15,189,21,192,190:8:1 0,30,255,30,255,255:10:0 17 370 . C <*> . . END=374;MinDP=8;QS=3,0 PL:DP 0,30,255:10 0,24,201:8 0,30,255:10 -17 375 . A T,<*> 0 . DP=31;I16=17,13,0,1,1138,43798,14,196,1676,96964,60,3600,547,12177,4,16;QS=2.9661,0.0338983,0;SGB=-0.556633;RPBZ=-1.45432;MQBZ=0.3849;MQSBZ=-1.26404;BQBZ=-1.68488;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,36,255,36,255,255:12:0 0,24,218,24,218,218:8:0 0,18,255,30,255,255:11:1 +17 375 . A T,<*> 0 . DP=31;I16=17,13,0,1,1138,43798,14,196,1676,96964,60,3600,547,12177,4,16;QS=2.9661,0.0338983,0;SGB=-0.556633;RPBZ=-1.45432;MQBZ=0.3849;MQSBZ=-1.26404;BQBZ=-1.68488;SCBZ=0;MQ0F=0 PL:DP:DV 0,36,255,36,255,255:12:0 0,24,218,24,218,218:8:0 0,18,255,30,255,255:11:1 17 376 . G <*> . . END=383;MinDP=7;QS=3,0 PL:DP 0,36,255:12 0,21,172:7 0,30,255:10 -17 384 . A C,<*> 0 . DP=31;I16=19,11,0,1,1077,39885,4,16,1738,102482,60,3600,504,10988,25,625;QS=2.98419,0.0158103,0;SGB=-0.556633;RPBZ=0.615229;MQBZ=0.262613;MQSBZ=-0.333409;BQBZ=-1.68746;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,39,255,39,255,255:13:0 0,15,171,21,174,171:8:1 0,30,255,30,255,255:10:0 +17 384 . A C,<*> 0 . DP=31;I16=19,11,0,1,1077,39885,4,16,1738,102482,60,3600,504,10988,25,625;QS=2.98419,0.0158103,0;SGB=-0.556633;RPBZ=0.615229;MQBZ=0.262613;MQSBZ=-0.333409;BQBZ=-1.68746;SCBZ=0;MQ0F=0 PL:DP:DV 0,39,255,39,255,255:13:0 0,15,171,21,174,171:8:1 0,30,255,30,255,255:10:0 17 385 . C <*> . . END=400;MinDP=5;QS=3,0 PL:DP 0,36,255:12 0,15,133:5 0,30,255:10 -17 401 . A C,<*> 0 . DP=29;I16=17,11,0,1,1063,41001,8,64,1587,92523,60,3600,501,11113,25,625;QS=2.97985,0.0201511,0;SGB=-0.556633;RPBZ=-0.478622;MQBZ=0.339683;MQSBZ=0.29364;BQBZ=-1.68267;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,39,255,39,255,255:13:0 0,15,160,15,160,160:5:0 0,22,255,30,255,255:11:1 +17 401 . A C,<*> 0 . DP=29;I16=17,11,0,1,1063,41001,8,64,1587,92523,60,3600,501,11113,25,625;QS=2.97985,0.0201511,0;SGB=-0.556633;RPBZ=-0.478622;MQBZ=0.339683;MQSBZ=0.29364;BQBZ=-1.68267;SCBZ=0;MQ0F=0 PL:DP:DV 0,39,255,39,255,255:13:0 0,15,160,15,160,160:5:0 0,22,255,30,255,255:11:1 17 402 . T <*> . . END=404;MinDP=5;QS=3,0 PL:DP 0,39,255:13 0,15,131:5 0,33,255:11 17 405 . T <*> . . END=411;MinDP=4;QS=3,0 PL:DP 0,39,255:13 0,12,109:4 0,30,244:10 -17 412 . C T,<*> 0 . DP=30;I16=17,12,1,0,1094,42458,14,196,1678,98882,60,3600,495,10659,25,625;QS=2.97455,0.0254545,0;SGB=-0.556633;RPBZ=-0.40473;MQBZ=0.267261;MQSBZ=-0.293785;BQBZ=-1.6942;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,30,255,42,255,255:15:1 0,12,124,12,124,124:4:0 0,33,255,33,255,255:11:0 +17 412 . C T,<*> 0 . DP=30;I16=17,12,1,0,1094,42458,14,196,1678,98882,60,3600,495,10659,25,625;QS=2.97455,0.0254545,0;SGB=-0.556633;RPBZ=-0.40473;MQBZ=0.267261;MQSBZ=-0.293785;BQBZ=-1.6942;SCBZ=0;MQ0F=0 PL:DP:DV 0,30,255,42,255,255:15:1 0,12,124,12,124,124:4:0 0,33,255,33,255,255:11:0 17 413 . A <*> . . END=436;MinDP=3;QS=3,0 PL:DP 0,45,255:15 0,9,98:3 0,27,223:9 -17 437 . T G,<*> 0 . DP=28;I16=13,14,1,0,990,36832,6,36,1558,91682,29,841,549,12435,16,256;QS=2.9781,0.0218978,0;SGB=-0.556633;RPBZ=-1.36214;MQBZ=-2.88675;MQSBZ=0.6;BQBZ=-1.67909;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,48,255,48,255,255:16:0 0,9,109,9,109,109:3:0 0,17,200,24,203,201:9:1 +17 437 . T G,<*> 0 . DP=28;I16=13,14,1,0,990,36832,6,36,1558,91682,29,841,549,12435,16,256;QS=2.9781,0.0218978,0;SGB=-0.556633;RPBZ=-1.36214;MQBZ=-2.88675;MQSBZ=0.6;BQBZ=-1.67909;SCBZ=0;MQ0F=0 PL:DP:DV 0,48,255,48,255,255:16:0 0,9,109,9,109,109:3:0 0,17,200,24,203,201:9:1 17 438 . A <*> . . END=464;MinDP=2;QS=3,0 PL:DP 0,48,255:16 0,6,97:2 0,27,198:9 -17 465 . C T,<*> 0 . DP=33;I16=19,12,0,1,1173,45601,4,16,1775,103851,60,3600,589,12909,6,36;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.67982;MQBZ=0.321288;MQSBZ=0.341466;BQBZ=-1.68493;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,51,255,51,255,255:17:0 0,15,158,15,158,158:5:0 0,20,224,27,227,224:10:1 +17 465 . C T,<*> 0 . DP=33;I16=19,12,0,1,1173,45601,4,16,1775,103851,60,3600,589,12909,6,36;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.67982;MQBZ=0.321288;MQSBZ=0.341466;BQBZ=-1.68493;SCBZ=0;MQ0F=0 PL:DP:DV 0,51,255,51,255,255:17:0 0,15,158,15,158,158:5:0 0,20,224,27,227,224:10:1 17 466 . A <*> . . END=470;MinDP=5;QS=3,0 PL:DP 0,54,255:18 0,15,165:5 0,30,238:10 -17 471 . T G,C,<*> 0 . DP=36;I16=21,12,0,2,1220,46380,18,162,1918,113282,97,4969,611,13281,16,256;QS=2.94529,0.0273556,0.0273556,0;VDB=0.96;SGB=0.346553;RPBZ=0.497712;MQBZ=-1.9761;MQSBZ=0.312094;BQBZ=-2.35032;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,57,255,57,255,255,57,255,255,255:19:0 0,15,169,15,169,169,15,169,169,169:5:0 0,19,219,19,221,219,27,222,222,221:11:2 +17 471 . T G,C,<*> 0 . DP=36;I16=21,12,0,2,1220,46380,18,162,1918,113282,97,4969,611,13281,16,256;QS=2.94529,0.0273556,0.0273556,0;VDB=0.96;SGB=0.346553;RPBZ=0.497712;MQBZ=-1.9761;MQSBZ=0.312094;BQBZ=-2.35032;SCBZ=0;MQ0F=0 PL:DP:DV 0,57,255,57,255,255,57,255,255,255:19:0 0,15,169,15,169,169,15,169,169,169:5:0 0,19,219,19,221,219,27,222,222,221:11:2 17 472 . T <*> . . END=487;MinDP=5;QS=3,0 PL:DP 0,51,255:17 0,15,146:5 0,30,241:10 -17 488 . A G,<*> 0 . DP=35;I16=22,12,1,0,1278,48412,4,16,1986,117410,29,841,646,14380,25,625;QS=2.98947,0.0105263,0;SGB=-0.556633;RPBZ=0.594463;MQBZ=-3.36505;MQSBZ=0.10737;BQBZ=-1.69552;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,54,255,54,255,255:18:0 0,18,177,18,177,177:6:0 0,23,255,30,255,255:11:1 +17 488 . A G,<*> 0 . DP=35;I16=22,12,1,0,1278,48412,4,16,1986,117410,29,841,646,14380,25,625;QS=2.98947,0.0105263,0;SGB=-0.556633;RPBZ=0.594463;MQBZ=-3.36505;MQSBZ=0.10737;BQBZ=-1.69552;SCBZ=0;MQ0F=0 PL:DP:DV 0,54,255,54,255,255:18:0 0,18,177,18,177,177:6:0 0,23,255,30,255,255:11:1 17 489 . A <*> . . END=511;MinDP=6;QS=3,0 PL:DP 0,51,255:17 0,18,175:6 0,24,221:8 -17 512 . A C,<*> 0 . DP=33;I16=22,10,0,1,1133,41513,13,169,1866,110210,60,3600,628,14340,9,81;QS=2.97766,0.0223368,0;SGB=-0.556633;RPBZ=-1.47079;MQBZ=0.253876;MQSBZ=-0.461593;BQBZ=-1.68442;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,39,255,51,255,255:18:1 0,21,183,21,183,183:7:0 0,24,231,24,231,231:8:0 -17 513 . A T,<*> 0 . DP=32;I16=21,10,1,0,1125,42283,12,144,1806,106610,60,3600,623,14249,15,225;QS=2.97966,0.020339,0;SGB=-0.556633;RPBZ=-1.24609;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.57376;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,37,255,48,255,255:17:1 0,21,177,21,177,177:7:0 0,24,233,24,233,233:8:0 -17 514 . A T,<*> 0 . DP=32;I16=22,9,0,1,1086,40204,16,256,1806,106610,60,3600,627,14381,11,121;QS=2.97127,0.0287253,0;SGB=-0.556633;RPBZ=-1.4628;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.46657;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,34,255,48,255,255:17:1 0,21,172,21,172,172:7:0 0,24,235,24,235,235:8:0 +17 512 . A C,<*> 0 . DP=33;I16=22,10,0,1,1133,41513,13,169,1866,110210,60,3600,628,14340,9,81;QS=2.97766,0.0223368,0;SGB=-0.556633;RPBZ=-1.47079;MQBZ=0.253876;MQSBZ=-0.461593;BQBZ=-1.68442;SCBZ=0;MQ0F=0 PL:DP:DV 0,39,255,51,255,255:18:1 0,21,183,21,183,183:7:0 0,24,231,24,231,231:8:0 +17 513 . A T,<*> 0 . DP=32;I16=21,10,1,0,1125,42283,12,144,1806,106610,60,3600,623,14249,15,225;QS=2.97966,0.020339,0;SGB=-0.556633;RPBZ=-1.24609;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.57376;SCBZ=0;MQ0F=0 PL:DP:DV 0,37,255,48,255,255:17:1 0,21,177,21,177,177:7:0 0,24,233,24,233,233:8:0 +17 514 . A T,<*> 0 . DP=32;I16=22,9,0,1,1086,40204,16,256,1806,106610,60,3600,627,14381,11,121;QS=2.97127,0.0287253,0;SGB=-0.556633;RPBZ=-1.4628;MQBZ=0.258065;MQSBZ=-0.532795;BQBZ=-1.46657;SCBZ=0;MQ0F=0 PL:DP:DV 0,34,255,48,255,255:17:1 0,21,172,21,172,172:7:0 0,24,235,24,235,235:8:0 17 515 . C <*> . . END=522;MinDP=5;QS=3,0 PL:DP 0,51,255:17 0,21,169:7 0,15,170:5 -17 523 . T G,<*> 0 . DP=32;I16=23,8,1,0,1184,45708,15,225,1837,109369,60,3600,626,14446,25,625;QS=2.9794,0.0206044,0;SGB=-0.556633;RPBZ=1.13742;MQBZ=0.179605;MQSBZ=-1.73205;BQBZ=-1.68805;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,44,255,57,255,255:20:1 0,21,191,21,191,191:7:0 0,15,166,15,166,166:5:0 +17 523 . T G,<*> 0 . DP=32;I16=23,8,1,0,1184,45708,15,225,1837,109369,60,3600,626,14446,25,625;QS=2.9794,0.0206044,0;SGB=-0.556633;RPBZ=1.13742;MQBZ=0.179605;MQSBZ=-1.73205;BQBZ=-1.68805;SCBZ=0;MQ0F=0 PL:DP:DV 0,44,255,57,255,255:20:1 0,21,191,21,191,191:7:0 0,15,166,15,166,166:5:0 17 524 . T <*> . . END=534;MinDP=5;QS=3,0 PL:DP 0,54,255:18 0,21,172:7 0,15,133:5 -17 535 . A G,<*> 0 . DP=31;I16=24,6,0,1,1080,39870,8,64,1777,105769,60,3600,611,13341,25,625;QS=2.98623,0.0137694,0;SGB=-0.556633;RPBZ=-0.894788;MQBZ=0.182574;MQSBZ=-1.85164;BQBZ=-1.6854;SCBZ=0;FS=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,21,194,21,194,194:7:0 0,18,189,18,189,189:6:0 +17 535 . A G,<*> 0 . DP=31;I16=24,6,0,1,1080,39870,8,64,1777,105769,60,3600,611,13341,25,625;QS=2.98623,0.0137694,0;SGB=-0.556633;RPBZ=-0.894788;MQBZ=0.182574;MQSBZ=-1.85164;BQBZ=-1.6854;SCBZ=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,21,194,21,194,194:7:0 0,18,189,18,189,189:6:0 17 536 . C <*> . . END=547;MinDP=6;QS=3,0 PL:DP 0,54,255:18 0,21,166:7 0,18,157:6 -17 548 . A C,<*> 0 . DP=33;I16=23,9,1,0,1153,42673,9,81,1866,110210,60,3600,561,12489,3,9;QS=2.98607,0.0139319,0;SGB=-0.556633;RPBZ=1.57584;MQBZ=0.253876;MQSBZ=-2.34521;BQBZ=-1.68939;SCBZ=3.80814;FS=0;MQ0F=0 PL:DP:DV 0,44,255,54,255,255:19:1 0,21,181,21,181,181:7:0 0,21,211,21,211,211:7:0 -17 549 . T G,<*> 0 . DP=32;I16=23,8,0,1,1135,42143,20,400,1806,106610,60,3600,532,11720,25,625;QS=2.96918,0.0308166,0;SGB=-0.556633;RPBZ=-0.487556;MQBZ=0.258065;MQSBZ=-2.29695;BQBZ=-1.68602;SCBZ=-0.258065;FS=0;MQ0F=0 PL:DP:DV 0,34,255,51,255,255:18:1 0,21,168,21,168,168:7:0 0,21,208,21,208,208:7:0 +17 548 . A C,<*> 0 . DP=33;I16=23,9,1,0,1153,42673,9,81,1866,110210,60,3600,561,12489,3,9;QS=2.98607,0.0139319,0;SGB=-0.556633;RPBZ=1.57584;MQBZ=0.253876;MQSBZ=-2.34521;BQBZ=-1.68939;SCBZ=3.80814;MQ0F=0 PL:DP:DV 0,44,255,54,255,255:19:1 0,21,181,21,181,181:7:0 0,21,211,21,211,211:7:0 +17 549 . T G,<*> 0 . DP=32;I16=23,8,0,1,1135,42143,20,400,1806,106610,60,3600,532,11720,25,625;QS=2.96918,0.0308166,0;SGB=-0.556633;RPBZ=-0.487556;MQBZ=0.258065;MQSBZ=-2.29695;BQBZ=-1.68602;SCBZ=-0.258065;MQ0F=0 PL:DP:DV 0,34,255,51,255,255:18:1 0,21,168,21,168,168:7:0 0,21,208,21,208,208:7:0 17 550 . T <*> . . END=558;MinDP=6;QS=3,0 PL:DP 0,45,255:15 0,18,143:6 0,18,177:6 -17 559 . C A,<*> 0 . DP=27;I16=18,8,0,1,915,33775,14,196,1560,93600,29,841,473,10141,25,625;QS=2.92708,0.0729167,0;SGB=-0.556633;RPBZ=-1.02726;MQBZ=-5.09902;MQSBZ=-1.41421;BQBZ=-1.54776;SCBZ=5.09902;FS=0;MQ0F=0 PL:DP:DV 0,45,255,45,255,255:15:0 0,4,116,15,119,123:6:1 0,18,169,18,169,169:6:0 +17 559 . C A,<*> 0 . DP=27;I16=18,8,0,1,915,33775,14,196,1560,93600,29,841,473,10141,25,625;QS=2.92708,0.0729167,0;SGB=-0.556633;RPBZ=-1.02726;MQBZ=-5.09902;MQSBZ=-1.41421;BQBZ=-1.54776;SCBZ=5.09902;MQ0F=0 PL:DP:DV 0,45,255,45,255,255:15:0 0,4,116,15,119,123:6:1 0,18,169,18,169,169:6:0 17 560 . C <*> . . END=565;MinDP=5;QS=3,0 PL:DP 0,45,255:15 0,15,121:5 0,21,154:7 -17 566 . C A,<*> 0 . DP=29;I16=16,12,1,0,920,33998,9,81,1649,98041,60,3600,454,9734,25,625;QS=2.98321,0.016791,0;SGB=-0.556633;RPBZ=0.239193;MQBZ=0.188982;MQSBZ=-1.19024;BQBZ=-1.43942;SCBZ=-0.188982;FS=0;MQ0F=0 PL:DP:DV 0,38,255,48,255,255:17:1 0,15,155,15,155,155:5:0 0,21,170,21,170,170:7:0 +17 566 . C A,<*> 0 . DP=29;I16=16,12,1,0,920,33998,9,81,1649,98041,60,3600,454,9734,25,625;QS=2.98321,0.016791,0;SGB=-0.556633;RPBZ=0.239193;MQBZ=0.188982;MQSBZ=-1.19024;BQBZ=-1.43942;SCBZ=-0.188982;MQ0F=0 PL:DP:DV 0,38,255,48,255,255:17:1 0,15,155,15,155,155:5:0 0,21,170,21,170,170:7:0 17 567 . C <*> . . END=573;MinDP=6;QS=3,0 PL:DP 0,48,255:16 0,18,156:6 0,18,175:6 -17 574 . C A,<*> 0 . DP=31;I16=18,11,0,1,1088,41328,15,225,1740,104400,29,841,478,10422,25,625;QS=2.94071,0.0592885,0;SGB=-0.556633;RPBZ=-0.173514;MQBZ=-5.38516;MQSBZ=-1.22474;BQBZ=-1.68578;SCBZ=3.60588;FS=0;MQ0F=0 PL:DP:DV 0,48,255,48,255,255:16:0 0,9,170,21,173,177:8:1 0,18,173,18,173,173:6:0 -17 575 . T C,<*> 0 . DP=30;I16=17,11,0,1,1048,41548,9,81,1680,100800,29,841,480,10426,25,625;QS=2.96786,0.0321429,0;SGB=-0.556633;RPBZ=-0.119685;MQBZ=-5.2915;MQSBZ=-1.19024;BQBZ=-1.68121;SCBZ=3.53589;FS=0;MQ0F=0 PL:DP:DV 0,48,255,48,255,255:16:0 0,13,200,21,203,202:8:1 0,15,163,15,163,163:5:0 +17 574 . C A,<*> 0 . DP=31;I16=18,11,0,1,1088,41328,15,225,1740,104400,29,841,478,10422,25,625;QS=2.94071,0.0592885,0;SGB=-0.556633;RPBZ=-0.173514;MQBZ=-5.38516;MQSBZ=-1.22474;BQBZ=-1.68578;SCBZ=3.60588;MQ0F=0 PL:DP:DV 0,48,255,48,255,255:16:0 0,9,170,21,173,177:8:1 0,18,173,18,173,173:6:0 +17 575 . T C,<*> 0 . DP=30;I16=17,11,0,1,1048,41548,9,81,1680,100800,29,841,480,10426,25,625;QS=2.96786,0.0321429,0;SGB=-0.556633;RPBZ=-0.119685;MQBZ=-5.2915;MQSBZ=-1.19024;BQBZ=-1.68121;SCBZ=3.53589;MQ0F=0 PL:DP:DV 0,48,255,48,255,255:16:0 0,13,200,21,203,202:8:1 0,15,163,15,163,163:5:0 17 576 . G <*> . . END=579;MinDP=5;QS=3,0 PL:DP 0,48,255:16 0,24,198:8 0,15,144:5 -17 580 . A C,<*> 0 . DP=30;I16=15,14,1,0,1060,39178,16,256,1709,101641,60,3600,510,11078,17,289;QS=2.97338,0.0266223,0;SGB=-0.556633;RPBZ=1.32953;MQBZ=0.185695;MQSBZ=-1.06904;BQBZ=-1.69093;SCBZ=-0.267102;FS=0;MQ0F=0 PL:DP:DV 0,34,255,48,255,255:17:1 0,24,221,24,221,221:8:0 0,15,155,15,155,155:5:0 +17 580 . A C,<*> 0 . DP=30;I16=15,14,1,0,1060,39178,16,256,1709,101641,60,3600,510,11078,17,289;QS=2.97338,0.0266223,0;SGB=-0.556633;RPBZ=1.32953;MQBZ=0.185695;MQSBZ=-1.06904;BQBZ=-1.69093;SCBZ=-0.267102;MQ0F=0 PL:DP:DV 0,34,255,48,255,255:17:1 0,24,221,24,221,221:8:0 0,15,155,15,155,155:5:0 17 581 . A <*> . . MinDP=5;QS=3,0 PL:DP 0,54,255:18 0,24,223:8 0,15,153:5 -17 582 . C G,<*> 0 . DP=31;I16=15,15,1,0,1080,39870,8,64,1769,105241,60,3600,519,11211,15,225;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.34259;MQBZ=0.182574;MQSBZ=-1.0328;BQBZ=-1.68266;SCBZ=-0.262467;FS=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,24,207,24,207,207:8:0 0,15,151,15,151,151:5:0 +17 582 . C G,<*> 0 . DP=31;I16=15,15,1,0,1080,39870,8,64,1769,105241,60,3600,519,11211,15,225;QS=2.98734,0.0126582,0;SGB=-0.556633;RPBZ=1.34259;MQBZ=0.182574;MQSBZ=-1.0328;BQBZ=-1.68266;SCBZ=-0.262467;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,24,207,24,207,207:8:0 0,15,151,15,151,151:5:0 17 583 . T <*> . . END=592;MinDP=5;QS=3,0 PL:DP 0,51,255:17 0,21,209:7 0,15,155:5 -17 593 . C A,<*> 0 . DP=31;I16=16,14,0,1,1071,39925,7,49,1769,105241,29,841,561,12253,25,625;QS=2.97021,0.0297872,0;SGB=-0.556633;RPBZ=0.559355;MQBZ=-3.80789;MQSBZ=-0.0464238;BQBZ=-1.57464;SCBZ=3.67454;FS=0;MQ0F=0 PL:DP:DV 0,54,255,54,255,255:18:0 0,12,184,18,187,185:7:1 0,18,174,18,174,174:6:0 -17 594 . A G,<*> 0 . DP=33;I16=16,16,1,0,1161,42757,4,16,1858,109682,60,3600,572,12672,15,225;QS=2.99359,0.00641026,0;SGB=-0.556633;RPBZ=-0.998367;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68954;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:DV 0,42,255,51,255,255:18:1 0,21,205,21,205,205:7:0 0,24,213,24,213,213:8:0 +17 593 . C A,<*> 0 . DP=31;I16=16,14,0,1,1071,39925,7,49,1769,105241,29,841,561,12253,25,625;QS=2.97021,0.0297872,0;SGB=-0.556633;RPBZ=0.559355;MQBZ=-3.80789;MQSBZ=-0.0464238;BQBZ=-1.57464;SCBZ=3.67454;MQ0F=0 PL:DP:DV 0,54,255,54,255,255:18:0 0,12,184,18,187,185:7:1 0,18,174,18,174,174:6:0 +17 594 . A G,<*> 0 . DP=33;I16=16,16,1,0,1161,42757,4,16,1858,109682,60,3600,572,12672,15,225;QS=2.99359,0.00641026,0;SGB=-0.556633;RPBZ=-0.998367;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68954;SCBZ=-0.253876;MQ0F=0 PL:DP:DV 0,42,255,51,255,255:18:1 0,21,205,21,205,205:7:0 0,24,213,24,213,213:8:0 17 595 . A <*> . . MinDP=7;QS=3,0 PL:DP 0,54,255:18 0,21,198:7 0,24,218:8 -17 596 . A G,<*> 0 . DP=33;I16=16,16,1,0,1061,37187,8,64,1858,109682,60,3600,590,12952,1,1;QS=2.98564,0.0143627,0;SGB=-0.556633;RPBZ=1.68146;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68357;SCBZ=-0.253876;FS=0;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,21,169,21,169,169:7:0 0,24,231,24,231,231:8:0 +17 596 . A G,<*> 0 . DP=33;I16=16,16,1,0,1061,37187,8,64,1858,109682,60,3600,590,12952,1,1;QS=2.98564,0.0143627,0;SGB=-0.556633;RPBZ=1.68146;MQBZ=0.254;MQSBZ=-0.0435607;BQBZ=-1.68357;SCBZ=-0.253876;MQ0F=0 PL:DP:DV 0,41,255,51,255,255:18:1 0,21,169,21,169,169:7:0 0,24,231,24,231,231:8:0 17 597 . C <*> . . END=600;MinDP=7;QS=3,0 PL:DP 0,51,255:17 0,21,194:7 0,24,220:8 diff --git a/test/mpileup/mpileup.7.out b/test/mpileup/mpileup.7.out index 0df1f5a8a..df76ba6d5 100644 --- a/test/mpileup/mpileup.7.out +++ b/test/mpileup/mpileup.7.out @@ -12,7 +12,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -34,7 +33,7 @@ 17 112 . C <*> 0 . DP=9;I16=7,1,0,0,295,11875,0,0,449,26041,0,0,150,3170,0,0;QS=2,0;MQ0F=0 PL 0,9,103 0,15,135 17 113 . A <*> 0 . DP=9;I16=7,1,0,0,301,12565,0,0,449,26041,0,0,147,3101,0,0;QS=2,0;MQ0F=0 PL 0,9,102 0,15,139 17 114 . C <*> 0 . DP=9;I16=7,1,0,0,306,12386,0,0,449,26041,0,0,144,3042,0,0;QS=2,0;MQ0F=0 PL 0,9,113 0,15,133 -17 115 . C A,<*> 0 . DP=11;I16=7,2,1,0,321,13261,12,144,509,29641,29,841,117,2369,25,625;QS=1.88785,0.11215,0;SGB=-0.516033;RPBZ=0.174608;MQBZ=-2;MQSBZ=-1.125;BQBZ=-1.23359;SCBZ=-0.496904;FS=0;MQ0F=0 PL 3,0,86,9,89,93 0,21,153,21,153,153 +17 115 . C A,<*> 0 . DP=11;I16=7,2,1,0,321,13261,12,144,509,29641,29,841,117,2369,25,625;QS=1.88785,0.11215,0;SGB=-0.516033;RPBZ=0.174608;MQBZ=-2;MQSBZ=-1.125;BQBZ=-1.23359;SCBZ=-0.496904;MQ0F=0 PL 3,0,86,9,89,93 0,21,153,21,153,153 17 116 . A <*> 0 . DP=11;I16=8,2,0,0,354,14068,0,0,538,30482,0,0,141,2959,0,0;QS=2,0;MQ0F=0 PL 0,9,102 0,21,175 17 117 . G <*> 0 . DP=11;I16=8,2,0,0,356,14150,0,0,538,30482,0,0,140,2938,0,0;QS=2,0;MQ0F=0 PL 0,9,97 0,21,177 17 118 . G <*> 0 . DP=11;I16=8,2,0,0,303,11685,0,0,538,30482,0,0,139,2931,0,0;QS=2,0;MQ0F=0 PL 0,9,65 0,21,162 diff --git a/test/mpileup/mpileup.8.out b/test/mpileup/mpileup.8.out index e6c16c17c..7e3667c97 100644 --- a/test/mpileup/mpileup.8.out +++ b/test/mpileup/mpileup.8.out @@ -12,7 +12,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -22,29 +21,29 @@ 17 100 . C <*> 0 . DP=9;I16=9,0,0,0,350,14094,0,0,509,29641,0,0,159,3427,0,0;QS=1,0;MQ0F=0 PL 0,27,189 17 101 . C <*> 0 . DP=9;I16=9,0,0,0,331,12701,0,0,509,29641,0,0,159,3349,0,0;QS=1,0;MQ0F=0 PL 0,27,182 17 102 . C <*> 0 . DP=9;I16=9,0,0,0,349,13977,0,0,509,29641,0,0,159,3283,0,0;QS=1,0;MQ0F=0 PL 0,27,188 -17 103 . T C,<*> 0 . DP=9;I16=8,0,1,0,338,14304,6,36,480,28800,29,841,153,3193,6,36;QS=0.982558,0.0174419,0;SGB=-0.379885;RPBZ=-0.774597;MQBZ=-2.82843;BQBZ=-1.62549;SCBZ=2.82843;FS=0;MQ0F=0 PL 0,17,184,24,187,185 -17 104 . G C,<*> 0 . DP=9;I16=8,0,1,0,310,12224,3,9,480,28800,29,841,152,3138,7,49;QS=0.987261,0.0127389,0;SGB=-0.379885;RPBZ=-0.774597;MQBZ=-2.82843;BQBZ=-1.56227;SCBZ=2.82843;FS=0;MQ0F=0 PL 0,18,173,24,176,173 +17 103 . T C,<*> 0 . DP=9;I16=8,0,1,0,338,14304,6,36,480,28800,29,841,153,3193,6,36;QS=0.982558,0.0174419,0;SGB=-0.379885;RPBZ=-0.774597;MQBZ=-2.82843;BQBZ=-1.62549;SCBZ=2.82843;MQ0F=0 PL 0,17,184,24,187,185 +17 104 . G C,<*> 0 . DP=9;I16=8,0,1,0,310,12224,3,9,480,28800,29,841,152,3138,7,49;QS=0.987261,0.0127389,0;SGB=-0.379885;RPBZ=-0.774597;MQBZ=-2.82843;BQBZ=-1.56227;SCBZ=2.82843;MQ0F=0 PL 0,18,173,24,176,173 17 105 . G <*> 0 . DP=10;I16=10,0,0,0,318,11136,0,0,569,33241,0,0,159,3157,0,0;QS=1,0;MQ0F=0 PL 0,30,171 17 106 . G <*> 0 . DP=10;I16=10,0,0,0,372,14438,0,0,569,33241,0,0,160,3140,0,0;QS=1,0;MQ0F=0 PL 0,30,190 17 107 . C <*> 0 . DP=10;I16=10,0,0,0,372,14922,0,0,569,33241,0,0,161,3137,0,0;QS=1,0;MQ0F=0 PL 0,30,192 17 108 . C <*> 0 . DP=10;I16=10,0,0,0,367,14465,0,0,569,33241,0,0,162,3148,0,0;QS=1,0;MQ0F=0 PL 0,30,190 -17 109 . T C,<*> 0 . DP=10;I16=9,0,1,0,367,15083,2,4,540,32400,29,841,151,3029,12,144;QS=0.989218,0.0107817,0;SGB=-0.379885;RPBZ=-0.522233;MQBZ=-3;BQBZ=-1.59099;SCBZ=3;FS=0;MQ0F=0 PL 0,20,191,27,194,191 +17 109 . T C,<*> 0 . DP=10;I16=9,0,1,0,367,15083,2,4,540,32400,29,841,151,3029,12,144;QS=0.989218,0.0107817,0;SGB=-0.379885;RPBZ=-0.522233;MQBZ=-3;BQBZ=-1.59099;SCBZ=3;MQ0F=0 PL 0,20,191,27,194,191 17 110 . G <*> 0 . DP=10;I16=10,0,0,0,376,15242,0,0,569,33241,0,0,164,3212,0,0;QS=1,0;MQ0F=0 PL 0,30,194 17 111 . G <*> 0 . DP=10;I16=10,0,0,0,316,10760,0,0,569,33241,0,0,165,3265,0,0;QS=1,0;MQ0F=0 PL 0,30,167 -17 112 . C G,<*> 0 . DP=10;I16=9,0,1,0,362,14690,2,4,540,32400,29,841,151,3107,15,225;QS=0.989071,0.010929,0;SGB=-0.379885;RPBZ=-0.174078;MQBZ=-3;BQBZ=-1.61126;SCBZ=3;FS=0;MQ0F=0 PL 0,20,187,27,190,187 -17 113 . A G,<*> 0 . DP=10;I16=9,0,1,0,334,12490,4,16,540,32400,29,841,150,3106,16,256;QS=0.988166,0.0118343,0;SGB=-0.379885;RPBZ=-0.174078;MQBZ=-3;BQBZ=-1.57628;SCBZ=3;FS=0;MQ0F=0 PL 0,20,172,27,175,172 +17 112 . C G,<*> 0 . DP=10;I16=9,0,1,0,362,14690,2,4,540,32400,29,841,151,3107,15,225;QS=0.989071,0.010929,0;SGB=-0.379885;RPBZ=-0.174078;MQBZ=-3;BQBZ=-1.61126;SCBZ=3;MQ0F=0 PL 0,20,187,27,190,187 +17 113 . A G,<*> 0 . DP=10;I16=9,0,1,0,334,12490,4,16,540,32400,29,841,150,3106,16,256;QS=0.988166,0.0118343,0;SGB=-0.379885;RPBZ=-0.174078;MQBZ=-3;BQBZ=-1.57628;SCBZ=3;MQ0F=0 PL 0,20,172,27,175,172 17 114 . C <*> 0 . DP=10;I16=10,0,0,0,354,13490,0,0,569,33241,0,0,166,3404,0,0;QS=1,0;MQ0F=0 PL 0,30,181 17 115 . C <*> 0 . DP=10;I16=10,0,0,0,367,14165,0,0,569,33241,0,0,166,3458,0,0;QS=1,0;MQ0F=0 PL 0,30,189 -17 116 . A C,<*> 0 . DP=10;I16=9,0,1,0,351,13723,2,4,540,32400,29,841,146,3114,19,361;QS=0.988732,0.0112676,0;SGB=-0.379885;RPBZ=0.174078;MQBZ=-3;BQBZ=-1.59099;SCBZ=3;FS=0;MQ0F=0 PL 0,20,179,27,182,179 +17 116 . A C,<*> 0 . DP=10;I16=9,0,1,0,351,13723,2,4,540,32400,29,841,146,3114,19,361;QS=0.988732,0.0112676,0;SGB=-0.379885;RPBZ=0.174078;MQBZ=-3;BQBZ=-1.59099;SCBZ=3;MQ0F=0 PL 0,20,179,27,182,179 17 117 . G <*> 0 . DP=10;I16=10,0,0,0,359,13895,0,0,569,33241,0,0,164,3506,0,0;QS=1,0;MQ0F=0 PL 0,30,185 17 118 . G <*> 0 . DP=9;I16=9,0,0,0,317,11785,0,0,509,29641,0,0,164,3550,0,0;QS=1,0;MQ0F=0 PL 0,27,175 17 119 . G <*> 0 . DP=9;I16=9,0,0,0,320,12116,0,0,509,29641,0,0,164,3606,0,0;QS=1,0;MQ0F=0 PL 0,27,176 -17 120 . A G,<*> 0 . DP=9;I16=8,0,1,0,311,12135,4,16,480,28800,29,841,141,3145,23,529;QS=0.987302,0.0126984,0;SGB=-0.379885;RPBZ=0.387298;MQBZ=-2.82843;BQBZ=-1.55569;SCBZ=2.82843;FS=0;MQ0F=0 PL 0,18,171,24,174,171 +17 120 . A G,<*> 0 . DP=9;I16=8,0,1,0,311,12135,4,16,480,28800,29,841,141,3145,23,529;QS=0.987302,0.0126984,0;SGB=-0.379885;RPBZ=0.387298;MQBZ=-2.82843;BQBZ=-1.55569;SCBZ=2.82843;MQ0F=0 PL 0,18,171,24,174,171 17 121 . G <*> 0 . DP=9;I16=9,0,0,0,327,12691,0,0,509,29641,0,0,163,3703,0,0;QS=1,0;MQ0F=0 PL 0,27,181 17 122 . C <*> 0 . DP=9;I16=9,0,0,0,324,12880,0,0,509,29641,0,0,162,3742,0,0;QS=1,0;MQ0F=0 PL 0,27,180 17 123 . T <*> 0 . DP=8;I16=8,0,0,0,288,11074,0,0,449,26041,0,0,161,3739,0,0;QS=1,0;MQ0F=0 PL 0,24,170 17 124 . T <*> 0 . DP=9;I16=9,0,0,0,276,9034,0,0,509,29641,0,0,160,3742,0,0;QS=1,0;MQ0F=0 PL 0,27,154 -17 125 . A T,<*> 0 . DP=8;I16=7,0,1,0,253,9195,4,16,420,25200,29,841,136,3126,25,625;QS=0.984436,0.0155642,0;SGB=-0.379885;RPBZ=1.09109;MQBZ=-2.64575;BQBZ=-1.5367;SCBZ=2.64575;FS=0;MQ0F=0 PL 0,15,149,21,152,149 +17 125 . A T,<*> 0 . DP=8;I16=7,0,1,0,253,9195,4,16,420,25200,29,841,136,3126,25,625;QS=0.984436,0.0155642,0;SGB=-0.379885;RPBZ=1.09109;MQBZ=-2.64575;BQBZ=-1.5367;SCBZ=2.64575;MQ0F=0 PL 0,15,149,21,152,149 17 126 . A <*> 0 . DP=8;I16=8,0,0,0,275,9967,0,0,449,26041,0,0,162,3766,0,0;QS=1,0;MQ0F=0 PL 0,24,162 17 127 . C <*> 0 . DP=8;I16=8,0,0,0,280,10340,0,0,449,26041,0,0,163,3787,0,0;QS=1,0;MQ0F=0 PL 0,24,163 17 128 . A <*> 0 . DP=8;I16=8,0,0,0,295,11123,0,0,449,26041,0,0,164,3814,0,0;QS=1,0;MQ0F=0 PL 0,24,169 diff --git a/test/mpileup/mpileup.9.out b/test/mpileup/mpileup.9.out index 42656823d..afb2ec816 100644 --- a/test/mpileup/mpileup.9.out +++ b/test/mpileup/mpileup.9.out @@ -12,7 +12,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -34,7 +33,7 @@ 17 112 . C <*> 0 . DP=9;I16=7,1,0,0,295,11875,0,0,449,26041,0,0,150,3170,0,0;QS=2,0;MQ0F=0 PL 0,9,103 0,15,135 17 113 . A <*> 0 . DP=9;I16=7,1,0,0,301,12565,0,0,449,26041,0,0,147,3101,0,0;QS=2,0;MQ0F=0 PL 0,9,102 0,15,139 17 114 . C <*> 0 . DP=9;I16=7,1,0,0,306,12386,0,0,449,26041,0,0,144,3042,0,0;QS=2,0;MQ0F=0 PL 0,9,113 0,15,133 -17 115 . C A,<*> 0 . DP=11;I16=7,2,1,0,321,13261,12,144,509,29641,29,841,117,2369,25,625;QS=1.88785,0.11215,0;SGB=-0.516033;RPBZ=0.174608;MQBZ=-2;MQSBZ=-1.125;BQBZ=-1.23359;SCBZ=-0.496904;FS=0;MQ0F=0 PL 3,0,86,9,89,93 0,21,153,21,153,153 +17 115 . C A,<*> 0 . DP=11;I16=7,2,1,0,321,13261,12,144,509,29641,29,841,117,2369,25,625;QS=1.88785,0.11215,0;SGB=-0.516033;RPBZ=0.174608;MQBZ=-2;MQSBZ=-1.125;BQBZ=-1.23359;SCBZ=-0.496904;MQ0F=0 PL 3,0,86,9,89,93 0,21,153,21,153,153 17 116 . A <*> 0 . DP=11;I16=8,2,0,0,354,14068,0,0,538,30482,0,0,141,2959,0,0;QS=2,0;MQ0F=0 PL 0,9,102 0,21,175 17 117 . G <*> 0 . DP=11;I16=8,2,0,0,356,14150,0,0,538,30482,0,0,140,2938,0,0;QS=2,0;MQ0F=0 PL 0,9,97 0,21,177 17 118 . G <*> 0 . DP=11;I16=8,2,0,0,303,11685,0,0,538,30482,0,0,139,2931,0,0;QS=2,0;MQ0F=0 PL 0,9,65 0,21,162 From 73a25b0ac281cd57627a7ad090d053b439c53991 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Thu, 15 Dec 2022 16:49:44 +0100 Subject: [PATCH 63/84] Minor usage page clarification --- plugins/split-vep.c | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/plugins/split-vep.c b/plugins/split-vep.c index 5914d27c4..a0517a5c8 100644 --- a/plugins/split-vep.c +++ b/plugins/split-vep.c @@ -202,7 +202,8 @@ static const char *usage_text(void) " \"tab\", \"space\" or an arbitrary string.\n" " -c, --columns [LIST|-][:TYPE] Extract the fields listed either as 0-based indexes or names, \"-\" to extract all\n" " fields. See --columns-types for the defaults. Supported types are String/Str,\n" - " Integer/Int and Float/Real. Unlisted fields are set to String.\n" + " Integer/Int and Float/Real. Unlisted fields are set to String. Existing header\n" + " definitions will not be overwritten, remove first with `bcftools annotate -x`\n" " --columns-types -|FILE Pass \"-\" to print the default -c types or FILE to override the presets\n" " -d, --duplicate Output per transcript/allele consequences on a new line rather rather than\n" " as comma-separated fields on a single line\n" From d80188cdf5bd0ff1a08e595ad37ff3b22b0bb0af Mon Sep 17 00:00:00 2001 From: "Dr. K. D. Murray" <1560490+kdm9@users.noreply.github.com> Date: Mon, 19 Dec 2022 11:53:49 +0100 Subject: [PATCH 64/84] concat: don't always error when setting --verbose Currently giving `--verbose` with any argument errors out. This check implements the conditional which the error message describes. --- vcfconcat.c | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/vcfconcat.c b/vcfconcat.c index 0246b59f5..74fd036b8 100644 --- a/vcfconcat.c +++ b/vcfconcat.c @@ -1018,8 +1018,8 @@ int main_vcfconcat(int argc, char *argv[]) if ( args->regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg); break; case 'v': - args->verbose = strtol(optarg, 0, 0); - error("Error: currently only --verbose 0 or --verbose 1 is supported\n"); + args->verbose = strtol(optarg, &tmp, 0); + if ( *tmp || args->verbose<0 || args->verbose>1 ) error("Error: currently only --verbose 0 or --verbose 1 is supported\n"); break; case 'h': case '?': usage(args); break; From 1f50f07a65ecc2e6137bda4d5d3df41b0900cdaf Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Tue, 3 Jan 2023 11:35:48 +0000 Subject: [PATCH 65/84] Split complex indels Originally copmlex indels C>GGGG would not be atomized, newly they are split properly as C>G C>CGGG Resolves #1832 --- NEWS | 5 ++++- abuf.c | 21 +++++++++++++++++---- test/atomize.split.4.1.out | 12 ++++++++++++ test/atomize.split.4.vcf | 6 ++++++ test/test.pl | 3 ++- 5 files changed, 41 insertions(+), 6 deletions(-) create mode 100644 test/atomize.split.4.1.out create mode 100644 test/atomize.split.4.vcf diff --git a/NEWS b/NEWS index 455a6b827..6024aa77a 100644 --- a/NEWS +++ b/NEWS @@ -47,7 +47,7 @@ Changes affecting specific commands: function of the plugin is the same but the command line options and the output format has changed, and for this was introduced as a new plugin. -* mpileup +* bcftools mpileup - Most of the annotations generated by mpileup are now optional via the `-a, --annotate` option and add several new (mostly experimental) annotations. @@ -68,6 +68,9 @@ Changes affecting specific commands: - Fixed a bug in `-m -` which does not split missing FORMAT values correctly and could lead to empty FORMAT fields such as `::` instead of the correct `:.:` (#1818) + - The `--atomize` option previously would not split complex indels such as C>GGG. + Newly these will be split into two records C>G and C>CGG (#1832) + * bcftools query - Fix a rare bug where the printing of SAMPLE field with `query` was incorrectly diff --git a/abuf.c b/abuf.c index 78682d667..7958cf570 100644 --- a/abuf.c +++ b/abuf.c @@ -1,6 +1,6 @@ /* The MIT License - Copyright (c) 2021-2022 Genome Research Ltd. + Copyright (c) 2021-2023 Genome Research Ltd. Author: Petr Danecek @@ -154,8 +154,19 @@ static void _atomize_allele(abuf_t *buf, bcf1_t *rec, int ial) assert(atom); if ( altb!='-' ) kputc(altb, &atom->alt); if ( refb!='-' ) { kputc(refb, &atom->ref); atom->end++; } + continue; } - else + buf->natoms++; + hts_expand0(atom_t,buf->natoms,buf->matoms,buf->atoms); + atom = &buf->atoms[buf->natoms-1]; + atom->ref.l = 0; + atom->alt.l = 0; + kputc(refb, &atom->ref); + kputc(altb, &atom->alt); + atom->beg = atom->end = i; + atom->ial = ial; + + if ( rlen!=alen && (i+1>=rlen || i+1>=alen) ) // the next base is an indel combined with SNV, e.g. C>GGG? { buf->natoms++; hts_expand0(atom_t,buf->natoms,buf->matoms,buf->atoms); @@ -163,13 +174,13 @@ static void _atomize_allele(abuf_t *buf, bcf1_t *rec, int ial) atom->ref.l = 0; atom->alt.l = 0; kputc(refb, &atom->ref); - kputc(altb, &atom->alt); + kputc(refb, &atom->alt); atom->beg = atom->end = i; atom->ial = ial; } continue; } - if ( i+1>=rlen || i+1>=alen ) // is the next base a deletion? + if ( i+1>=rlen || i+1>=alen ) // is the next base an indel? { buf->natoms++; hts_expand0(atom_t,buf->natoms,buf->matoms,buf->atoms); @@ -742,6 +753,8 @@ void _abuf_split(abuf_t *buf, bcf1_t *rec) _split_table_overlap(buf, j, atom); } } + // _split_table_print(buf); + // _split_table_print_atoms(buf); assert( !buf->rbuf.n ); // all records should be flushed first in the SPLIT mode // Create the output records, transferring all annotations: diff --git a/test/atomize.split.4.1.out b/test/atomize.split.4.1.out new file mode 100644 index 000000000..84b94e2b8 --- /dev/null +++ b/test/atomize.split.4.1.out @@ -0,0 +1,12 @@ +##fileformat=VCFv4.3 +##FILTER= +##contig= +##INFO= +#CHROM POS ID REF ALT QUAL FILTER INFO +11 100 . C G . . OLD_REC=11|100|CC|GG|1 +11 101 . C G . . OLD_REC=11|100|CC|GG|1 +11 200 . C G . . OLD_REC=11|200|CC|GGGG|1 +11 201 . C CGG . . OLD_REC=11|200|CC|GGGG +11 201 . C G . . OLD_REC=11|200|CC|GGGG +11 300 . C CGGG . . OLD_REC=11|300|C|GGGG +11 300 . C G . . OLD_REC=11|300|C|GGGG diff --git a/test/atomize.split.4.vcf b/test/atomize.split.4.vcf new file mode 100644 index 000000000..daf39ef93 --- /dev/null +++ b/test/atomize.split.4.vcf @@ -0,0 +1,6 @@ +##fileformat=VCFv4.3 +##contig= +#CHROM POS ID REF ALT QUAL FILTER INFO +11 100 . CC GG . . . +11 200 . CC GGGG . . . +11 300 . C GGGG . . . diff --git a/test/test.pl b/test/test.pl index 75559e1be..c2a0793b8 100755 --- a/test/test.pl +++ b/test/test.pl @@ -1,6 +1,6 @@ #!/usr/bin/env perl # -# Copyright (C) 2012-2022 Genome Research Ltd. +# Copyright (C) 2012-2023 Genome Research Ltd. # # Author: Petr Danecek # @@ -262,6 +262,7 @@ run_test(\&test_vcf_norm,$opts,in=>'atomize.split.2',out=>'atomize.split.2.1.out',args=>'--atomize --old-rec-tag OLD_REC'); run_test(\&test_vcf_norm,$opts,in=>'atomize.split.2',out=>'atomize.split.2.2.out',args=>'--atomize --atom-overlaps . --old-rec-tag OLD_REC'); run_test(\&test_vcf_norm,$opts,in=>'atomize.split.3',out=>'atomize.split.3.1.out',args=>'--atomize --atom-overlaps .'); +run_test(\&test_vcf_norm,$opts,in=>'atomize.split.4',out=>'atomize.split.4.1.out',args=>'--atomize --atom-overlaps . --old-rec-tag OLD_REC'); run_test(\&test_vcf_norm,$opts,in=>'norm.4',out=>'norm.4.1.out',args=>'-m +both'); run_test(\&test_vcf_norm,$opts,in=>'norm.4',out=>'norm.4.2.out',args=>'-m +any'); run_test(\&test_vcf_norm,$opts,in=>'norm.5',out=>'norm.5.1.out',args=>'-m - --multi-overlaps 0'); From be18428bd2cd8f6ef2a297e945cf3f7157154bda Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Tue, 3 Jan 2023 16:40:19 +0000 Subject: [PATCH 66/84] Add error checks to prevent incorrect use of vector arithmetics in -i/-e. For example, when evaluating the sum of two vectors A and B, the resulting vector could contain nonsense values when the input vectors were not of the same length. The fix introduces the following logic: - evaluate to C_i = A_i + B_i when length(A)==B(A) and set length(C)=length(A) - evaluate to C_i = A_i + B_0 when length(B)=1 and set length(C)=length(A) - evaluate to C_i = A_0 + B_i when length(A)=1 and set length(C)=length(B) - throw an error when length(A)!=length(B) AND length(A)!=1 AND length(B)!=1 Also fixes a related issue in the fill-tags plugin where custom expressions (`-t TAG:Number=Type(EXPR)`) could assign values to incorrect samples. --- NEWS | 14 ++++++++++++++ doc/bcftools.txt | 7 +++++++ filter.c | 43 ++++++++++++++++++++++++++++++++++++------- plugins/fill-tags.c | 6 +++--- 4 files changed, 60 insertions(+), 10 deletions(-) diff --git a/NEWS b/NEWS index 6024aa77a..8d228c369 100644 --- a/NEWS +++ b/NEWS @@ -1,5 +1,19 @@ ## Release a.b +Changes affecting the whole of bcftools, or multiple commands: + +* The -i/-e filtering expressions + + - Error checks were added to prevent incorrect use of vector arithmetics. For example, + when evaluating the sum of two vectors A and B, the resulting vector could contain + nonsense values when the input vectors were not of the same length. The fix introduces + the following logic: + - evaluate to C_i = A_i + B_i when length(A)==B(A) and set length(C)=length(A) + - evaluate to C_i = A_i + B_0 when length(B)=1 and set length(C)=length(A) + - evaluate to C_i = A_0 + B_i when length(A)=1 and set length(C)=length(B) + - throw an error when length(A)!=length(B) AND length(A)!=1 AND length(B)!=1 + + Changes affecting specific commands: * bcftools annotate diff --git a/doc/bcftools.txt b/doc/bcftools.txt index cf7d9085e..7a0e572f7 100644 --- a/doc/bcftools.txt +++ b/doc/bcftools.txt @@ -3593,6 +3593,13 @@ used on the result. For example, when querying "TAG=1,2,3,4", it will be evaluat -e 'TAG[0]=1' .. false -e 'TAG[0]!=1' .. true +* When arithmetic operators are used on vectors A and B, the following logic is used to + compute the resulting vector C: + + - C_i = A_i + B_i when length(A)==B(A) and sets length(C)=length(A) + - C_i = A_i + B_0 when length(B)=1 and sets length(C)=length(A) + - C_i = A_0 + B_i when length(A)=1 and sets length(C)=length(B) + - throw an error when length(A)!=length(B) AND length(A)!=1 AND length(B)!=1 *Examples:* diff --git a/filter.c b/filter.c index d54560896..c87e44777 100644 --- a/filter.c +++ b/filter.c @@ -1,6 +1,6 @@ /* filter.c -- filter expressions. - Copyright (C) 2013-2022 Genome Research Ltd. + Copyright (C) 2013-2023 Genome Research Ltd. Author: Petr Danecek @@ -1974,18 +1974,47 @@ inline static void tok_init_samples(token_t *atok, token_t *btok, token_t *rtok) { \ tok_init_values(atok, btok, rtok); \ tok_init_samples(atok, btok, rtok); \ - if ( (atok->nsamples && btok->nsamples) || (!atok->nsamples && !btok->nsamples)) \ + if ( !atok->nsamples && !btok->nsamples ) \ { \ - assert( atok->nsamples==btok->nsamples ); \ - for (i=0; invalues; i++) \ + if ( atok->nvalues!=btok->nvalues && atok->nvalues!=1 && btok->nvalues!=1 ) \ + error("Cannot run numeric operator in -i/-e filtering on vectors of different lengths: %d vs %d\n",atok->nvalues,btok->nvalues); \ + int ir,ia = 0, ib = 0; \ + for (ir=0; irnvalues; ir++) \ { \ - if ( bcf_double_is_missing_or_vector_end(atok->values[i]) || bcf_double_is_missing_or_vector_end(btok->values[i]) ) \ + if ( atok->nvalues > 1 ) ia = ir; \ + if ( btok->nvalues > 1 ) ib = ir; \ + if ( bcf_double_is_missing_or_vector_end(atok->values[ia]) || bcf_double_is_missing_or_vector_end(btok->values[ib]) ) \ { \ - bcf_double_set_missing(rtok->values[i]); \ + bcf_double_set_missing(rtok->values[ir]); \ continue; \ } \ has_values = 1; \ - rtok->values[i] = TYPE atok->values[i] AOP TYPE btok->values[i]; \ + rtok->values[ir] = TYPE atok->values[ia] AOP TYPE btok->values[ib]; \ + } \ + } \ + else if ( atok->nsamples && btok->nsamples ) \ + { \ + assert( atok->nsamples==btok->nsamples ); \ + if ( atok->nval1!=btok->nval1 && atok->nval1!=1 && btok->nval1!=1 ) \ + error("Cannot run numeric operator in -i/-e filtering on vectors of different lengths: %d vs %d\n",atok->nval1,btok->nval1); \ + for (i=0; insamples; i++) \ + { \ + double *rval = rtok->values + i*rtok->nval1; \ + double *aval = atok->values + i*atok->nval1; \ + double *bval = btok->values + i*btok->nval1; \ + int ir,ia = 0, ib = 0; \ + for (ir=0; irnval1; ir++) \ + { \ + if ( atok->nval1 > 1 ) ia = ir; \ + if ( btok->nval1 > 1 ) ib = ir; \ + if ( bcf_double_is_missing_or_vector_end(aval[ia]) || bcf_double_is_missing_or_vector_end(bval[ib]) ) \ + { \ + bcf_double_set_missing(rval[ir]); \ + continue; \ + } \ + has_values = 1; \ + rval[ir] = TYPE aval[ia] AOP TYPE bval[ib]; \ + } \ } \ } \ else if ( atok->nsamples ) \ diff --git a/plugins/fill-tags.c b/plugins/fill-tags.c index 79aeebdd6..124595b75 100644 --- a/plugins/fill-tags.c +++ b/plugins/fill-tags.c @@ -1,6 +1,6 @@ /* The MIT License - Copyright (c) 2015-2022 Genome Research Ltd. + Copyright (c) 2015-2023 Genome Research Ltd. Author: Petr Danecek @@ -318,7 +318,7 @@ int ftf_filter_expr(args_t *args, bcf1_t *rec, pop_t *pop, ftf_t *ftf) hts_expand(float,nfill*rec->n_sample,ftf->nfval,ftf->fval); for (k=0; kn_sample; k++) { - float *dst = ftf->fval + k*nval1; + float *dst = ftf->fval + k*nfill; const double *src = val + k*nval1; for (j=0; jn_sample,ftf->nival,ftf->ival); for (k=0; kn_sample; k++) { - int32_t *dst = ftf->ival + k*nval1; + int32_t *dst = ftf->ival + k*nfill; const double *src = val + k*nval1; for (j=0; j Date: Wed, 4 Jan 2023 16:31:07 +0000 Subject: [PATCH 67/84] Fix overflow for indels longer than 512bp. Fixes #1837 --- NEWS | 5 +++++ plugins/allele-length.c | 9 +++++++-- test/query.allele-length.tsv | 6 +++--- test/query.nucleotide.vcf | 1 + 4 files changed, 16 insertions(+), 5 deletions(-) diff --git a/NEWS b/NEWS index 8d228c369..00e164dd8 100644 --- a/NEWS +++ b/NEWS @@ -16,6 +16,11 @@ Changes affecting the whole of bcftools, or multiple commands: Changes affecting specific commands: +* bcftools +allele-length + + - fix overflow for indels longer than 512bp and aggregate alleles equal or larger than + that in the same bin (#1837) + * bcftools annotate - Support sample reordering of annotation file (#1785) diff --git a/plugins/allele-length.c b/plugins/allele-length.c index 718fb8250..b9372080d 100644 --- a/plugins/allele-length.c +++ b/plugins/allele-length.c @@ -1,6 +1,7 @@ /* plugins/allele-length.c -- Calculate stats about the length of alleles Copyright (C) 2017-2018 GENOMICS plc. + Copyright (C) 2023 Genome Research Ltd. Author: Nicola Asuni @@ -89,12 +90,16 @@ bcf1_t *process(bcf1_t *rec) { int rl = strlen(rec->d.allele[0]); int al = strlen(rec->d.allele[1]); + int ral = rl + al; + if ( rl >= MAXLEN ) rl = MAXLEN - 1; + if ( al >= MAXLEN ) al = MAXLEN - 1; + if ( ral >= MAXLEN ) ral = MAXLEN - 1; reflen[rl] += 1; altlen[al] += 1; - refaltlen[(rl + al)] += 1; + refaltlen[ral] += 1; if ((contain_non_base(rec->d.allele[0])) || (contain_non_base(rec->d.allele[1]))) { - xrefaltlen[(rl + al)] += 1; + xrefaltlen[ral] += 1; numxvar++; } numvar++; diff --git a/test/query.allele-length.tsv b/test/query.allele-length.tsv index c9fcdcb79..27c6b09ea 100644 --- a/test/query.allele-length.tsv +++ b/test/query.allele-length.tsv @@ -1,6 +1,6 @@ LENGTH REF ALT REF+ALT REF+ALT WITH NON-BASE NUCLEOTIDES 0 0 0 0 0 -1 53 56 0 0 +1 53 57 0 0 2 9 10 43 0 3 1 0 19 1 4 0 0 1 0 @@ -510,5 +510,5 @@ LENGTH REF ALT REF+ALT REF+ALT WITH NON-BASE NUCLEOTIDES 508 0 0 0 0 509 0 0 0 0 510 0 0 0 0 -511 0 0 0 0 - 66 1 +511 1 0 1 0 + 67 1 diff --git a/test/query.nucleotide.vcf b/test/query.nucleotide.vcf index a3d30efae..fd9beaa41 100644 --- a/test/query.nucleotide.vcf +++ b/test/query.nucleotide.vcf @@ -148,3 +148,4 @@ 1 11014 rs28484712 G A . . RS=28484712;RSPOS=11014;dbSNPBuildID=125;SSR=0;SAO=0;VP=0x050000020005000002000100;GENEINFO=DDX11L1:100287102;WGT=1;VC=SNV;R5;ASP 1 11022 rs28775022 G A . . RS=28775022;RSPOS=11022;dbSNPBuildID=125;SSR=0;SAO=0;VP=0x050000020005000002000100;GENEINFO=DDX11L1:100287102;WGT=1;VC=SNV;R5;ASP 1 11063 rs561109771 T G . . RS=561109771;RSPOS=11063;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000020005040024000100;GENEINFO=DDX11L1:100287102;WGT=1;VC=SNV;R5;ASP;VLD;KGPhase3;CAF=0.997,0.002995;COMMON=1 +1 22222 . AGTTCAGGGCCTGGAGAGAAGGCTGGGAGGCAGGAGCTGGGTCTAAAGAGGCCATTGTAACGATGGAGCTGTGCCTGTGGAGGCTGTTGTGAGGCAGTAGCCTCATCTGCGGAGGCTGCCGTGACATAGGGTATGGGCCTAAATAGGCCATTGTGAGTCATGAGCTTGGTCTGTAGAGGCTGACTGGAGAAAGTTCTGGGCCTGGAGAGGCTGCCGGGAGGTAGGAGCTGGGCCAAAAGATGTAAGCACATTTGCATTTATTAGGCACTTTATTTCCATTATTACACTGTAATATATAATAAAATAATTATAGAACTCACCATAATGTAGAATTAGTGGGCGTGTTAAGCTTGTTTTCCTGCAACTGAATGGTCCCACCTGAGCGTGATGGGAGAAAGTGACAGATCAATAGGTATTAGATTCTCATAAGGACAGCGCAACCTCGATCCCTCACATGCACGGTTCACAACAGGGTGCGTTCTCCTATGAGCATCTAATGCTGCTGCTCATCTGAGAAGGTGGAGCTCAGGTGGGAATGTGAGCAAAGGGGAGTGGCTCTAAATACAGACGAAGCTTCCCTCACTCCCTCACTCGACACCGCTCACCTCCTGCTGTGTGGCTCCTTGCGGCTCCATGGCTCAGGGGTTGGGGACCCCTGCTCAAGTGCATCCAAAGCGACCCTTCCCACACCAGTCTTCACAGTGGTCAAGGGCAGCAACCACTTAGCTCCCAAGGCATGTGCCTCAGCTGGCATTTCGTCACAATCAACAGTAAGTGGTAGCTTGAGTCACTGTGAGGTCACCTACTGGAAATCACCAGCACCCCATTTCCCACTGGCAAAGAGCTCAGCACTGCCCCCTGGGAAACCAAACCTATGCCCAAATCCCATCTGTGTGGGTCTACCTCCTGGGACCCTTCCTAACATATTAGTCAGAGTCCAATCAGGAAGCATAAACCACTCAAAAGTTTAAAGTGGTAAAATTTAATACAGAGAATTATTCATTATAACAGGTGAACAGCATAATGAGAGATTGGCTAGCACAGAGTAAAGAGAACTCTAGAGAATATGGGACTAGCCCAGGCCAGGCATGGTGGCTCATGCCTGAAATTCCAGCCATTACAGAAGCTAATGCAGGAGGATTGCTTAAGGCCAGGAGCTAGAGACCGGTCTGGACGACACAGTGAGACCCTGTCTCTATCCAAAAGAAGAAAAAAGTTAGCTGGGGGTGGTGGTGCACACTTGTAGTCCCAGCTACTCAGAATGCTGAAGTTTGAGCCTGGGAGGTCAAGGCTGCAGTGAGGCATGATTATGCCACTACAGTCCAGCCGGATGACAGAGCAAGACCCTGTCTCAAAGAACAAAACCACAACAACCATTTACAGACAGAAAAGAAATAGAGCTAATAAGCTGAGGAAAGATGTTGAAATGTGACAAGTAAAGTAATATGAGGTCTTTTGTCTATTTAAAATAATCAAACAAAAAATGGCTTACGAAATTATAATACCCTGTGCTGGCAAAGGTGCAGTGAAATGGGCACTTTCTTATACTATGAGGGGTGGTTAAATTGTGTATAAGCCTTCCAGGGTAAAGCCTGTCAATTTTTTAAAATAATGGAGACAGGGTCTCACCATACTGCCATACTGCCTCCTCCAACTCTTGGCCTCAAGCAATCCTCCTCTCTTAGCCTCCCAAAGTGCTAAGATTATAGCTGGGAGGCACCCAAAACCCTGTCAATTTACATCAAGGGTAAGGAGAATGTCCATTCACCATGACTCACAGTAATCTTACTTCTGGGGAGACAATTCAATCTAAGCAAAAGGTCATCTGTACACACACAGTAAAAATCTGGGAGTAACTGAAGACAGAGTTGGTAAGTGAAATAAGAAACAGTTATAAGAAATTAAACTATGGTATCAATAGGCACCTGGTAAAAGGTCAGTTGATGTTAGCTGCTACTTTTTTGTTGTTTTGAGACAGGGTCTCACTCTGTCACCCAGGCTGGAGTGCAGAGGCCTGATCATGACTCACTGCAGTCTCAGCCTCCCTGGGCTCAAGTGATCCTCCCACCTCAGCCTCCCAAGTAGCTGGGACTACAGGAACATGCCACCACACTAGGCTAATTCATGTATTTTTCTGTAGGGATGGTGACTCCCCCTTTGTTTCCAAGGCCTATCGCAAACTCTTGGCCTCGAGCCATCCTCCTGCCTCAGCCTCCCAAAGTGTTGTGATTACCAGTGTGAGCCACCACACCTGGCCAGCTGCTACTTTTATCAATATTATTCTTATTCCACTCAATTAAAAATTATTATTTTCAAGGCTATGCAACAGTATGTATCCTACAGCGTAATTGTAAAAACATACACAGTCGTCATCCCTCAGTATACAGAATTAGTTCCAGCCCCCCATCTCTGCATATACCAAAATCCATGCTTACTCACGTTTCGCTGTCACCCCTCTAGAATCCACGTATACGAAAATTCCAAATGTTAGTTGGGCATAGTGGCAAGCACCTGTAGTCTCAGCCACGTGGGAGGTTGAGGTGGGAGGATCGCTTCAGCCTGGAAGGTTGAGGCTGCAGTCAGCTGCGATAGCACTACTACACTCCAGCCTTGGACAACAGAGGGAGACCCTGTCTCAGAAAAAAAAACAAAATAAAACAGGTTAGAAATTGTAATGAGGTCTGCTGGGCAAAATTCCATATAAGCAATGTATAAATTAATAAAGCAAATCGTGATAAATTAGTACGATTGACTTTCTGGAGTTTCTGACAATAAAAGTAAGGAAAATGCAGAACACAAAGACAGAGAGTAAAAAGAGAAATTAGGAAAGCATTCTACATGTTGAATAGGAAGACACTGGCCATGTTCGTGCAGCGGCAGTATGTCGTGACATGACATACCTTGGAGAGAAGTTAACAGATGAGGAAGTTGATAAAAATCATCAGAGAAGCAAAATACTGGTAGCGACACTCAAGTAAACCATGAAATTTCCATAACTTATGTCAGCAAAGTGGGAATATTGTACAGTGTGTGTTGAAGTTCCTATACAACATTGTTTATCTGCCTTTTGTTTGTTTGTAAGGAATGTACATACTAAAAGTTCTTCTTGCTGTCAAAAGAATATGCGTGAATAAGTCATTTTAACTTATTCTTCTGTTTTTCTTTTATCTTCCTGCCATCATCCCACAGCCTTACTTTAGAAATTTCTTTTTTAGAAAATTGAACAAGTGCTCCCTGTGGTGGCACATACCTCGAGGATGGGAGGCAGGGGTGGAAGGGTCACTTGAGGCCATTAGTTTGACACCAGCCTGGCCAACAAAGTGAGACCCCGTGTCTACAAAACAATTTAAAAATTAGCCAAGTATCGTCATGTATACCTACAGTCCCAGCTATCTGAACTTACTGAGAAT A . . . From 959265512db00b0e8e9c3cba6492d6c7a185c491 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Mon, 9 Jan 2023 09:49:12 +0000 Subject: [PATCH 68/84] Per-sample stats (PSC) would not be computed when the `-i/-e` filtering options and the `-s -` were given unless the expression included sample columns. This was a consequence of misfired performance optimization that tells htslib to excludes sample columns from parsing when they are not needed. Fixes #1835 --- NEWS | 5 +++++ test/stats.counts.2.chk | 36 ++++++++++++++++++++++++++++++++++++ test/test.pl | 1 + vcfstats.c | 3 ++- 4 files changed, 44 insertions(+), 1 deletion(-) create mode 100644 test/stats.counts.2.chk diff --git a/NEWS b/NEWS index 00e164dd8..70c3b01bf 100644 --- a/NEWS +++ b/NEWS @@ -107,6 +107,11 @@ Changes affecting specific commands: - New `-H, --print-header` option to print the header with `-f` +* bcftools stats + + - The per-sample stats (PSC) would not be computed when `-i/-e` filtering options and + the `-s -` option were given but the expression did not include sample columns (1835) + * bcftools +trio-dnm2 - New `-n, --strictly-novel` option to downplay alleles which violate Mendelian diff --git a/test/stats.counts.2.chk b/test/stats.counts.2.chk new file mode 100644 index 000000000..e86630791 --- /dev/null +++ b/test/stats.counts.2.chk @@ -0,0 +1,36 @@ +SN 0 number of samples: 3 +SN 0 number of records: 5 +SN 0 number of no-ALTs: 0 +SN 0 number of SNPs: 5 +SN 0 number of MNPs: 0 +SN 0 number of indels: 0 +SN 0 number of others: 0 +SN 0 number of multiallelic sites: 2 +SN 0 number of multiallelic SNP sites: 2 +TSTV 0 3 4 0.75 2 3 0.67 +SiS 0 1 2 1 1 0 0 0 0 +AF 0 0.000000 3 1 2 0 0 0 0 +AF 0 0.330000 2 1 1 0 0 0 0 +AF 0 0.490000 2 1 1 0 0 0 0 +QUAL 0 . 5 2 3 0 +ST 0 A>C 0 +ST 0 A>G 0 +ST 0 A>T 0 +ST 0 C>A 2 +ST 0 C>G 1 +ST 0 C>T 1 +ST 0 G>A 2 +ST 0 G>C 1 +ST 0 G>T 0 +ST 0 T>A 0 +ST 0 T>C 0 +ST 0 T>G 0 +PSC 0 A 4 0 0 0 0 0 0.0 0 0 0 1 +PSC 0 B 0 1 2 2 1 0 0.0 0 2 0 0 +PSC 0 C 0 3 0 2 1 0 0.0 0 0 1 1 +PSI 0 A 0 0 0 0.00 0 0 0 0 +PSI 0 B 0 0 0 0.00 0 0 0 0 +PSI 0 C 0 0 0 0.00 0 0 0 0 +HWE 0 0.000000 2 0.000000 0.000000 0.000000 +HWE 0 0.330000 1 0.000000 0.000000 0.000000 +HWE 0 0.490000 1 0.330000 0.330000 0.330000 diff --git a/test/test.pl b/test/test.pl index c2a0793b8..fce6ec470 100755 --- a/test/test.pl +++ b/test/test.pl @@ -47,6 +47,7 @@ run_test(\&test_vcf_stats,$opts,in=>['stats.a','stats.b'],out=>'stats.chk',args=>'-s -'); run_test(\&test_vcf_stats,$opts,in=>['stats.a','stats.b'],out=>'stats.B.chk',args=>'-s B'); run_test(\&test_vcf_stats,$opts,in=>['stats.counts'],out=>'stats.counts.chk',args=>'-s -'); +run_test(\&test_vcf_stats,$opts,in=>['stats.counts'],out=>'stats.counts.2.chk',args=>q[-s - -i 'type="snp"']); run_test(\&test_vcf_isec,$opts,in=>['isec.a','isec.b'],out=>'isec.ab.out',args=>'-n =2'); run_test(\&test_vcf_isec,$opts,in=>['isec.a','isec.b'],out=>'isec.ab.flt.out',args=>'-n =2 -i"STRLEN(REF)==2"'); run_test(\&test_vcf_isec,$opts,in=>['isec.a','isec.b'],out=>'isec.ab.both.out',args=>'-n =2 -c both'); diff --git a/vcfstats.c b/vcfstats.c index 6a7272fa8..10189fef9 100644 --- a/vcfstats.c +++ b/vcfstats.c @@ -1,6 +1,6 @@ /* vcfstats.c -- Produces stats which can be plotted using plot-vcfstats. - Copyright (C) 2012-2022 Genome Research Ltd. + Copyright (C) 2012-2023 Genome Research Ltd. Author: Petr Danecek @@ -1881,6 +1881,7 @@ int main_vcfstats(int argc, char *argv[]) if ( args->split_by_id ) error("Only one file can be given with -i.\n"); } if ( !args->samples_list ) args->files->max_unpack = BCF_UN_INFO; + else args->files->max_unpack = BCF_UN_FMT; if ( args->targets_list ) { bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap); From f6acc129be1d4f33b5e6444fb2e7102558a24320 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Wed, 11 Jan 2023 11:48:46 +0000 Subject: [PATCH 69/84] Make GFF file parsing more flexible. Add new misc/gff2gff script - newly ids in a GFF file can be just 'XXX' rather than, for example, 'gene:XXX' - The new gff2gff perl script is intended to fix GFF formatting differences. Eventually it should replace the current gff2gff.py which has a dependencay on external pyothn package gffutils --- NEWS | 5 ++ csq.c | 78 ++++++++++++++++++++---- misc/gff2gff | 163 +++++++++++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 234 insertions(+), 12 deletions(-) create mode 100755 misc/gff2gff diff --git a/NEWS b/NEWS index 70c3b01bf..1c76f5b23 100644 --- a/NEWS +++ b/NEWS @@ -50,6 +50,11 @@ Changes affecting specific commands: - Fix a bug where a MNV with multiple consequences (e.g. missense + stop_gained) would report only the less severe one (#1810) + - GFF file parsing was made slightly more flexible, newly ids can be just 'XXX' + rather than, for example, 'gene:XXX' + + - New gff2gff perl script to fix GFF formatting differences + * bcftools - More of the available annotations are now added by the `-t all` option diff --git a/csq.c b/csq.c index 7105a4be1..49812d4de 100644 --- a/csq.c +++ b/csq.c @@ -1,6 +1,6 @@ /* The MIT License - Copyright (c) 2016-2022 Genome Research Ltd. + Copyright (c) 2016-2023 Genome Research Ltd. Author: Petr Danecek @@ -256,6 +256,7 @@ const char *csq_strings[] = // GFF line types +#define GFF_UNKN_LINE 0 #define GFF_TSCRIPT_LINE 1 #define GFF_GENE_LINE 2 @@ -755,10 +756,11 @@ static void gff_id_destroy(id_tbl_t *tbl) khash_str2int_destroy_free(tbl->str2id); free(tbl->str); } -static inline uint32_t gff_id_parse(id_tbl_t *tbl, const char *line, const char *needle, char *ss) +// returns 0 on success, -1 on failure +static inline int gff_id_parse(id_tbl_t *tbl, const char *needle, char *ss, uint32_t *id_ptr) { ss = strstr(ss,needle); // e.g. "ID=transcript:" - if ( !ss ) error("[%s:%d %s] Could not parse the line, \"%s\" not present: %s\n",__FILE__,__LINE__,__FUNCTION__,needle,line); + if ( !ss ) return -1; ss += strlen(needle); char *se = ss; @@ -775,8 +777,8 @@ static inline uint32_t gff_id_parse(id_tbl_t *tbl, const char *line, const char khash_str2int_set(tbl->str2id, tbl->str[id], id); } *se = tmp; - - return id; + *id_ptr = id; + return 0; } static inline int gff_parse_type(char *line) { @@ -931,13 +933,34 @@ void gff_parse_transcript(args_t *args, const char *line, char *ss, ftr_t *ftr) int biotype = gff_parse_biotype(ss); if ( biotype <= 0 ) { - if ( !gff_ignored_biotype(args, ss) && args->verbosity > 0 ) fprintf(stderr,"ignored transcript: %s\n",line); + if ( !gff_ignored_biotype(args, ss) && args->verbosity > 0 ) fprintf(stderr,"ignored transcript, unknown biotype: %s\n",line); return; } // create a mapping from transcript_id to gene_id - uint32_t trid = gff_id_parse(&args->tscript_ids, line, "ID=transcript:", ss); - uint32_t gene_id = gff_id_parse(&args->init.gene_ids, line, "Parent=gene:", ss); + uint32_t trid, gene_id; + if ( gff_id_parse(&args->tscript_ids, "ID=transcript:", ss, &trid) ) + { + if ( gff_id_parse(&args->tscript_ids, "ID=", ss, &trid) ) + error("[%s:%d %s] Could not parse the line, neither \"ID=transcript:\" nor \"ID=\" substring is present: %s\n",__FILE__,__LINE__,__FUNCTION__,line); + static int warned = 0; + if ( !warned && args->verbosity > 0 ) + { + fprintf(stderr,"Warning: non-standard transcript ID notation in the GFF, expected \"ID=transcript:XXX\", found %s\n",line); + warned = 1; + } + } + if ( gff_id_parse(&args->init.gene_ids, "Parent=gene:", ss, &gene_id) ) + { + if ( gff_id_parse(&args->init.gene_ids, "Parent=", ss, &gene_id) ) + error("[%s:%d %s] Could not parse the line, neither \"Parent=gene:\" nor \"Parent=\" substring is present: %s\n",__FILE__,__LINE__,__FUNCTION__,line); + static int warned = 0; + if ( !warned && args->verbosity > 0 ) + { + fprintf(stderr,"Warning: non-standard transcript Parent notation in the GFF, expected \"Parent=gene:XXX\", found %s\n",line); + warned = 1; + } + } tscript_t *tr = (tscript_t*) calloc(1,sizeof(tscript_t)); tr->id = trid; @@ -957,14 +980,26 @@ void gff_parse_gene(args_t *args, const char *line, char *ss, char *chr_beg, cha int biotype = gff_parse_biotype(ss); if ( biotype <= 0 ) { - if ( !gff_ignored_biotype(args, ss) && args->verbosity > 0 ) fprintf(stderr,"ignored gene: %s\n",line); + if ( !gff_ignored_biotype(args, ss) && args->verbosity > 0 ) fprintf(stderr,"ignored gene, unknown biotype: %s\n",line); return; } aux_t *aux = &args->init; // substring search for "ID=gene:ENSG00000437963" - uint32_t gene_id = gff_id_parse(&aux->gene_ids, line, "ID=gene:", ss); + uint32_t gene_id; + if ( gff_id_parse(&aux->gene_ids, "ID=gene:", ss, &gene_id) ) + { + if ( gff_id_parse(&aux->gene_ids, "ID=", ss, &gene_id) ) + error("[%s:%d %s] Could not parse the line, neither \"ID=gene:\" nor \"ID=\" substring is present: %s\n",__FILE__,__LINE__,__FUNCTION__,line); + static int warned = 0; + if ( !warned && args->verbosity > 0 ) + { + fprintf(stderr,"Warning: non-standard gene ID notation in the GFF, expected \"ID=gene:XXX\", found %s\n",line); + warned = 1; + } + } + gf_gene_t *gene = gene_init(aux, gene_id); assert( !gene->name ); // the gene_id should be unique @@ -1012,10 +1047,13 @@ int gff_parse(args_t *args, char *line, ftr_t *ftr) else if ( !strncmp("five_prime_UTR\t",ss,15) ) { ftr->type = GF_UTR5; ss += 15; } else { + int type = GFF_UNKN_LINE; + if ( !strncmp("gene\t",ss,4) ) type = GFF_GENE_LINE; + else if ( !strncmp("transcript\t",ss,4) ) type = GFF_TSCRIPT_LINE; ss = gff_skip(line, ss); ss = gff_parse_beg_end(line, ss, &ftr->beg,&ftr->end); ss = gff_skip(line, ss); - int type = gff_parse_type(ss); + if ( type==GFF_UNKN_LINE ) type = gff_parse_type(ss); // determine type from ID=transcript: or ID=gene: if ( type!=GFF_TSCRIPT_LINE && type!=GFF_GENE_LINE ) { // we ignore these, debug print to see new types: @@ -1057,7 +1095,18 @@ int gff_parse(args_t *args, char *line, ftr_t *ftr) ss += 2; // substring search for "Parent=transcript:ENST00000437963" - ftr->trid = gff_id_parse(&args->tscript_ids, line, "Parent=transcript:", ss); + if ( gff_id_parse(&args->tscript_ids, "Parent=transcript:", ss, &ftr->trid) ) + { + if ( gff_id_parse(&args->tscript_ids, "Parent=", ss, &ftr->trid) ) + error("[%s:%d %s] Could not parse the line, neither \"Parent=transcript:\" nor \"Parent=\" substring is present: %s\n",__FILE__,__LINE__,__FUNCTION__,line); + static int warned = 0; + if ( !warned && args->verbosity > 0 ) + { + fprintf(stderr,"Warning: non-standard gene Parent notation in the GFF, expected \"Parent=transcript:XXX\", found %s\n",line); + warned = 1; + } + } + ftr->iseq = feature_set_seq(args, chr_beg,chr_end); return 0; } @@ -1380,6 +1429,11 @@ void init_gff(args_t *args) regidx_nregs(args->idx_cds), regidx_nregs(args->idx_utr)); } + if ( !regidx_nregs(args->idx_tscript) ) + fprintf(stderr, + "Warning: No usable transcripts found, likely a failure to parse a non-standard GFF file. Please check if the misc/gff2gff\n" + " or misc/gff2gff.py script can fix the problem (both do different things). See also the man page for the description\n" + " of the expected format http://samtools.github.io/bcftools/bcftools-man.html#csq\n"); free(aux->ftr); khash_str2int_destroy_free(aux->seq2int); diff --git a/misc/gff2gff b/misc/gff2gff new file mode 100755 index 000000000..27485fad8 --- /dev/null +++ b/misc/gff2gff @@ -0,0 +1,163 @@ +#!/usr/bin/env perl +# +# Copyright (C) 2023 Genome Research Ltd. +# +# Author: Petr Danecek +# +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to deal +# in the Software without restriction, including without limitation the rights +# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +# copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in +# all copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER +# DEALINGS IN THE SOFTWARE. + + +use strict; +use warnings; +use Carp; + +my $opts = parse_params(); +gff2gff($opts); + +exit; + +#-------------------------------- + +sub error +{ + my (@msg) = @_; + if ( scalar @msg ) { confess @msg; } + print + "About: Attempt to fix a GFF file to be correctly parse by bcftools/csq, see\n", + " the man page for the description of the expected format\n", + " http://samtools.github.io/bcftools/bcftools-man.html#csq\n", + "Usage: gff2gff [OPTIONS]\n", + "Options:\n", + " -h, -?, --help This help message\n", + "Example:\n", + " zcat in.gff.gz | gff2gff | gzip -c > out.gff.gz\n", + "\n"; + exit -1; +} +sub parse_params +{ + my $opts = {}; + if ( -t STDIN && !@ARGV ) { error(); } + while (defined(my $arg=shift(@ARGV))) + { + if ( $arg eq '-?' or $arg eq '-h' or $arg eq '--help' ) { error(); } + error("Unknown parameter \"$arg\". Run -h for help.\n"); + } + return $opts; +} + +sub gff2gff +{ + my ($opts) = @_; + while (my $line=) + { + if ( $line=~/^#/ ) { print $line; next; } + my @row = split(/\t/,$line); + chomp($row[-1]); + if ( $row[2] eq 'gene' ) { fix_gene($opts,$line,\@row); } + elsif ( $row[2] eq 'transcript' ) { fix_transcript($opts,$line,\@row); } + print join("\t",@row)."\n"; + } +} +sub fix_gene +{ + my ($opts,$line,$row) = @_; + my ($id,$biotype,$name); + my $id_ok = 0; + my $biotype_ok = 0; + my $name_ok = 0; + + if ( $$row[8] =~ /ID=([^;]+)/ ) { $id = $1; $id_ok = 1; } + if ( !$id_ok && $$row[8] =~ /gene_id=([^;]+)/i ) { $id = $1; } + if ( $$row[8] =~ /biotype=([^;]+)/ ) { $biotype = $1; $biotype_ok = 1; } + if ( !$biotype_ok && $$row[8] =~ /gene_type=([^;]+)/i ) { $biotype = $1; } + if ( $$row[8] =~ /Name=([^;]+)/ ) { $name = $1; $name_ok = 1; } + if ( !$biotype_ok && $$row[8] =~ /gene_name=([^;]+)/i ) { $name = $1; } + + if ( !$id_ok ) + { + if ( defined $id ) { $$row[8] .= ";ID=$id"; } + elsif ( !$$opts{gene_id_warned} ) + { + print STDERR "Unable to determine gene ID, see e.g. $line\n"; + $$opts{gene_id_warned} = 1; + } + } + if ( !$biotype_ok ) + { + if ( defined $biotype ) { $$row[8] .= ";biotype=$biotype"; } + elsif ( !$$opts{gene_biotype_warned} ) + { + print STDERR "Unable to determine gene biotype/type, see e.g. $line\n"; + $$opts{gene_biotype_warned} = 1; + } + } + if ( !$name_ok ) + { + if ( defined $name ) { $$row[8] .= ";Name=$name"; } + elsif ( !$$opts{gene_name_warned} ) + { + print STDERR "Unable to determine gene name, see e.g. $line\n"; + $$opts{gene_name_warned} = 1; + } + } +} +sub fix_transcript +{ + my ($opts,$line,$row) = @_; + my ($id,$biotype,$parent); + my $id_ok = 0; + my $biotype_ok = 0; + my $parent_ok = 0; + + if ( $$row[8] =~ /ID=([^;]+)/ ) { $id = $1; $id_ok = 1; } + if ( !$id_ok && $$row[8] =~ /transcript_id=([^;]+)/i ) { $id = $1; } + if ( $$row[8] =~ /biotype=([^;]+)/ ) { $biotype = $1; $biotype_ok = 1; } + if ( !$biotype_ok && $$row[8] =~ /transcript_type=([^;]+)/i ) { $biotype = $1; } + if ( $$row[8] =~ /Parent=([^;]+)/ ) { $parent = $1; $parent_ok = 1; } + + if ( !$id_ok ) + { + if ( defined $id ) { $$row[8] .= ";ID=$id"; } + elsif ( !$$opts{tscript_id_warned} ) + { + print STDERR "Unable to determine transcript ID, see e.g. $line\n"; + $$opts{tscript_id_warned} = 1; + } + } + if ( !$biotype_ok ) + { + if ( defined $biotype ) { $$row[8] .= ";biotype=$biotype"; } + elsif ( !$$opts{tscript_biotype_warned} ) + { + print STDERR "Unable to determine transcript biotype/type, see e.g. $line\n"; + $$opts{tscript_biotype_warned} = 1; + } + } + if ( !$parent_ok ) + { + if ( defined $parent ) { $$row[8] .= ";Parent=$parent"; } # currently cannot happen + elsif ( !$$opts{tscript_parent_warned} ) + { + print STDERR "Unable to determine transcript Parent, see e.g. $line\n"; + $$opts{tscript_parent_warned} = 1; + } + } +} + From 38792f87170cd9b3dfc1f46de8b3786ed97fd3e9 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Thu, 12 Jan 2023 13:22:43 +0000 Subject: [PATCH 70/84] Revamp or +tag2tag The plugin now supports wider range of tag conversions, specifically all combinations from FORMAT/GL,PL,GP to FORMAT/GL,PL,GP,GT. Note that this comes at a (small) performance cost, internally the source tag is first converted to GL and then to the requested tag. Resolves #1845 --- NEWS | 5 + plugins/tag2tag.c | 388 ++++++++++++++++++++++++-------------------- test/test.pl | 1 + test/view.GL-GP.vcf | 30 ++++ 4 files changed, 249 insertions(+), 175 deletions(-) create mode 100644 test/view.GL-GP.vcf diff --git a/NEWS b/NEWS index 1c76f5b23..1901d3d8b 100644 --- a/NEWS +++ b/NEWS @@ -117,6 +117,11 @@ Changes affecting specific commands: - The per-sample stats (PSC) would not be computed when `-i/-e` filtering options and the `-s -` option were given but the expression did not include sample columns (1835) +* bcftools +tag2tag + + - Revamp of the plugin to allo wider range of tag conversions, specifically all combinations + from FORMAT/GL,PL,GP to FORMAT/GL,PL,GP,GT + * bcftools +trio-dnm2 - New `-n, --strictly-novel` option to downplay alleles which violate Mendelian diff --git a/plugins/tag2tag.c b/plugins/tag2tag.c index fc3520138..92ee2e478 100644 --- a/plugins/tag2tag.c +++ b/plugins/tag2tag.c @@ -1,6 +1,6 @@ /* plugins/tag2tag.c -- convert between similar tags - Copyright (C) 2014-2021 Genome Research Ltd. + Copyright (C) 2014-2023 Genome Research Ltd. Author: Petr Danecek @@ -31,20 +31,36 @@ DEALINGS IN THE SOFTWARE. */ #include #include "bcftools.h" +typedef struct +{ + int type; + const char *str, *hdr; +} +tag_t; +enum tag { UNKN, GP, GL, PL, GT, QRQA, QS }; +tag_t tags[] = +{ + [UNKN] = { .type = 0 , .str = NULL, .hdr = NULL }, + [GP] = { .type = BCF_HT_REAL, .str = "GP", .hdr = "##FORMAT=" }, + [GL] = { .type = BCF_HT_REAL, .str = "GL", .hdr = "##FORMAT=" }, + [PL] = { .type = BCF_HT_INT, .str = "PL", .hdr = "##FORMAT=" }, + [GT] = { .type = BCF_HT_STR, .str = "GT", .hdr = "##FORMAT=" }, + [QRQA] = { .type = BCF_HT_INT, .str = NULL, .hdr = NULL }, + [QS] = { .type = BCF_HT_INT, .str = "QS", .hdr = "##FORMAT=" }, +}; + +typedef struct +{ + enum tag src, dst; + int drop_src; + bcf_hdr_t *in_hdr, *out_hdr; + float *farr, gp_th; + int32_t *iarr, *iarr2, *iarr3; + int mfarr, miarr, miarr2, miarr3; +} +args_t; -#define GP_TO_GL 1 -#define GL_TO_PL 2 -#define GP_TO_GT 3 -#define PL_TO_GL 4 -#define QRQA_TO_QS 5 - -static int mode = 0, drop_source_tag = 0; -static bcf_hdr_t *in_hdr, *out_hdr; -static float *farr = NULL, thresh = 0.1; -static int32_t *iarr = NULL; -static int32_t *iarr2 = NULL; -static int32_t *iarr3 = NULL; -static int mfarr = 0, miarr = 0, miarr2 = 0, miarr3 = 0; +static args_t *args; const char *about(void) { @@ -53,7 +69,7 @@ const char *about(void) const char *usage(void) { - return + return "\n" "About: Convert between similar tags such as GL,PL,GP or QR,QA,QS.\n" "Usage: bcftools +tag2tag [General Options] -- [Plugin Options]\n" @@ -61,181 +77,226 @@ const char *usage(void) " run \"bcftools plugin\" for a list of common options\n" "\n" "Plugin options:\n" - " --GP-to-GL convert FORMAT/GP to FORMAT/GL\n" - " --GP-to-GT convert FORMAT/GP to FORMAT/GT by taking argmax of GP\n" - " --GL-to-PL convert FORMAT/GL to FORMAT/PL\n" - " --PL-to-GL convert FORMAT/PL to FORMAT/GL\n" - " --QR-QA-to-QS convert FORMAT/QR,QA to FORMAT/QS\n" - " -r, --replace drop the source tag\n" - " -t, --threshold threshold for GP to GT hard-call [0.1]\n" + " --ORI-to-NEW Convert from source tags FORMAT/GL,PL,GP to FORMAT/GL,PL,GP,GT\n" + " --QR-QA-to-QS Convert FORMAT/QR,QA to FORMAT/QS\n" + " -r, --replace Drop the source tag\n" + " -t, --threshold FLOAT Threshold for GP to GT hard-call [0.1]\n" "\n" "Example:\n" - " bcftools +tag2tag in.vcf -- -r --gp-to-gl\n" + " bcftools +tag2tag in.vcf -- -r --GP-to-GL\n" + " bcftools +tag2tag in.vcf -- --PL-to-GT\n" "\n"; } - -static void init_header(bcf_hdr_t *hdr, const char *ori, int ori_type, const char *new_hdr_line) +static int parse_ori2new_option(args_t *args, char *optarg) { - if ( ori ) - bcf_hdr_remove(hdr,ori_type,ori); - - bcf_hdr_append(hdr, new_hdr_line); + if ( args->src!=UNKN ) error("Multiple modes selected: %s\n",optarg); + if ( strncmp("--",optarg,2) ) return -1; + + char *tmp = optarg+2; + if ( !strncasecmp("GL-to-",tmp,6) ) args->src = GL, tmp += 6; + else if ( !strncasecmp("PL-to-",tmp,6) ) args->src = PL, tmp += 6; + else if ( !strncasecmp("GP-to-",tmp,6) ) args->src = GP, tmp += 6; + if ( args->src==UNKN ) error("The conversion is not supported: %s\n",optarg); + + if ( !strcasecmp("GL",tmp) ) args->dst = GL; + else if ( !strcasecmp("PL",tmp) ) args->dst = PL; + else if ( !strcasecmp("GP",tmp) ) args->dst = GP; + else if ( !strcasecmp("GT",tmp) ) args->dst = GT; + if ( args->dst==UNKN || args->src==args->dst ) error("The conversion is not supported: %s\n",optarg); + return 0; } int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out) { + args = (args_t*) calloc(1,sizeof(args_t)); + args->in_hdr = in; + args->out_hdr = out; + args->src = args->dst = UNKN; + static struct option loptions[] = { {"replace",no_argument,NULL,'r'}, - {"gp-to-gl",no_argument,NULL,1}, - {"GP-to-GL",no_argument,NULL,1}, - {"gl-to-pl",no_argument,NULL,2}, - {"GL-to-PL",no_argument,NULL,2}, - {"gp-to-gt",no_argument,NULL,3}, - {"GP-to-GT",no_argument,NULL,3}, - {"pl-to-gl",no_argument,NULL,4}, - {"PL-to-GL",no_argument,NULL,4}, - {"qr-qa-to-qs",no_argument,NULL,5}, - {"QR-QA-to-QS",no_argument,NULL,5}, + {"qr-qa-to-qs",no_argument,NULL,1}, + {"QR-QA-to-QS",no_argument,NULL,1}, {"threshold",required_argument,NULL,'t'}, {NULL,0,NULL,0} }; + opterr = 0; int c; - char *src_tag = "GP"; - int src_type = BCF_HT_REAL; while ((c = getopt_long(argc, argv, "?hrt:",loptions,NULL)) >= 0) { - switch (c) + switch (c) { - case 1 : src_tag = "GP"; mode = GP_TO_GL; src_type = BCF_HT_REAL; break; - case 2 : src_tag = "GL"; mode = GL_TO_PL; src_type = BCF_HT_REAL; break; - case 3 : src_tag = "GP"; mode = GP_TO_GT; src_type = BCF_HT_REAL; break; - case 4 : src_tag = "PL"; mode = PL_TO_GL; src_type = BCF_HT_INT; break; - case 5 : src_tag = "QR"; mode = QRQA_TO_QS; src_type = BCF_HT_INT; break; - case 'r': drop_source_tag = 1; break; - case 't': thresh = atof(optarg); break; - case 'h': - case '?': - default: error("%s", usage()); break; + case 1 : args->src = QRQA; args->dst = QS; break; + case 'r': args->drop_src = 1; break; + case 't': + args->gp_th = atof(optarg); + if ( args->gp_th<0 || args->gp_th>1 ) error("Expected value between [0-1] for -t, --threshold, got %f\n",args->gp_th); + break; + case 'h': error("%s", usage()); break; + default: + if ( optind<=0 || parse_ori2new_option(args,argv[optind-1])<0 ) error("%s", usage()); + break; } } - if ( !mode ) mode = GP_TO_GL; - - in_hdr = in; - out_hdr = out; - - if ( mode==GP_TO_GL ) - init_header(out_hdr,drop_source_tag?"GP":NULL,BCF_HL_FMT,"##FORMAT="); - else if ( mode==GL_TO_PL ) - init_header(out_hdr,drop_source_tag?"GL":NULL,BCF_HL_FMT,"##FORMAT="); - else if ( mode==PL_TO_GL ) - init_header(out_hdr,drop_source_tag?"PL":NULL,BCF_HL_FMT,"##FORMAT="); - else if ( mode==GP_TO_GT ) + if ( args->src==UNKN ) error("%s", usage()); + int tag_id; + if ( args->src==QRQA ) { - if (thresh<0||thresh>1) error("--threshold must be in the range [0,1]: %f\n", thresh); - init_header(out_hdr,drop_source_tag?"GP":NULL,BCF_HL_FMT,"##FORMAT="); + if ( (tag_id=bcf_hdr_id2int(args->in_hdr,BCF_DT_ID,"QR"))<0 || !bcf_hdr_idinfo_exists(args->in_hdr,BCF_HL_FMT,tag_id) ) error("The source tag does not exist: QR\n"); + if ( bcf_hdr_id2type(args->in_hdr,BCF_HL_FMT,tag_id)!=tags[args->src].type ) error("The source tag is of different type than required by the VCF specification\n"); + if ( (tag_id=bcf_hdr_id2int(args->in_hdr,BCF_DT_ID,"QA"))<0 || !bcf_hdr_idinfo_exists(args->in_hdr,BCF_HL_FMT,tag_id) ) error("The source tag does not exist: QA\n"); + if ( bcf_hdr_id2type(args->in_hdr,BCF_HL_FMT,tag_id)!=tags[args->src].type ) error("The source tag is of different type than required by the VCF specification\n"); } - else if ( mode==QRQA_TO_QS ) + else { - if ( drop_source_tag ) - { - bcf_hdr_remove(out_hdr,BCF_HL_FMT,"QR"); - bcf_hdr_remove(out_hdr,BCF_HL_FMT,"QA"); - } - bcf_hdr_append(out_hdr, "##FORMAT="); + if ( (tag_id=bcf_hdr_id2int(args->in_hdr,BCF_DT_ID,tags[args->src].str))<0 || !bcf_hdr_idinfo_exists(args->in_hdr,BCF_HL_FMT,tag_id) ) error("The source tag does not exist: %s\n",tags[args->src].str); + if ( bcf_hdr_id2type(args->in_hdr,BCF_HL_FMT,tag_id)!=tags[args->src].type ) error("The source tag is of different type than required by the VCF specification\n"); } - - int tag_id; - if ( (tag_id=bcf_hdr_id2int(in_hdr,BCF_DT_ID,src_tag))<0 || !bcf_hdr_idinfo_exists(in_hdr,BCF_HL_FMT,tag_id) ) - error("The source tag does not exist: %s\n", src_tag); - if ( bcf_hdr_id2type(in_hdr,BCF_HL_FMT,tag_id) != src_type ) - error("The source tag type does not match the VCF specification, expected Type=%s. Use `bcftools reheader` to fix.\n",src_type==BCF_HT_REAL?"Float":"Integer"); - if ( mode==QRQA_TO_QS ) + if ( args->drop_src ) { - src_tag = "QA"; - if ( (tag_id=bcf_hdr_id2int(in_hdr,BCF_DT_ID,src_tag))<0 || !bcf_hdr_idinfo_exists(in_hdr,BCF_HL_FMT,tag_id) ) - error("The source tag does not exist: %s\n", src_tag); - if ( bcf_hdr_id2type(in_hdr,BCF_HL_FMT,tag_id) != src_type ) - error("The source tag type does not match the VCF specification, expected Type=%s. Use `bcftools reheader` to fix.\n",src_type==BCF_HT_REAL?"Float":"Integer"); + if ( args->src==QRQA ) + { + bcf_hdr_remove(args->out_hdr,BCF_HL_FMT,"QR"); + bcf_hdr_remove(args->out_hdr,BCF_HL_FMT,"QA"); + } + else + bcf_hdr_remove(args->out_hdr,BCF_HL_FMT,tags[args->src].str); } + assert( tags[args->dst].hdr ); + bcf_hdr_append(args->out_hdr,tags[args->dst].hdr); return 0; } bcf1_t *process(bcf1_t *rec) { - int i, n; - if ( mode==GP_TO_GL ) + int i,j,n; + if ( args->src==QRQA ) { - n = bcf_get_format_float(in_hdr,rec,"GP",&farr,&mfarr); + int nals = rec->n_allele; + int nsmpl = bcf_hdr_nsamples(args->in_hdr); + + n = bcf_get_format_int32(args->in_hdr,rec,"QR",&args->iarr,&args->miarr); if ( n<=0 ) return rec; - for (i=0; iin_hdr,rec),rec->pos+1); + if ( nals==1 ) + bcf_update_format_int32(args->out_hdr,rec,"QS",args->iarr,nsmpl); + else + { + int n2 = bcf_get_format_int32(args->in_hdr,rec,"QA",&args->iarr2,&args->miarr2); + if ( n2<=0 ) return rec; + if ( n*(nals-1) != n2 ) error("Unexpected number of QR vs QA values at %s:%"PRIhts_pos"\n",bcf_seqname(args->in_hdr,rec),rec->pos+1); + hts_expand(int32_t,nsmpl*nals,args->miarr3,args->iarr3); + for (i=0; iiarr3[i*nals] = args->iarr[i]; + for (j=1; jiarr3[i*nals+j] = args->iarr2[i*(nals-1)+j-1]; + } + bcf_update_format_int32(args->out_hdr,rec,"QS",args->iarr3,nals*nsmpl); + } + if ( args->drop_src ) { - if ( bcf_float_is_missing(farr[i]) || bcf_float_is_vector_end(farr[i]) ) continue; - farr[i] = farr[i] ? log10(farr[i]) : -99; + bcf_update_format_int32(args->out_hdr,rec,"QR",NULL,0); + bcf_update_format_int32(args->out_hdr,rec,"QA",NULL,0); } - bcf_update_format_float(out_hdr,rec,"GL",farr,n); - if ( drop_source_tag ) - bcf_update_format_float(out_hdr,rec,"GP",NULL,0); + return rec; } - else if ( mode==PL_TO_GL ) + + // convert source tags to GL. If performance is an issue, can be smarter + if ( tags[args->src].type==BCF_HT_REAL ) { - n = bcf_get_format_int32(in_hdr,rec,"PL",&iarr,&miarr); + // from GL,GP to something + n = bcf_get_format_float(args->in_hdr,rec,tags[args->src].str,&args->farr,&args->mfarr); if ( n<=0 ) return rec; - hts_expand(float, n, mfarr, farr); - for (i=0; isrc==GP ) { - if ( iarr[i]==bcf_int32_missing ) - bcf_float_set_missing(farr[i]); - else if ( iarr[i]==bcf_int32_vector_end ) - bcf_float_set_vector_end(farr[i]); - else - farr[i] = -0.1 * iarr[i]; + for (i=0; ifarr[i]) || bcf_float_is_vector_end(args->farr[i]) ) continue; + args->farr[i] = args->farr[i] ? log10(args->farr[i]) : -99; + } } - bcf_update_format_float(out_hdr,rec,"GL",farr,n); - if ( drop_source_tag ) - bcf_update_format_int32(out_hdr,rec,"PL",NULL,0); } - else if ( mode==GL_TO_PL ) + else if ( tags[args->src].type==BCF_HT_INT ) { - n = bcf_get_format_float(in_hdr,rec,"GL",&farr,&mfarr); + // from PL to something + n = bcf_get_format_int32(args->in_hdr,rec,tags[args->src].str,&args->iarr,&args->miarr); if ( n<=0 ) return rec; - hts_expand(int32_t, n, miarr, iarr); + hts_expand(float, n, args->mfarr, args->farr); + + // convert to GL for (i=0; iiarr[i]==bcf_int32_missing ) + bcf_float_set_missing(args->farr[i]); + else if ( args->iarr[i]==bcf_int32_vector_end ) + bcf_float_set_vector_end(args->farr[i]); else - iarr[i] = lroundf(-10 * farr[i]); + args->farr[i] = -0.1 * args->iarr[i]; } - bcf_update_format_int32(out_hdr,rec,"PL",iarr,n); - if ( drop_source_tag ) - bcf_update_format_float(out_hdr,rec,"GL",NULL,0); } - else if ( mode==GP_TO_GT ) - { - int nals = rec->n_allele; - int nsmpl = bcf_hdr_nsamples(in_hdr); - hts_expand(int32_t,nsmpl*2,miarr,iarr); - - n = bcf_get_format_float(in_hdr,rec,"GP",&farr,&mfarr); - if ( n<=0 ) return rec; + else error("fixme: expected BCF_HT_REAL or BCF_HT_INT for source tag\n"); - n /= nsmpl; + if ( args->dst==GL ) + bcf_update_format_float(args->out_hdr,rec,"GL",args->farr,n); + else if ( args->dst==PL ) + { + hts_expand(int32_t, n, args->miarr, args->iarr); + for (i=0; ifarr[i]) ) args->iarr[i] = bcf_int32_missing; + else if ( bcf_float_is_vector_end(args->farr[i]) ) args->iarr[i] = bcf_int32_vector_end; + else args->iarr[i] = lroundf(-10*args->farr[i]); + } + bcf_update_format_int32(args->out_hdr,rec,"PL",args->iarr,n); + } + else if ( args->dst==GP || args->dst==GT ) + { + int nsmpl = bcf_hdr_nsamples(args->in_hdr); + int n1 = n / nsmpl; for (i=0; ifarr + i*n1; + float sum = 0; + for (j=0; jdst==GP ) + bcf_update_format_float(args->out_hdr,rec,"GP",args->farr,n); + } + if ( args->dst==GT ) + { + // farr contains GP. If performance is an issue, note that if the src was GP, we made an unnecessary conversion GP->GL->GP + int nsmpl = bcf_hdr_nsamples(args->in_hdr); + int n1 = n / nsmpl; + int nals = rec->n_allele; + hts_expand(int32_t,nsmpl*2,args->miarr,args->iarr); + for (i=0; ifarr + i*n1; if ( bcf_float_is_missing(ptr[0]) ) { - iarr[2*i] = iarr[2*i+1] = bcf_gt_missing; + args->iarr[2*i] = args->iarr[2*i+1] = bcf_gt_missing; continue; } - - int j, jmax = 0; - for (j=1; j ptr[jmax] ) jmax = j; @@ -244,76 +305,53 @@ bcf1_t *process(bcf1_t *rec) // haploid genotype if ( j==nals ) { - iarr[2*i] = ptr[jmax] < 1-thresh ? bcf_gt_missing : bcf_gt_unphased(jmax); - iarr[2*i+1] = bcf_int32_vector_end; + args->iarr[2*i] = ptr[jmax] < 1 - args->gp_th ? bcf_gt_missing : bcf_gt_unphased(jmax); + args->iarr[2*i+1] = bcf_int32_vector_end; continue; } if ( j!=nals*(nals+1)/2 ) error("Wrong number of GP values for diploid genotype at %s:%"PRId64", expected %d, found %d\n", - bcf_seqname(in_hdr,rec),(int64_t) rec->pos+1, nals*(nals+1)/2,j); + bcf_seqname(args->in_hdr,rec), rec->pos+1, nals*(nals+1)/2,j); - if (ptr[jmax] < 1-thresh) + if ( ptr[jmax] < 1 - args->gp_th ) { - iarr[2*i] = iarr[2*i+1] = bcf_gt_missing; + args->iarr[2*i] = args->iarr[2*i+1] = bcf_gt_missing; continue; } // most common case: RR if ( jmax==0 ) { - iarr[2*i] = iarr[2*i+1] = bcf_gt_unphased(0); + args->iarr[2*i] = args->iarr[2*i+1] = bcf_gt_unphased(0); continue; } int a,b; bcf_gt2alleles(jmax,&a,&b); - iarr[2*i] = bcf_gt_unphased(a); - iarr[2*i+1] = bcf_gt_unphased(b); + args->iarr[2*i] = bcf_gt_unphased(a); + args->iarr[2*i+1] = bcf_gt_unphased(b); } - bcf_update_genotypes(out_hdr,rec,iarr,nsmpl*2); - if ( drop_source_tag ) - bcf_update_format_float(out_hdr,rec,"GP",NULL,0); + bcf_update_genotypes(args->out_hdr,rec,args->iarr,nsmpl*2); } - else if ( mode==QRQA_TO_QS ) - { - int nals = rec->n_allele; - int nsmpl = bcf_hdr_nsamples(in_hdr); - n = bcf_get_format_int32(in_hdr,rec,"QR",&iarr,&miarr); - if ( n<=0 ) return rec; - if ( n!=nsmpl ) error("Unexpected number of QR values at %s:%"PRIhts_pos"\n",bcf_seqname(in_hdr,rec),rec->pos+1); - if ( nals==1 ) - bcf_update_format_int32(out_hdr,rec,"QS",iarr,nsmpl); - else - { - int n2 = bcf_get_format_int32(in_hdr,rec,"QA",&iarr2,&miarr2); - if ( n2<=0 ) return rec; - if ( n*(nals-1) != n2 ) error("Unexpected number of QR vs QA values at %s:%"PRIhts_pos"\n",bcf_seqname(in_hdr,rec),rec->pos+1); - hts_expand(int32_t,nsmpl*nals,miarr3,iarr3); - for (i=0; idrop_src ) + { + if ( tags[args->src].type==BCF_HT_REAL ) + bcf_update_format_float(args->out_hdr,rec,tags[args->src].str,NULL,0); + else if ( tags[args->src].type==BCF_HT_INT ) + bcf_update_format_int32(args->out_hdr,rec,tags[args->src].str,NULL,0); } return rec; } void destroy(void) { - free(farr); - free(iarr); - free(iarr2); - free(iarr3); + free(args->farr); + free(args->iarr); + free(args->iarr2); + free(args->iarr3); + free(args); } diff --git a/test/test.pl b/test/test.pl index fce6ec470..c829f9195 100755 --- a/test/test.pl +++ b/test/test.pl @@ -530,6 +530,7 @@ run_test(\&test_vcf_plugin,$opts,in=>'view.PL',out=>'guess-ploidy.PL.out',cmd=>'+guess-ploidy',args=>'-vrX | grep -v bcftools'); run_test(\&test_vcf_plugin,$opts,in=>'view.GL',out=>'guess-ploidy.GL.out',cmd=>'+guess-ploidy',args=>'-vrX | grep -v bcftools'); run_test(\&test_vcf_plugin,$opts,in=>'view.GL',out=>'view.PL.vcf',cmd=>'+tag2tag --no-version',args=>'-- -r --gl-to-pl'); +run_test(\&test_vcf_plugin,$opts,in=>'view.GL',out=>'view.GL-GP.vcf',cmd=>'+tag2tag --no-version',args=>'-- --gl-to-gp'); run_test(\&test_vcf_plugin,$opts,in=>'view.GP',out=>'view.GT.vcf',cmd=>'+tag2tag --no-version',args=>'-- -r --gp-to-gt -t 0.2'); run_test(\&test_vcf_plugin,$opts,in=>'query.variantkey',out=>'query.add-variantkey.vcf',cmd=>'+add-variantkey',args=>''); run_test(\&test_vcf_plugin,$opts,in=>'query.variantkey',out=>'variantkey-hex.out',cmd=>'+variantkey-hex',args=>'test/'); diff --git a/test/view.GL-GP.vcf b/test/view.GL-GP.vcf new file mode 100644 index 000000000..600c7bbd6 --- /dev/null +++ b/test/view.GL-GP.vcf @@ -0,0 +1,30 @@ +##fileformat=VCFv4.1 +##FILTER= +##reference=file:///seq/references/1000Genomes-NCBI37.fasta +##contig= +##contig= +##contig= +##contig= +##FORMAT= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +11 2343543 . A . 999 PASS . GL:GP 0:1 0:1 0:1 +11 5464562 . C T 999 PASS . GL:GP 0,0,0:0.333333,0.333333,0.333333 0,0,0:0.333333,0.333333,0.333333 0,0,0:0.333333,0.333333,0.333333 +20 76962 rs6111385 T C 999 PASS . GL:GP -25.5,0,-25.5:3.16228e-26,1,3.16228e-26 -25.5,-25.5,0:3.16228e-26,3.16228e-26,1 -25.5,-25.5,0:3.16228e-26,3.16228e-26,1 +20 126310 . ACC A 999 StrandBias;EndDistBias . GL:GP -25.5,0,-13.2:3.16228e-26,1,6.30958e-14 -25.5,0,-13.9:3.16228e-26,1,1.25893e-14 -25.5,-21.3,0:3.16228e-26,5.01188e-22,1 +20 138125 rs2298108 G T 999 PASS . GL:GP -13.5,0,-16.3:3.16228e-14,1,5.01188e-17 -14,0,-25.5:1e-14,1,3.16228e-26 -25.5,-19.9,0:3.16228e-26,1.25893e-20,1 +20 138148 rs2298109 C T 999 PASS . GL:GP -19.5,0,-25.5:3.16228e-20,1,3.16228e-26 -19.2,0,-25.5:6.30956e-20,1,3.16228e-26 -25.5,-23.5,0:3.16228e-26,3.16228e-24,1 +20 271225 . T TTTA,TA 999 StrandBias . GL:GP -15.1,-5.3,-20.3,0,-5.2,-15.9:7.94319e-16,5.01181e-06,5.01182e-21,0.999989,6.3095e-06,1.25891e-16 -25.5,0,-21.3,-25.5,-25.5,-25.5:3.16228e-26,1,5.01188e-22,3.16228e-26,3.16228e-26,3.16228e-26 -25.5,-25.5,-25.5,-25.5,0,-24.1:3.16228e-26,3.16228e-26,3.16228e-26,3.16228e-26,1,7.94328e-25 +20 304568 . C T 999 PASS . GL:GP -9.5,0,-25.5:3.16228e-10,1,3.16228e-26 -19.2,0,-25.5:6.30956e-20,1,3.16228e-26 -25.5,-9.5,0:3.16228e-26,3.16228e-10,1 +20 326891 . A AC 999 PASS . GL:GP -25.5,0,-13.2:3.16228e-26,1,6.30958e-14 -25.5,0,-13.9:3.16228e-26,1,1.25893e-14 .,.,.:.,.,. +X 2928329 rs62584840 C T 999 PASS . GL:GP 0,-5.6:0.999997,2.51188e-06 0,-8.1:1,7.94328e-09 -7.3,0,-1.9:4.94956e-08,0.987567,0.0124327 +X 2933066 rs61746890 G C 999 PASS . GL:GP 0,-25.5:1,3.16228e-26 0,-25.5:1,3.16228e-26 -25.5,-25.5,-25.5:0.333333,0.333333,0.333333 +X 2942109 rs5939407 T C 999 PASS . GL:GP 0,-25.5:1,3.16228e-26 -25.5,0:3.16228e-26,1 -25.5,-15.7,0:3.16228e-26,1.99526e-16,1 +X 3048719 . T C 999 PASS . GL:GP 0,-25.5:1,3.16228e-26 -25.5,0:3.16228e-26,1 -25.5,0,-15.7:3.16228e-26,1,1.99526e-16 +Y 8657215 . C A 999 PASS . GL:GP 0,-25.5:1,3.16228e-26 -25.5,0:3.16228e-26,1 .:. +Y 10011673 rs78249411 G A 999 MinAB . GL:GP -12.6,-10.1:0.00315231,0.996848 -9.5,0:3.16228e-10,1 .:. From 17be4eba2330b794c1b9d4ba2c7eb85071c64eee Mon Sep 17 00:00:00 2001 From: Rob Davies Date: Thu, 12 Jan 2023 16:21:17 +0000 Subject: [PATCH 71/84] Happy New Year --- LICENSE | 2 +- main.c | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/LICENSE b/LICENSE index f223b096a..6d40ae2d1 100644 --- a/LICENSE +++ b/LICENSE @@ -9,7 +9,7 @@ the INSTALL document), the use of this software is governed by the GPL license. The MIT/Expat License -Copyright (C) 2012-2021 Genome Research Ltd. +Copyright (C) 2012-2023 Genome Research Ltd. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/main.c b/main.c index 3a0d557b7..a0213589f 100644 --- a/main.c +++ b/main.c @@ -265,7 +265,7 @@ int main(int argc, char *argv[]) if (argc < 2) { usage(stderr); return 1; } if (strcmp(argv[1], "version") == 0 || strcmp(argv[1], "--version") == 0 || strcmp(argv[1], "-v") == 0) { - printf("bcftools %s\nUsing htslib %s\nCopyright (C) 2022 Genome Research Ltd.\n", bcftools_version(), hts_version()); + printf("bcftools %s\nUsing htslib %s\nCopyright (C) 2023 Genome Research Ltd.\n", bcftools_version(), hts_version()); #if USE_GPL printf("License GPLv3+: GNU GPL version 3 or later \n"); #else From dfdb09230e6009a7c792346af09eef22f7ef551d Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Fri, 13 Jan 2023 10:18:47 +0000 Subject: [PATCH 72/84] Make the `-t ./x` mode select both phased and unphased genotypes, as advertised by the usage page. Fixes #1844 --- NEWS | 5 ++++- plugins/setGT.c | 4 ++-- test/setGT.6.1.out | 7 +++++++ test/setGT.6.vcf | 6 ++++++ test/test.pl | 2 ++ 5 files changed, 21 insertions(+), 3 deletions(-) create mode 100644 test/setGT.6.1.out create mode 100644 test/setGT.6.vcf diff --git a/NEWS b/NEWS index 1901d3d8b..0c57b1356 100644 --- a/NEWS +++ b/NEWS @@ -105,6 +105,9 @@ Changes affecting specific commands: - Add new `--new-gt X` option (#1800) + - Fix a bug where `-t ./x` mode was advertised as selecting both phased and unphased + half-missing genotypes, but was in fact selecting only unphased genotypes (#1844) + * bcftools +split-vep - New options `-g, --gene-list` and `--gene-list-fields` which allow to prioritize @@ -119,7 +122,7 @@ Changes affecting specific commands: * bcftools +tag2tag - - Revamp of the plugin to allo wider range of tag conversions, specifically all combinations + - Revamp of the plugin to allow wider range of tag conversions, specifically all combinations from FORMAT/GL,PL,GP to FORMAT/GL,PL,GP,GT * bcftools +trio-dnm2 diff --git a/plugins/setGT.c b/plugins/setGT.c index ddcbb388d..68b28c39b 100644 --- a/plugins/setGT.c +++ b/plugins/setGT.c @@ -1,6 +1,6 @@ /* plugins/setGT.c -- set gentoypes to given values - Copyright (C) 2015-2022 Genome Research Ltd. + Copyright (C) 2015-2023 Genome Research Ltd. Author: Petr Danecek @@ -570,7 +570,7 @@ bcf1_t *process(bcf1_t *rec) { if ( ptr[j]==bcf_int32_vector_end ) break; ploidy++; - if ( ptr[j]==bcf_gt_missing ) nmiss++; + if ( bcf_gt_is_missing(ptr[j]) ) nmiss++; } int do_set = 0; diff --git a/test/setGT.6.1.out b/test/setGT.6.1.out new file mode 100644 index 000000000..af8d7d3ea --- /dev/null +++ b/test/setGT.6.1.out @@ -0,0 +1,7 @@ +##fileformat=VCFv4.2 +##FILTER= +##contig= +##reference=file:ref.fa +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B C D +1 1890 . A G . . . GT ./. ./. 1/1 1|1 diff --git a/test/setGT.6.vcf b/test/setGT.6.vcf new file mode 100644 index 000000000..33f348d2a --- /dev/null +++ b/test/setGT.6.vcf @@ -0,0 +1,6 @@ +##fileformat=VCFv4.2 +##contig= +##reference=file:ref.fa +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B C D +1 1890 . A G . . . GT 1/. 1|. 1/1 1|1 diff --git a/test/test.pl b/test/test.pl index c829f9195..9b2a6b9b0 100755 --- a/test/test.pl +++ b/test/test.pl @@ -522,6 +522,8 @@ run_test(\&test_vcf_plugin,$opts,in=>'setGT.4',out=>'setGT.4.1.out',cmd=>'+setGT --no-version',args=>q[-- -t q -n . -e 'FMT/DP>90']); run_test(\&test_vcf_plugin,$opts,in=>'setGT.4',out=>'setGT.4.2.out',cmd=>'+setGT --no-version',args=>q[-- -t q -n . -e 'FMT/DP>100']); run_test(\&test_vcf_plugin,$opts,in=>'setGT.5',out=>'setGT.5.1.out',cmd=>'+setGT --no-version',args=>q[-- -t a -n X]); +run_test(\&test_vcf_plugin,$opts,in=>'setGT.6',out=>'setGT.6.1.out',cmd=>'+setGT --no-version',args=>q[-- -t ./x -n .]); +run_test(\&test_vcf_plugin,$opts,in=>'setGT.6',out=>'setGT.6.1.out',cmd=>'+setGT --no-version',args=>q[-- -t . -n .]); run_test(\&test_vcf_plugin,$opts,in=>'plugin1',out=>'fill-AN-AC.out',cmd=>'+fill-AN-AC --no-version'); run_test(\&test_vcf_plugin,$opts,in=>'dosage',out=>'dosage.1.out',cmd=>'+dosage',args=>'-- -t PL'); run_test(\&test_vcf_plugin,$opts,in=>'dosage',out=>'dosage.2.out',cmd=>'+dosage',args=>'-- -t GL'); From 8f545450ecbf8a90894e8c91ac688ab7020d283a Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Thu, 19 Jan 2023 08:43:08 +0000 Subject: [PATCH 73/84] Update man page to prevent future confusion as in #1851 --- doc/bcftools.txt | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/doc/bcftools.txt b/doc/bcftools.txt index 7a0e572f7..7cfc8e337 100644 --- a/doc/bcftools.txt +++ b/doc/bcftools.txt @@ -3279,9 +3279,9 @@ Convert between VCF and BCF. Former *bcftools subset*. Note that filter options below dealing with counting the number of alleles will, for speed, first check for the values of AC and AN in the INFO column to avoid parsing all the genotype (FORMAT/GT) fields in the VCF. This means -that a filter like '--min-af 0.1' will be calculated from INFO/AC and INFO/AN -when available or FORMAT/GT otherwise. However, it will not attempt to use any other existing -field, like INFO/AF for example. For that, use '--exclude AF<0.1' instead. +that filters like '--uncalled', --exclude-uncalled', or '--min-af 0.1' will be calculated from INFO/AC and +INFO/AN when available or FORMAT/GT otherwise. However, it will not attempt to use any other existing field, +like INFO/AF for example. For that, use '--exclude AF<0.1' instead. Also note that one must be careful when sample subsetting and filtering is performed in a single command because the order of internal operations can influence the result. For example, the *-i/-e* filtering @@ -3357,10 +3357,14 @@ when piping!) most frequent ('nonmajor') alleles. *-u, --uncalled*:: - print sites without a called genotype + print sites without a called genotype, i.e. print sites with all genotypes + missing. Note that the missingness is determined from INFO/AN and AC tags + when available to avoid parsing sample fields. *-U, --exclude-uncalled*:: - exclude sites without a called genotype + exclude sites without a called genotype, i.e. print sites with at least one + non-missing genotype. Note that the missingness is determined from INFO/AN + and AC tags when available to avoid parsing sample fields. *-v, --types* 'snps'|'indels'|'mnps'|'other':: comma-separated list of variant types to select. Site is selected if From 868aefbad7a9f97e51c49d5383c7168e97aa952e Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Mon, 23 Jan 2023 09:21:29 +0000 Subject: [PATCH 74/84] Output missing FORMAT/VAF values in non-trio samples, rather than random nonsense values --- NEWS | 2 ++ plugins/trio-dnm2.c | 3 ++- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/NEWS b/NEWS index 0c57b1356..7c8d73e2b 100644 --- a/NEWS +++ b/NEWS @@ -133,6 +133,8 @@ Changes affecting specific commands: - Allow to set the `--pn` and `--pns` options separately for SNVs and indels and make the indel settings more strict by default + - Output missing FORMAT/VAF values in non-trio samples, rather than random nonsense values + * bcftools +variant-distance - New option `-d, --direction` to choose the directionality: forward, reverse, nearest (the default) diff --git a/plugins/trio-dnm2.c b/plugins/trio-dnm2.c index 8928046b1..4783458b2 100644 --- a/plugins/trio-dnm2.c +++ b/plugins/trio-dnm2.c @@ -1,6 +1,6 @@ /* The MIT License - Copyright (c) 2018-2022 Genome Research Ltd. + Copyright (c) 2018-2023 Genome Research Ltd. Author: Petr Danecek @@ -1375,6 +1375,7 @@ static void process_record(args_t *args, bcf1_t *rec) else for (i=0; idnm_qual_int[i] = bcf_int32_missing; for (i=0; idnm_allele[i] = bcf_int32_missing; + for (i=0; ivaf[i] = bcf_int32_missing; for (i=0; intrio; i++) { if ( args->filter && !args->trio[i].pass ) continue; From 5202e44f246699dfda43d2e3f100ac15202651eb Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Mon, 23 Jan 2023 15:18:24 +0000 Subject: [PATCH 75/84] Add new `--target-gt r:FLOAT` option to randomly select a proportion of genotypes Resolves #1850 --- NEWS | 2 ++ plugins/setGT.c | 72 ++++++++++++++++++++++++++++++++++--------------- test/test.pl | 1 + 3 files changed, 54 insertions(+), 21 deletions(-) diff --git a/NEWS b/NEWS index 7c8d73e2b..8529b2a5b 100644 --- a/NEWS +++ b/NEWS @@ -105,6 +105,8 @@ Changes affecting specific commands: - Add new `--new-gt X` option (#1800) + - Add new `--target-gt r:FLOAT` option to randomly select a proportion of genotypes (#1850) + - Fix a bug where `-t ./x` mode was advertised as selecting both phased and unphased half-missing genotypes, but was in fact selecting only unphased genotypes (#1844) diff --git a/plugins/setGT.c b/plugins/setGT.c index 68b28c39b..b0da58617 100644 --- a/plugins/setGT.c +++ b/plugins/setGT.c @@ -27,6 +27,7 @@ DEALINGS IN THE SOFTWARE. */ #include #include #include +#include #include #include #include @@ -58,9 +59,9 @@ typedef struct int m_allele, M_allele, *gt, *phased, ploidy; char *gt_str; } custom; - int filter_logic; + int filter_logic, rand_seed; uint8_t *smpl_pass; - double binom_val; + double binom_val, rand_frac; char *binom_tag; cmp_f binom_cmp; } @@ -80,6 +81,7 @@ args_t *args = NULL; #define GT_MINOR (1<<9) #define GT_CUSTOM (1<<10) #define GT_X_VAF (1<<11) +#define GT_RAND (1<<12) #define MINOR_ALLELE -1 #define MAJOR_ALLELE -2 @@ -93,30 +95,32 @@ const char *usage(void) { return "About: Sets genotypes. The target genotypes can be specified as:\n" - " ./. .. completely missing (\".\" or \"./.\", depending on ploidy)\n" - " ./x .. partially missing (e.g., \"./0\" or \".|1\" but not \"./.\")\n" - " . .. partially or completely missing\n" - " a .. all genotypes\n" - " b .. heterozygous genotypes failing two-tailed binomial test (example below)\n" - " q .. select genotypes using -i/-e options\n" + " ./. .. completely missing (\".\" or \"./.\", depending on ploidy)\n" + " ./x .. partially missing (e.g., \"./0\" or \".|1\" but not \"./.\")\n" + " . .. partially or completely missing\n" + " a .. all genotypes\n" + " b .. heterozygous genotypes failing two-tailed binomial test (example below)\n" + " q .. select genotypes using -i/-e options\n" + " r:FLOAT .. select randomly a proportion of FLOAT genotypes (can be combined with other modes)\n" " and the new genotype can be one of:\n" - " . .. missing (\".\" or \"./.\", keeps ploidy)\n" - " 0 .. reference allele (e.g. 0/0 or 0, keeps ploidy)\n" - " c:GT .. custom genotype (e.g. 0/0, 0, 0/1, m/M, overrides ploidy)\n" - " m .. minor (the second most common) allele as determined from INFO/AC or FMT/GT (e.g. 1/1 or 1, keeps ploidy)\n" - " M .. major allele as determined from INFO/AC or FMT/GT (e.g. 1/1 or 1, keeps ploidy)\n" - " X .. allele with bigger read depth as determined from FMT/AD\n" - " p .. phase genotype (0/1 becomes 0|1)\n" - " u .. unphase genotype and sort by allele (1|0 becomes 0/1)\n" + " . .. missing (\".\" or \"./.\", keeps ploidy)\n" + " 0 .. reference allele (e.g. 0/0 or 0, keeps ploidy)\n" + " c:GT .. custom genotype (e.g. 0/0, 0, 0/1, m/M, overrides ploidy)\n" + " m .. minor (the second most common) allele as determined from INFO/AC or FMT/GT (e.g. 1/1 or 1, keeps ploidy)\n" + " M .. major allele as determined from INFO/AC or FMT/GT (e.g. 1/1 or 1, keeps ploidy)\n" + " X .. allele with bigger read depth as determined from FMT/AD\n" + " p .. phase genotype (0/1 becomes 0|1)\n" + " u .. unphase genotype and sort by allele (1|0 becomes 0/1)\n" "Usage: bcftools +setGT [General Options] -- [Plugin Options]\n" "Options:\n" " run \"bcftools plugin\" for a list of common options\n" "\n" "Plugin options:\n" - " -e, --exclude Exclude a genotype if true (requires -t q)\n" - " -i, --include include a genotype if true (requires -t q)\n" - " -n, --new-gt Genotypes to set, see above\n" - " -t, --target-gt Genotypes to change, see above\n" + " -e, --exclude EXPR Exclude a genotype if true (requires -t q)\n" + " -i, --include EXPR include a genotype if true (requires -t q)\n" + " -n, --new-gt TYPE Genotypes to set, see above\n" + " -s, --seed INT Random seed to use with -t r [0]\n" + " -t, --target-gt TYPE Genotypes to change, see above\n" "\n" "Example:\n" " # set missing genotypes (\"./.\") to phased ref genotypes (\"0|0\")\n" @@ -196,6 +200,7 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out) args->in_hdr = in; args->out_hdr = out; + char *tmp; int c; static struct option loptions[] = { @@ -203,12 +208,17 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out) {"exclude",required_argument,NULL,'e'}, {"new-gt",required_argument,NULL,'n'}, {"target-gt",required_argument,NULL,'t'}, + {"seed",required_argument,NULL,'s'}, {NULL,0,NULL,0} }; - while ((c = getopt_long(argc, argv, "?hn:t:i:e:",loptions,NULL)) >= 0) + while ((c = getopt_long(argc, argv, "?hn:t:i:e:s:",loptions,NULL)) >= 0) { switch (c) { + case 's': + args->rand_seed = strtol(optarg,&tmp,10); + if ( *tmp ) error("Could not parse: -s %s\n",optarg); + break; case 'e': if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n"); args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; @@ -233,6 +243,13 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out) if ( !strcmp(optarg,"a") ) args->tgt_mask |= GT_ALL; if ( !strcmp(optarg,"q") ) args->tgt_mask |= GT_QUERY; if ( !strcmp(optarg,"?") ) args->tgt_mask |= GT_QUERY; // for backward compatibility + if ( !strncmp(optarg,"r:",2) ) + { + args->rand_frac = strtod(optarg+2,&tmp); + if ( *tmp ) error("Could not parse: -t %s\n", optarg); + if ( args->rand_frac<=0 || args->rand_frac>=1 ) error("Expected value between 0 and 1 with -t\n"); + args->tgt_mask |= GT_RAND; + } if ( strchr(optarg,'b') ) parse_binom_expr(args, strchr(optarg,'b')); if ( args->tgt_mask==0 ) error("Unknown parameter to --target-gt: %s\n", optarg); break; @@ -244,6 +261,11 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out) if ( !args->new_mask ) error("Expected -n option\n"); if ( !args->tgt_mask ) error("Expected -t option\n"); + if ( args->tgt_mask & GT_RAND ) + { + if ( args->tgt_mask==GT_RAND ) args->tgt_mask |= GT_ALL; + hts_srand48(args->rand_seed); + } if ( args->new_mask & GT_MISSING ) args->new_gt = bcf_gt_missing; if ( args->new_mask & GT_REF ) args->new_gt = args->new_mask>_PHASED ? bcf_gt_phased(0) : bcf_gt_unphased(0); @@ -389,6 +411,11 @@ static inline double calc_binom(int na, int nb) return prob; } +static inline int random_draw(args_t *args) +{ + return hts_drand48() > args->rand_frac ? 1 : 0; // reversed random draw +} + bcf1_t *process(bcf1_t *rec) { if ( !rec->n_sample ) return rec; @@ -510,6 +537,7 @@ bcf1_t *process(bcf1_t *rec) double prob = calc_binom(args->iarr[i*nbinom+ia],args->iarr[i*nbinom+ib]); if ( !args->binom_cmp(prob,args->binom_val) ) continue; + if ( args->tgt_mask>_RAND && random_draw(args) ) continue; if ( args->new_mask>_UNPHASED ) changed += unphase_gt(ptr, ngts); @@ -548,6 +576,7 @@ bcf1_t *process(bcf1_t *rec) for (i=0; in_sample; i++) { if ( args->smpl_pass && !args->smpl_pass[i] ) continue; + if ( args->tgt_mask>_RAND && random_draw(args) ) continue; if ( args->new_mask>_UNPHASED ) changed += unphase_gt(args->gts + i*ngts, ngts); else if ( args->new_mask==GT_PHASED ) @@ -579,6 +608,7 @@ bcf1_t *process(bcf1_t *rec) else if ( args->tgt_mask>_MISSING && ploidy==nmiss ) do_set = 1; if ( !do_set ) continue; + if ( args->tgt_mask>_RAND && random_draw(args) ) continue; if ( args->new_mask>_UNPHASED ) changed += unphase_gt(ptr, ngts); diff --git a/test/test.pl b/test/test.pl index 9b2a6b9b0..1b7428c80 100755 --- a/test/test.pl +++ b/test/test.pl @@ -524,6 +524,7 @@ run_test(\&test_vcf_plugin,$opts,in=>'setGT.5',out=>'setGT.5.1.out',cmd=>'+setGT --no-version',args=>q[-- -t a -n X]); run_test(\&test_vcf_plugin,$opts,in=>'setGT.6',out=>'setGT.6.1.out',cmd=>'+setGT --no-version',args=>q[-- -t ./x -n .]); run_test(\&test_vcf_plugin,$opts,in=>'setGT.6',out=>'setGT.6.1.out',cmd=>'+setGT --no-version',args=>q[-- -t . -n .]); +run_test(\&test_vcf_plugin,$opts,in=>'setGT.6',out=>'setGT.6.2.out',cmd=>'+setGT --no-version',args=>q[-- -t r:0.5 -n .]); run_test(\&test_vcf_plugin,$opts,in=>'plugin1',out=>'fill-AN-AC.out',cmd=>'+fill-AN-AC --no-version'); run_test(\&test_vcf_plugin,$opts,in=>'dosage',out=>'dosage.1.out',cmd=>'+dosage',args=>'-- -t PL'); run_test(\&test_vcf_plugin,$opts,in=>'dosage',out=>'dosage.2.out',cmd=>'+dosage',args=>'-- -t GL'); From 19bb932a5c1cf5be731c85136e12ecb9c1d6d15a Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Tue, 24 Jan 2023 15:54:28 +0000 Subject: [PATCH 76/84] Arrays in Number=R tags can be now subscripted by alleles found in FORMAT/GT For example FORMAT/AD[GT] > 10 .. require support of more than 10 reads for each allele FORMAT/AD[0:GT] > 10 .. same as above, but in the first sample sSUM(FORMAT/AD[GT]) > 20 .. require total sample depth bigger than 20 Resolves #1849 --- NEWS | 6 +++ doc/bcftools.txt | 10 +++- filter.c | 116 +++++++++++++++++++++++++++++++++++++++++++-- test/query.92.out | 6 +++ test/query.93.out | 2 + test/query.94.out | 3 ++ test/setGT.6.2.out | 7 +++ test/test.pl | 3 ++ 8 files changed, 147 insertions(+), 6 deletions(-) create mode 100644 test/query.92.out create mode 100644 test/query.93.out create mode 100644 test/query.94.out create mode 100644 test/setGT.6.2.out diff --git a/NEWS b/NEWS index 8529b2a5b..443eb9ff7 100644 --- a/NEWS +++ b/NEWS @@ -13,6 +13,12 @@ Changes affecting the whole of bcftools, or multiple commands: - evaluate to C_i = A_0 + B_i when length(A)=1 and set length(C)=length(B) - throw an error when length(A)!=length(B) AND length(A)!=1 AND length(B)!=1 + - Arrays in Number=R tags can be now subscripted by alleles found in FORMAT/GT. For example, + + FORMAT/AD[GT] > 10 .. require support of more than 10 reads for each allele + FORMAT/AD[0:GT] > 10 .. same as above, but in the first sample + sSUM(FORMAT/AD[GT]) > 20 .. require total sample depth bigger than 20 + Changes affecting specific commands: diff --git a/doc/bcftools.txt b/doc/bcftools.txt index 7cfc8e337..755d67262 100644 --- a/doc/bcftools.txt +++ b/doc/bcftools.txt @@ -3505,7 +3505,7 @@ to require that all alleles are of the given type. Compare * array subscripts (0-based), "*" for any element, "-" to indicate a range. Note that for querying FORMAT vectors, the colon ":" can be used to select a sample and an -element of the vector, as shown in the examples below +element of the vector, as shown in the examples below. INFO/AF[0] > 0.3 .. first AF value bigger than 0.3 FORMAT/AD[0:0] > 30 .. first AD value of the first sample bigger than 30 @@ -3522,6 +3522,14 @@ element of the vector, as shown in the examples below (DP4[0]+DP4[1])/(DP4[2]+DP4[3]) > 0.3 CSQ[*] ~ "missense_variant.*deleterious" +* in addition to array subscripts shown above, it is possible to subscript arrays +of Number=R tags by alleles found in FORMAT/GT (starting with version 1.17). +For example + + FORMAT/AD[GT] > 10 .. require support of more than 10 reads for each allele + FORMAT/AD[0:GT] > 10 .. same as above, but in the first sample + sSUM(FORMAT/AD[GT]) > 20 .. require total sample depth bigger than 20 + * with many samples it can be more practical to provide a file with sample names, one sample name per line diff --git a/filter.c b/filter.c index c87e44777..b9174c3a0 100644 --- a/filter.c +++ b/filter.c @@ -69,6 +69,7 @@ typedef struct _token_t int hdr_id, tag_type; // BCF header lookup ID and one of BCF_HL_* types int idx; // 0-based index to VCF vectors, // -2: list (e.g. [0,1,2] or [1..3] or [1..] or any field[*], which is equivalent to [0..]) + // -3: select indices on the fly based on values in GT int *idxs; // set indexes to 0 to exclude, to 1 to include, and last element negative if unlimited; used by VCF retrievers only int nidxs, nuidxs; // size of idxs array and the number of elements set to 1 uint8_t *usmpl; // bitmask of used samples as set by idx, set for FORMAT fields, NULL otherwise @@ -100,6 +101,11 @@ struct _filter_t float *tmpf; kstring_t tmps; int max_unpack, mtmpi, mtmpf, nsamples; + struct { + bcf1_t *line; + int32_t *buf, nbuf, mbuf; // GTs as obtained by bcf_get_genotypes() + uint64_t *mask; // GTs as mask, e.g 0/0 is 1; 0/1 is 3, max 63 unique alleles + } cached_GT; #if ENABLE_PERL_FILTERS PerlInterpreter *perl; #endif @@ -350,6 +356,44 @@ char *expand_path(char *path) return strdup(path); } +static int filters_cache_genotypes(filter_t *flt, bcf1_t *line) +{ + if ( flt->cached_GT.line==line ) return flt->cached_GT.nbuf > 0 ? 0 : -1; + flt->cached_GT.line = line; + flt->cached_GT.nbuf = bcf_get_genotypes(flt->hdr, line, &flt->cached_GT.buf, &flt->cached_GT.mbuf); + if ( flt->cached_GT.nbuf<=0 ) return -1; + if ( !flt->cached_GT.mask ) + { + flt->cached_GT.mask = (uint64_t*) malloc(sizeof(*flt->cached_GT.mask)*flt->nsamples); + if ( !flt->cached_GT.mask ) error("Could not alloc %zu bytes\n",sizeof(*flt->cached_GT.mask)*flt->nsamples); + } + int i,j, ngt1 = flt->cached_GT.nbuf / line->n_sample; + for (i=0; in_sample; i++) + { + int32_t *ptr = flt->cached_GT.buf + i*ngt1; + flt->cached_GT.mask[i] = 0; + for (j=0; j 63 ) + { + static int warned = 0; + if ( !warned ) + { + fprintf(stderr,"Too many alleles, skipping GT filtering at this site %s:%"PRId64". " + "(This warning is printed only once.)\n", bcf_seqname(flt->hdr,line),line->pos+1); + warned = 1; + } + flt->cached_GT.nbuf = 0; + return -1; + } + flt->cached_GT.mask[i] |= 1<values[i] = ptr[tok->idx]; } } + else if ( tok->idx==-3 ) + { + if ( filters_cache_genotypes(flt,line)!=0 ) + { + tok->nvalues = 0; + return; + } + for (i=0; insamples; i++) + { + if ( !tok->usmpl[i] ) continue; + int32_t *src = flt->tmpi + i*nsrc1; + double *dst = tok->values + i*tok->nval1; + int k, j = 0; + for (k=0; kcached_GT.mask[i] & (1<nval1; j++) bcf_double_set_vector_end(dst[j]); + } + } else { int kend = tok->idxs[tok->nidxs-1] < 0 ? tok->nval1 : tok->nidxs; @@ -825,6 +890,33 @@ static void filters_set_format_float(filter_t *flt, bcf1_t *line, token_t *tok) tok->values[i] = ptr[tok->idx]; } } + else if ( tok->idx==-3 ) + { + if ( filters_cache_genotypes(flt,line)!=0 ) + { + tok->nvalues = 0; + return; + } + for (i=0; insamples; i++) + { + if ( !tok->usmpl[i] ) continue; + float *src = flt->tmpf + i*nsrc1; + double *dst = tok->values + i*tok->nval1; + int k, j = 0; + for (k=0; kcached_GT.mask[i] & (1<nval1; j++) bcf_double_set_vector_end(dst[j]); + } + } else { int kend = tok->idxs[tok->nidxs-1] < 0 ? tok->nval1 : tok->nidxs; @@ -989,9 +1081,9 @@ static void _filters_set_genotype(filter_t *flt, bcf1_t *line, token_t *tok, int tok->str_value.s[tok->str_value.l] = 0; tok->nval1 = nvals1; } -static void filters_set_genotype2(filter_t *flt, bcf1_t *line, token_t *tok) { _filters_set_genotype(flt, line, tok, 2); } -static void filters_set_genotype3(filter_t *flt, bcf1_t *line, token_t *tok) { _filters_set_genotype(flt, line, tok, 3); } -static void filters_set_genotype4(filter_t *flt, bcf1_t *line, token_t *tok) { _filters_set_genotype(flt, line, tok, 4); } +static void filters_set_genotype2(filter_t *flt, bcf1_t *line, token_t *tok) { _filters_set_genotype(flt, line, tok, 2); } // rr, ra, aa, aA etc +static void filters_set_genotype3(filter_t *flt, bcf1_t *line, token_t *tok) { _filters_set_genotype(flt, line, tok, 3); } // hap, hom, het +static void filters_set_genotype4(filter_t *flt, bcf1_t *line, token_t *tok) { _filters_set_genotype(flt, line, tok, 4); } // mis, alt, ref static void filters_set_genotype_string(filter_t *flt, bcf1_t *line, token_t *tok) { @@ -2480,6 +2572,14 @@ static int parse_idxs(char *tag_idx, int **idxs, int *nidxs, int *idx) *idx = -2; return 0; } + if ( !strcmp("GT", tag_idx) ) + { + *idxs = (int*) malloc(sizeof(int)); + (*idxs)[0] = -1; + *nidxs = 1; + *idx = -3; + return 0; + } // TAG[integer] .. one field; idx positive char *end, *beg = tag_idx; @@ -2595,7 +2695,7 @@ static void parse_tag_idx(bcf_hdr_t *hdr, int is_fmt, char *tag, char *tag_idx, tok->idxs = (int*) malloc(sizeof(int)); tok->idxs[0] = -1; tok->nidxs = 1; - tok->idx = -2; + tok->idx = idx1; } else if ( bcf_hdr_id2number(hdr,BCF_HL_FMT,tok->hdr_id)!=1 ) error("The FORMAT tag %s can have multiple subfields, run as %s[sample:subfield]\n", tag,tag); @@ -2620,7 +2720,7 @@ static void parse_tag_idx(bcf_hdr_t *hdr, int is_fmt, char *tag, char *tag_idx, if ( idx1 >= bcf_hdr_nsamples(hdr) ) error("The sample index is too large: %s\n", ori); tok->usmpl[idx1] = 1; } - else if ( idx1==-2 ) + else if ( idx1==-2 || idx1==-3 ) { for (i=0; ihdr, is_fmt, tmp.s, tmp.s+is_array, tok); + if ( tok->idx==-3 && bcf_hdr_id2length(filter->hdr,BCF_HL_FMT,tok->hdr_id)!=BCF_VL_R ) + error("Error: GT subscripts can be used only with Number=R tags\n"); + } else if ( is_fmt && !tok->nsamples ) { int i; @@ -3525,6 +3629,8 @@ void filter_destroy(filter_t *filter) free(filter->filters[i].regex); } } + free(filter->cached_GT.buf); + free(filter->cached_GT.mask); free(filter->filters); free(filter->flt_stack); free(filter->str); diff --git a/test/query.92.out b/test/query.92.out new file mode 100644 index 000000000..7ff098ba8 --- /dev/null +++ b/test/query.92.out @@ -0,0 +1,6 @@ +3000151 0/0 A 10,0,0 +3000151 0/0 B 10,0,0 +3000155 0/2 A 20,0,10 +3000155 0/2 B 200,0,10 +3000157 1/2 A 0,40,10 +3000157 1/2 B 0,400,10 diff --git a/test/query.93.out b/test/query.93.out new file mode 100644 index 000000000..7fa79af7b --- /dev/null +++ b/test/query.93.out @@ -0,0 +1,2 @@ +3000153 2/2 B 0,0,210 +3000155 0/2 B 200,0,10 diff --git a/test/query.94.out b/test/query.94.out new file mode 100644 index 000000000..7b419248b --- /dev/null +++ b/test/query.94.out @@ -0,0 +1,3 @@ +3000154 0/1 A 30,13,0 +3000156 1/0 A 30,14,0 +3000158 2/0 A 0,5,30 diff --git a/test/setGT.6.2.out b/test/setGT.6.2.out new file mode 100644 index 000000000..bf8530578 --- /dev/null +++ b/test/setGT.6.2.out @@ -0,0 +1,7 @@ +##fileformat=VCFv4.2 +##FILTER= +##contig= +##reference=file:ref.fa +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B C D +1 1890 . A G . . . GT ./. 1|. ./. 1|1 diff --git a/test/test.pl b/test/test.pl index 1b7428c80..4ef961c1a 100755 --- a/test/test.pl +++ b/test/test.pl @@ -184,6 +184,9 @@ run_test(\&test_vcf_query,$opts,in=>'query.filter.5',out=>'query.57.out',args=>q[-f'[%POS\\t%SAMPLE\\t%GT\\t%AD\\n]' -i'GT="het" & binom(FMT/AD)>0.01']); run_test(\&test_vcf_query,$opts,in=>'query.filter.5',out=>'query.58.out',args=>q[-f'[%POS\\t%SAMPLE\\t%GT\\t%AD\\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01']); run_test(\&test_vcf_query,$opts,in=>'query.filter.5',out=>'query.59.out',args=>q[-f'%POS\\t%AD\\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01']); +run_test(\&test_vcf_query,$opts,in=>'query.filter.5',out=>'query.92.out',args=>q[-f'[%POS\\t%GT\\t%SAMPLE\\t%AD\\n]' -i'FMT/AD[GT]==10']); +run_test(\&test_vcf_query,$opts,in=>'query.filter.5',out=>'query.93.out',args=>q[-f'[%POS\\t%GT\\t%SAMPLE\\t%AD\\n]' -i'sSUM(FMT/AD[GT])==210']); +run_test(\&test_vcf_query,$opts,in=>'query.filter.5',out=>'query.94.out',args=>q[-f'[%POS\\t%GT\\t%SAMPLE\\t%AD\\n]' -i'FMT/AD[0:GT]==30']); run_test(\&test_vcf_query,$opts,in=>'query',out=>'query.60.out',args=>q[-f'%CHROM %POS\\n' -i'CHROM="4"']); run_test(\&test_vcf_query,$opts,in=>'query.negative',out=>'query.61.out',args=>q[-f'%POS\\t%TAG1\\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)']); run_test(\&test_vcf_query,$opts,in=>'query.negative',out=>'query.61.out',args=>q[-f'%POS\\t%TAGV1\\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)']); From 9ae4fe87e1ee45ad156d307ad52d1fbd774988c3 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Mon, 6 Feb 2023 08:57:41 +0000 Subject: [PATCH 77/84] Exit when no matching sample is found --- consensus.c | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/consensus.c b/consensus.c index e48d5123f..397d45f98 100644 --- a/consensus.c +++ b/consensus.c @@ -1,6 +1,6 @@ /* The MIT License - Copyright (c) 2014-2022 Genome Research Ltd. + Copyright (c) 2014-2023 Genome Research Ltd. Author: Petr Danecek @@ -231,9 +231,15 @@ static void init_data(args_t *args) if ( !args->sample ) args->smpl = smpl_ilist_init(args->hdr,NULL,0,SMPL_NONE|SMPL_VERBOSE); else if ( args->sample && strcmp("-",args->sample) ) + { args->smpl = smpl_ilist_init(args->hdr,args->sample,0,SMPL_NONE|SMPL_VERBOSE); + if ( args->smpl && !args->smpl->n ) error("No matching sample found\n"); + } else if ( args->sample_fname ) + { args->smpl = smpl_ilist_init(args->hdr,args->sample_fname,1,SMPL_NONE|SMPL_VERBOSE); + if ( args->smpl && !args->smpl->n ) error("No matching sample found\n"); + } if ( args->smpl ) { if ( args->haplotype || args->allele ) From 02a39613666be62d4e2184ebe4c6d30062c1a784 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Mon, 6 Feb 2023 09:05:20 +0000 Subject: [PATCH 78/84] Drop offending space character in `query -H` output The header printed by `bcftools query -H` and `bcftools +split-vep -H` contained a space after the leading hash # [1]columnName The space is unnecessary and complicates machine processing, so is dropped to produce output like #[1]columnName Resolves #1856 --- NEWS | 7 ++++++- convert.c | 4 ++-- test/split-vep.12.2.out | 2 +- 3 files changed, 9 insertions(+), 4 deletions(-) diff --git a/NEWS b/NEWS index 443eb9ff7..d1730ee19 100644 --- a/NEWS +++ b/NEWS @@ -19,12 +19,17 @@ Changes affecting the whole of bcftools, or multiple commands: FORMAT/AD[0:GT] > 10 .. same as above, but in the first sample sSUM(FORMAT/AD[GT]) > 20 .. require total sample depth bigger than 20 +* The commands `consensus -H` and `+split-vep -H` + + - Drop unnecessary leading space in the first header column and newly print `#[1]columnName` + instead of the previous `# [1]columnName` (#1856) + Changes affecting specific commands: * bcftools +allele-length - - fix overflow for indels longer than 512bp and aggregate alleles equal or larger than + - Fix overflow for indels longer than 512bp and aggregate alleles equal or larger than that in the same bin (#1837) * bcftools annotate diff --git a/convert.c b/convert.c index 4ae57b7d4..80e54747d 100644 --- a/convert.c +++ b/convert.c @@ -1,6 +1,6 @@ /* convert.c -- functions for converting between VCF/BCF and related formats. - Copyright (C) 2013-2022 Genome Research Ltd. + Copyright (C) 2013-2023 Genome Research Ltd. Author: Petr Danecek @@ -1568,7 +1568,7 @@ int convert_header(convert_t *convert, kstring_t *str) if ( i!=convert->nfmt ) return str->l - l_ori; - kputs("# ", str); + kputc('#', str); for (i=0; infmt; i++) { // Genotype fields diff --git a/test/split-vep.12.2.out b/test/split-vep.12.2.out index 60a8c1996..9b2a0f8d5 100644 --- a/test/split-vep.12.2.out +++ b/test/split-vep.12.2.out @@ -1,4 +1,4 @@ -# [1]POS [2]Allele [3]Consequence [4]IMPACT [5]SYMBOL [6]Gene [7]Feature_type [8]Feature [9]BIOTYPE [10]EXON [11]INTRON [12]HGVSc [13]HGVSp [14]cDNA_position [15]CDS_position [16]Protein_position [17]Amino_acids [18]Codons [19]Existing_variation [20]ALLELE_NUM [21]DISTANCE [22]STRAND [23]FLAGS [24]VARIANT_CLASS [25]SYMBOL_SOURCE [26]HGNC_ID [27]CANONICAL [28]TSL [29]APPRIS [30]CCDS [31]ENSP [32]SWISSPROT [33]TREMBL [34]UNIPARC [35]SOURCE [36]GENE_PHENO [37]SIFT [38]PolyPhen [39]DOMAINS [40]miRNA [41]HGVS_OFFSET [42]AF [43]AFR_AF [44]AMR_AF [45]EAS_AF [46]EUR_AF [47]SAS_AF [48]AA_AF [49]EA_AF [50]gnomAD_AF [51]gnomAD_AFR_AF [52]gnomAD_AMR_AF [53]gnomAD_ASJ_AF [54]gnomAD_EAS_AF [55]gnomAD_FIN_AF [56]gnomAD_NFE_AF [57]gnomAD_OTH_AF [58]gnomAD_SAS_AF [59]MAX_AF [60]MAX_AF_POPS [61]CLIN_SIG [62]SOMATIC [63]PHENO [64]PUBMED [65]MOTIF_NAME [66]MOTIF_POS [67]HIGH_INF_POS [68]MOTIF_SCORE_CHANGE [69]LoF [70]LoF_filter [71]LoF_flags [72]LoF_info [73]CADD_PHRED [74]CADD_RAW [75]gnomAD2.1 [76]gnomAD2.1_AF_raw [77]gnomAD2.1_AF_popmax [78]gnomAD2.1_AF_afr [79]gnomAD2.1_AF_amr [80]gnomAD2.1_AF_asj [81]gnomAD2.1_AF_eas [82]gnomAD2.1_AF_fin [83]gnomAD2.1_AF_nfe [84]gnomAD2.1_AF_oth [85]gnomAD2.1_AF_sas +#[1]POS [2]Allele [3]Consequence [4]IMPACT [5]SYMBOL [6]Gene [7]Feature_type [8]Feature [9]BIOTYPE [10]EXON [11]INTRON [12]HGVSc [13]HGVSp [14]cDNA_position [15]CDS_position [16]Protein_position [17]Amino_acids [18]Codons [19]Existing_variation [20]ALLELE_NUM [21]DISTANCE [22]STRAND [23]FLAGS [24]VARIANT_CLASS [25]SYMBOL_SOURCE [26]HGNC_ID [27]CANONICAL [28]TSL [29]APPRIS [30]CCDS [31]ENSP [32]SWISSPROT [33]TREMBL [34]UNIPARC [35]SOURCE [36]GENE_PHENO [37]SIFT [38]PolyPhen [39]DOMAINS [40]miRNA [41]HGVS_OFFSET [42]AF [43]AFR_AF [44]AMR_AF [45]EAS_AF [46]EUR_AF [47]SAS_AF [48]AA_AF [49]EA_AF [50]gnomAD_AF [51]gnomAD_AFR_AF [52]gnomAD_AMR_AF [53]gnomAD_ASJ_AF [54]gnomAD_EAS_AF [55]gnomAD_FIN_AF [56]gnomAD_NFE_AF [57]gnomAD_OTH_AF [58]gnomAD_SAS_AF [59]MAX_AF [60]MAX_AF_POPS [61]CLIN_SIG [62]SOMATIC [63]PHENO [64]PUBMED [65]MOTIF_NAME [66]MOTIF_POS [67]HIGH_INF_POS [68]MOTIF_SCORE_CHANGE [69]LoF [70]LoF_filter [71]LoF_flags [72]LoF_info [73]CADD_PHRED [74]CADD_RAW [75]gnomAD2.1 [76]gnomAD2.1_AF_raw [77]gnomAD2.1_AF_popmax [78]gnomAD2.1_AF_afr [79]gnomAD2.1_AF_amr [80]gnomAD2.1_AF_asj [81]gnomAD2.1_AF_eas [82]gnomAD2.1_AF_fin [83]gnomAD2.1_AF_nfe [84]gnomAD2.1_AF_oth [85]gnomAD2.1_AF_sas 14464 T non_coding_transcript_exon_variant MODIFIER WASH7P ENSG00000227232 Transcript ENST00000423562 unprocessed_pseudogene 10/10 . ENST00000423562.1:n.1568T>A . 1568 . . . . rs546169444 1 . -1 . SNV HGNC 38034 . . . . . . . . . . . . . . . 0.0958 0.0144 0.1138 0.005 0.1859 0.1943 . . . . . . . . . . . 0.1943 SAS . . . . . . . . . . . . . . . . . . . . . . . . . 14464 T non_coding_transcript_exon_variant MODIFIER WASH7P ENSG00000227232 Transcript ENST00000438504 unprocessed_pseudogene 12/12 . ENST00000438504.2:n.1682T>A . 1682 . . . . rs546169444 1 . -1 . SNV HGNC 38034 YES . . . . . . . . . . . . . . 0.0958 0.0144 0.1138 0.005 0.1859 0.1943 . . . . . . . . . . . 0.1943 SAS . . . . . . . . . . . . . . . . . . . . . . . . . 14464 T downstream_gene_variant MODIFIER DDX11L1 ENSG00000223972 Transcript ENST00000456328 processed_transcript . . . . . . . . . rs546169444 1 55 1 . SNV HGNC 37102 YES . . . . . . . . . . . . . . 0.0958 0.0144 0.1138 0.005 0.1859 0.1943 . . . . . . . . . . . 0.1943 SAS . . . . . . . . . . . . . . . . . . . . . . . . . From d61277ecceb6c63f2ec2d3083e409bd91b608446 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Mon, 6 Feb 2023 13:52:53 +0000 Subject: [PATCH 79/84] Make +fill-tags recognise both `-t TAG` and `-t INFO/TAG`. Resolves #1857 --- plugins/fill-tags.c | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/plugins/fill-tags.c b/plugins/fill-tags.c index 124595b75..740313f5f 100644 --- a/plugins/fill-tags.c +++ b/plugins/fill-tags.c @@ -476,21 +476,21 @@ uint32_t parse_tags(args_t *args, const char *str) args->warned = ~(SET_END|SET_TYPE); args->unpack |= BCF_UN_FMT; } - else if ( !strcasecmp(tags[i],"AN") ) { flag |= SET_AN; args->unpack |= BCF_UN_FMT; } - else if ( !strcasecmp(tags[i],"AC") ) { flag |= SET_AC; args->unpack |= BCF_UN_FMT; } - else if ( !strcasecmp(tags[i],"NS") ) { flag |= SET_NS; args->unpack |= BCF_UN_FMT; } - else if ( !strcasecmp(tags[i],"AC_Hom") ) { flag |= SET_AC_Hom; args->unpack |= BCF_UN_FMT; } - else if ( !strcasecmp(tags[i],"AC_Het") ) { flag |= SET_AC_Het; args->unpack |= BCF_UN_FMT; } - else if ( !strcasecmp(tags[i],"AC_Hemi") ) { flag |= SET_AC_Hemi; args->unpack |= BCF_UN_FMT; } - else if ( !strcasecmp(tags[i],"AF") ) { flag |= SET_AF; args->unpack |= BCF_UN_FMT; } - else if ( !strcasecmp(tags[i],"MAF") ) { flag |= SET_MAF; args->unpack |= BCF_UN_FMT; } - else if ( !strcasecmp(tags[i],"HWE") ) { flag |= SET_HWE; args->unpack |= BCF_UN_FMT; } - else if ( !strcasecmp(tags[i],"ExcHet") ) { flag |= SET_ExcHet; args->unpack |= BCF_UN_FMT; } + else if ( !strcasecmp(tags[i],"AN") || !strcasecmp(tags[i],"INFO/AN") ) { flag |= SET_AN; args->unpack |= BCF_UN_FMT; } + else if ( !strcasecmp(tags[i],"AC") || !strcasecmp(tags[i],"INFO/AC") ) { flag |= SET_AC; args->unpack |= BCF_UN_FMT; } + else if ( !strcasecmp(tags[i],"NS") || !strcasecmp(tags[i],"INFO/NS") ) { flag |= SET_NS; args->unpack |= BCF_UN_FMT; } + else if ( !strcasecmp(tags[i],"AC_Hom") || !strcasecmp(tags[i],"INFO/AC_Hom") ) { flag |= SET_AC_Hom; args->unpack |= BCF_UN_FMT; } + else if ( !strcasecmp(tags[i],"AC_Het") || !strcasecmp(tags[i],"INFO/AC_Het") ) { flag |= SET_AC_Het; args->unpack |= BCF_UN_FMT; } + else if ( !strcasecmp(tags[i],"AC_Hemi") || !strcasecmp(tags[i],"INFO_Hemi") ) { flag |= SET_AC_Hemi; args->unpack |= BCF_UN_FMT; } + else if ( !strcasecmp(tags[i],"AF") || !strcasecmp(tags[i],"INFO/AF") ) { flag |= SET_AF; args->unpack |= BCF_UN_FMT; } + else if ( !strcasecmp(tags[i],"MAF") || !strcasecmp(tags[i],"INFO/MAF") ) { flag |= SET_MAF; args->unpack |= BCF_UN_FMT; } + else if ( !strcasecmp(tags[i],"HWE") || !strcasecmp(tags[i],"INFO/HWE") ) { flag |= SET_HWE; args->unpack |= BCF_UN_FMT; } + else if ( !strcasecmp(tags[i],"ExcHet") || !strcasecmp(tags[i],"INFO/ExcHet") ) { flag |= SET_ExcHet; args->unpack |= BCF_UN_FMT; } else if ( !strcasecmp(tags[i],"VAF") || !strcasecmp(tags[i],"FORMAT/VAF") ) { flag |= SET_VAF; args->unpack |= BCF_UN_FMT; } else if ( !strcasecmp(tags[i],"VAF1") || !strcasecmp(tags[i],"FORMAT/VAF1") ) { flag |= SET_VAF1; args->unpack |= BCF_UN_FMT; } - else if ( !strcasecmp(tags[i],"END") ) flag |= SET_END; - else if ( !strcasecmp(tags[i],"TYPE") ) flag |= SET_TYPE; - else if ( !strcasecmp(tags[i],"F_MISSING") ) { flag |= parse_func(args,"F_MISSING=F_MISSING","F_MISSING"); args->unpack |= BCF_UN_FMT; } + else if ( !strcasecmp(tags[i],"END") || !strcasecmp(tags[i],"INFO/END") ) flag |= SET_END; + else if ( !strcasecmp(tags[i],"TYPE") || !strcasecmp(tags[i],"INFO/TYPE") ) flag |= SET_TYPE; + else if ( !strcasecmp(tags[i],"F_MISSING") || !strcasecmp(tags[i],"INFO/F_MISSING") ) { flag |= parse_func(args,"F_MISSING=F_MISSING","F_MISSING"); args->unpack |= BCF_UN_FMT; } else if ( (ptr=strchr(tags[i],'=')) ) { flag |= parse_func(args,tags[i],ptr+1); args->unpack |= BCF_UN_FMT; } else { From f4fac3ce77aa34ebd96fc0f737cc3e61978f0249 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Wed, 8 Feb 2023 10:17:33 +0000 Subject: [PATCH 80/84] Replace assert with an error message to help with debugging. See #1044 --- vcfmerge.c | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/vcfmerge.c b/vcfmerge.c index 7296a0094..621f4102c 100644 --- a/vcfmerge.c +++ b/vcfmerge.c @@ -495,7 +495,7 @@ static int info_rules_add_values(args_t *args, bcf_hdr_t *hdr, bcf1_t *line, inf else if ( var_len==BCF_VL_G ) { args->maux->nagr_map = bcf_alleles2gt(line->n_allele-1,line->n_allele-1)+1; - assert( ret==line->n_allele || ret==args->maux->nagr_map ); + if ( ret!=line->n_allele && ret!=args->maux->nagr_map ) error("Wrong number of %s fields at %s:%"PRId64"\n",rule->hdr_tag,bcf_seqname(hdr,line),(int64_t) line->pos+1); if ( ret==line->n_allele ) // haploid { args->maux->nagr_map = line->n_allele; @@ -974,7 +974,7 @@ void merge_chrom2qual(args_t *args, bcf1_t *out) int k = 0; for (i=0; inals; i++) if ( i==0 || al_idxs[i] ) ma->out_als[k++] = strdup(ma->als[i]); - assert( k==ma->nout_als ); + if ( k!=ma->nout_als ) error("Error: could not merge alleles at %s:%"PRId64", sanity check failed: %d!=%d\n",bcf_seqname(out_hdr,out),out->pos+1,k,ma->nout_als); normalize_alleles(ma->out_als, ma->nout_als); bcf_update_alleles(out_hdr, out, (const char**) ma->out_als, ma->nout_als); free(al_idxs); From f0ad6aa062a949d7b0bd745d6733c8375bdc18fa Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Fri, 10 Feb 2023 12:06:52 +0000 Subject: [PATCH 81/84] Work around a bug in the LOFTEE VEP plugin used to annotate gnomAD VCFs The LoF_info subfield contains commas which, in general, makes it impossible to parse the VEP subfields in automated way. The +split-vep plugin can now work with such files, replacing the offending commas with slash (/) characters. Note that this makes two assumptions: 1) the number of subfields delimited by the pipe characters (|) are consistent with the header definition 2) the first subfield never contains a comma, otherwise it woud be impossible to distinguish between A|A,A,B,B|B and A|A,A,A,B|B See also https://github.com/Ensembl/ensembl-vep/issues/1351 --- NEWS | 5 +++ plugins/split-vep.c | 63 ++++++++++++++++++++++++++++------- test/split-vep.broken-LoF.out | 18 ++++++++++ test/split-vep.broken-LoF.vcf | 6 ++++ test/test.pl | 1 + 5 files changed, 81 insertions(+), 12 deletions(-) create mode 100644 test/split-vep.broken-LoF.out create mode 100644 test/split-vep.broken-LoF.vcf diff --git a/NEWS b/NEWS index d1730ee19..7d03c1eff 100644 --- a/NEWS +++ b/NEWS @@ -128,6 +128,11 @@ Changes affecting specific commands: - New `-H, --print-header` option to print the header with `-f` + - Work around a bug in the LOFTEE VEP plugin used to annotate gnomAD VCFs. There the + LoF_info subfield contains commas which, in general, makes it impossible to parse the + VEP subfields. The +split-vep plugin can now work with such files, replacing the offending + commas with slash (/) characters. See also https://github.com/Ensembl/ensembl-vep/issues/1351 + * bcftools stats - The per-sample stats (PSC) would not be computed when `-i/-e` filtering options and diff --git a/plugins/split-vep.c b/plugins/split-vep.c index a0517a5c8..387ebc8ee 100644 --- a/plugins/split-vep.c +++ b/plugins/split-vep.c @@ -1,6 +1,6 @@ /* The MIT License - Copyright (c) 2019-2022 Genome Research Ltd. + Copyright (c) 2019-2023 Genome Research Ltd. Author: Petr Danecek @@ -1095,6 +1095,55 @@ static void restrict_csqs_to_genes(args_t *args) } args->ncols_csq = nhit; } + +// Split the VEP annotation by transcript and by field, then check if the number of subfields looks alright. +// Unfortunately, we cannot enforce the number of subfields to match the header definition because that can +// be variable: `bcftools csq` outputs different number of fields for different consequence types. +// So we need to distinguish between this reasonable case and incorrectly formated consequences such +// as those reported for LoF_info subfield here https://github.com/Ensembl/ensembl-vep/issues/1351. +static void split_csq_fields(args_t *args, bcf1_t *rec, int csq_str_len) +{ + int i; + args->cols_tr = cols_split(args->csq_str, args->cols_tr, ','); + if ( args->cols_tr->n > args->mcols_csq ) + { + args->cols_csq = (cols_t**)realloc(args->cols_csq,args->cols_tr->n*sizeof(*args->cols_csq)); + for (i=args->mcols_csq; icols_tr->n; i++) args->cols_csq[i] = NULL; + args->mcols_csq = args->cols_tr->n; + } + args->ncols_csq = args->cols_tr->n; + int nfield_diff = 0, need_fix = 0; + for (i=0; icols_tr->n; i++) + { + args->cols_csq[i] = cols_split(args->cols_tr->off[i], args->cols_csq[i], '|'); + if ( args->csq_idx >= args->cols_csq[i]->n ) need_fix = 1; + if ( nfield_diff < abs(args->cols_csq[i]->n - args->nfield) ) nfield_diff = args->cols_csq[i]->n - args->nfield; + } + if ( !csq_str_len ) return; // called 2nd time, don't attempt to fix + if ( !need_fix ) return; + + static int warned = 0; + if ( !warned ) + fprintf(stderr,"Warning: The number of INFO/%s subfields at %s:%"PRIhts_pos" does not match the header definition,\n" + " expected %d subfields, found as %s as %d. (This warning is printed only once.)\n", + args->vep_tag,bcf_seqname(args->hdr,rec),rec->pos+1,args->nfield,nfield_diff>0?"much":"few",args->nfield+nfield_diff); + warned = 1; + + // One known failure mode is LoF_info subfield which can contain commas. Work around this by relying on + // the number of pipe delimiters matching the header definition, replacing offending commas with slash + // characters. This assumes that there is never a comma in the first subfield, otherwise it would be + // impossible to distinguish between A|A,A,B,B|B and A|A,A,A,B|B + int npipe = 0; + while ( csq_str_len > 0 ) + { + csq_str_len--; + if ( args->csq_str[csq_str_len]=='|' ) { npipe++; continue; } + if ( args->csq_str[csq_str_len]!=',' ) continue; + if ( npipe && !(npipe % (args->nfield-1)) ) { npipe = 0; continue; } // wholesome number of pipes encountered, this is a valid comma + args->csq_str[csq_str_len] = '/'; + } + split_csq_fields(args,rec,0); // try once more +} static void process_record(args_t *args, bcf1_t *rec) { int i,len = bcf_get_info_string(args->hdr,rec,args->vep_tag,&args->csq_str,&args->ncsq_str); @@ -1108,17 +1157,7 @@ static void process_record(args_t *args, bcf1_t *rec) return; } - // split by transcript and by field - args->cols_tr = cols_split(args->csq_str, args->cols_tr, ','); - if ( args->cols_tr->n > args->mcols_csq ) - { - args->cols_csq = (cols_t**)realloc(args->cols_csq,args->cols_tr->n*sizeof(*args->cols_csq)); - for (i=args->mcols_csq; icols_tr->n; i++) args->cols_csq[i] = NULL; - args->mcols_csq = args->cols_tr->n; - } - args->ncols_csq = args->cols_tr->n; - for (i=0; icols_tr->n; i++) - args->cols_csq[i] = cols_split(args->cols_tr->off[i], args->cols_csq[i], '|'); + split_csq_fields(args,rec,len); // restrict to -g genes if ( args->genes ) restrict_csqs_to_genes(args); diff --git a/test/split-vep.broken-LoF.out b/test/split-vep.broken-LoF.out new file mode 100644 index 000000000..04bb3f481 --- /dev/null +++ b/test/split-vep.broken-LoF.out @@ -0,0 +1,18 @@ +chr21:5032064 missense_variant . +chr21:5032064 missense_variant . +chr21:5032064 missense_variant . +chr21:5032064 3_prime_UTR_variant&NMD_transcript_variant . +chr21:5032064 missense_variant . +chr21:5032064 missense_variant . +chr21:5032064 missense_variant . +chr21:5032064 missense_variant . +chr21:5032064 missense_variant . +chr21:5032064 frameshift_variant PERCENTILE:0.773118279569892/GERP_DIST:-366.377766615897/BP_DIST:218/DIST_FROM_LAST_EXON:187/50_BP_RULE:PASS/ANN_ORF:-698.745/MAX_ORF:-698.745 +chr21:5032064 frameshift_variant PERCENTILE:0.635578583765112/GERP_DIST:-366.377766615897/BP_DIST:218/DIST_FROM_LAST_EXON:187/50_BP_RULE:PASS/ANN_ORF:-698.745/MAX_ORF:-698.745 +chr21:5032064 frameshift_variant PERCENTILE:0.659498207885305/GERP_DIST:-372.525567065179/BP_DIST:197/DIST_FROM_LAST_EXON:187/50_BP_RULE:PASS/ANN_ORF:-698.745/MAX_ORF:-698.745 +chr21:5032064 3_prime_UTR_variant&NMD_transcript_variant . +chr21:5032064 frameshift_variant PERCENTILE:0.790979097909791/GERP_DIST:-372.525567065179/BP_DIST:197/DIST_FROM_LAST_EXON:187/50_BP_RULE:PASS/ANN_ORF:-698.745/MAX_ORF:-698.745 +chr21:5032064 frameshift_variant PERCENTILE:0.790979097909791/GERP_DIST:-372.525567065179/BP_DIST:197/DIST_FROM_LAST_EXON:187/50_BP_RULE:PASS/PHYLOCSF_TOO_SHORT +chr21:5032064 frameshift_variant PERCENTILE:0.463571889103804/GERP_DIST:-1141.14512844086/BP_DIST:840/DIST_FROM_LAST_EXON:152/50_BP_RULE:PASS/PHYLOCSF_TOO_SHORT +chr21:5032064 frameshift_variant PERCENTILE:0.662062615101289/GERP_DIST:-354.294564935565/BP_DIST:374/DIST_FROM_LAST_EXON:187/50_BP_RULE:PASS/PHYLOCSF_TOO_SHORT +chr21:5032064 frameshift_variant PERCENTILE:0.785792349726776/GERP_DIST:-391.862466733158/BP_DIST:203/DIST_FROM_LAST_EXON:187/50_BP_RULE:PASS/PHYLOCSF_TOO_SHORT diff --git a/test/split-vep.broken-LoF.vcf b/test/split-vep.broken-LoF.vcf new file mode 100644 index 000000000..8ab605a95 --- /dev/null +++ b/test/split-vep.broken-LoF.vcf @@ -0,0 +1,6 @@ +##fileformat=VCFv4.2 +##INFO= +##contig= +#CHROM POS ID REF ALT QUAL FILTER INFO +chr21 5032064 . G A . . vep=A|missense_variant|MODERATE|FP565260.3|ENSG00000277117|Transcript|ENST00000612610|protein_coding|5/7||ENST00000612610.4:c.709G>A|ENSP00000483732.1:p.Gly237Arg|896|709|237|G/R|Gga/Aga|1||1|SNV||Clone_based_ensembl_gene|||1|A2||ENSP00000483732|||||||PANTHER:PTHR24100&PANTHER:PTHR24100|||||||||,A|missense_variant|MODERATE|FP565260.3|ENSG00000277117|Transcript|ENST00000620481|protein_coding|4/6||ENST00000620481.4:c.358G>A|ENSP00000484302.1:p.Gly120Arg|545|358|120|G/R|Gga/Aga|1||1|SNV||Clone_based_ensembl_gene|||5|||ENSP00000484302|||||||PANTHER:PTHR24100&PANTHER:PTHR24100|||||||||,A|missense_variant|MODERATE|FP565260.3|ENSG00000277117|Transcript|ENST00000623795|protein_coding|4/6||ENST00000623795.1:c.358G>A|ENSP00000485649.1:p.Gly120Arg|505|358|120|G/R|Gga/Aga|1||1|SNV||Clone_based_ensembl_gene|||2|||ENSP00000485649|||||||PANTHER:PTHR24100&PANTHER:PTHR24100|||||||||,A|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|FP565260.3|ENSG00000277117|Transcript|ENST00000623903|nonsense_mediated_decay|5/7||ENST00000623903.3:c.*323G>A||706|||||1||1|SNV||Clone_based_ensembl_gene|||2|||ENSP00000485557||||||||||||||||,A|missense_variant|MODERATE|FP565260.3|ENSG00000277117|Transcript|ENST00000623960|protein_coding|5/7||ENST00000623960.4:c.709G>A|ENSP00000485129.1:p.Gly237Arg|858|709|237|G/R|Gga/Aga|1||1|SNV||Clone_based_ensembl_gene||YES|1|P2|CCDS86973.1|ENSP00000485129|||||||PANTHER:PTHR24100&PANTHER:PTHR24100|||||||||,A|missense_variant|MODERATE|LOC102723996|102723996|Transcript|NM_001363770.2|protein_coding|5/7||NM_001363770.2:c.709G>A|NP_001350699.1:p.Gly237Arg|858|709|237|G/R|Gga/Aga|1||1|SNV||EntrezGene||YES||||NP_001350699.1||||||||||||||||,A|missense_variant|MODERATE|LOC102723996|102723996|Transcript|XM_006723899.2|protein_coding|5/6||XM_006723899.2:c.709G>A|XP_006723962.1:p.Gly237Arg|1345|709|237|G/R|Gga/Aga|1||1|SNV||EntrezGene||||||XP_006723962.1||||||||||||||||,A|missense_variant|MODERATE|LOC102723996|102723996|Transcript|XM_011546078.2|protein_coding|5/7||XM_011546078.2:c.709G>A|XP_011544380.1:p.Gly237Arg|1345|709|237|G/R|Gga/Aga|1||1|SNV||EntrezGene||||||XP_011544380.1||||||||||||||||,A|missense_variant|MODERATE|LOC102723996|102723996|Transcript|XM_011546079.1|protein_coding|5/7||XM_011546079.1:c.709G>A|XP_011544381.1:p.Gly237Arg|1345|709|237|G/R|Gga/Aga|1||1|SNV||EntrezGene||||||XP_011544381.1|||||||||||||||| +chr21 5032064 . G GGA . . vep=GA|frameshift_variant|HIGH|FP565260.3|ENSG00000277117|Transcript|ENST00000612610|protein_coding|5/7||ENST00000612610.4:c.718_719dup|ENSP00000483732.1:p.Asp240GlufsTer35|896-897|709-710|237|G/GX|gga/gGAga|1||1|insertion||Clone_based_ensembl_gene|||1|A2||ENSP00000483732|||||||PANTHER:PTHR24100&PANTHER:PTHR24100|10|||||HC||PHYLOCSF_WEAK|PERCENTILE:0.773118279569892,GERP_DIST:-366.377766615897,BP_DIST:218,DIST_FROM_LAST_EXON:187,50_BP_RULE:PASS,ANN_ORF:-698.745,MAX_ORF:-698.745,GA|frameshift_variant|HIGH|FP565260.3|ENSG00000277117|Transcript|ENST00000620481|protein_coding|4/6||ENST00000620481.4:c.367_368dup|ENSP00000484302.1:p.Asp123GlufsTer35|545-546|358-359|120|G/GX|gga/gGAga|1||1|insertion||Clone_based_ensembl_gene|||5|||ENSP00000484302|||||||PANTHER:PTHR24100&PANTHER:PTHR24100|10|||||HC||PHYLOCSF_WEAK|PERCENTILE:0.635578583765112,GERP_DIST:-366.377766615897,BP_DIST:218,DIST_FROM_LAST_EXON:187,50_BP_RULE:PASS,ANN_ORF:-698.745,MAX_ORF:-698.745,GA|frameshift_variant|HIGH|FP565260.3|ENSG00000277117|Transcript|ENST00000623795|protein_coding|4/6||ENST00000623795.1:c.367_368dup|ENSP00000485649.1:p.Asp123GlufsTer35|505-506|358-359|120|G/GX|gga/gGAga|1||1|insertion||Clone_based_ensembl_gene|||2|||ENSP00000485649|||||||PANTHER:PTHR24100&PANTHER:PTHR24100|10|||||HC||PHYLOCSF_WEAK|PERCENTILE:0.659498207885305,GERP_DIST:-372.525567065179,BP_DIST:197,DIST_FROM_LAST_EXON:187,50_BP_RULE:PASS,ANN_ORF:-698.745,MAX_ORF:-698.745,GA|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|FP565260.3|ENSG00000277117|Transcript|ENST00000623903|nonsense_mediated_decay|5/7||ENST00000623903.3:c.*332_*333dup||706-707|||||1||1|insertion||Clone_based_ensembl_gene|||2|||ENSP00000485557||||||||||||||||,GA|frameshift_variant|HIGH|FP565260.3|ENSG00000277117|Transcript|ENST00000623960|protein_coding|5/7||ENST00000623960.4:c.718_719dup|ENSP00000485129.1:p.Asp240GlufsTer35|858-859|709-710|237|G/GX|gga/gGAga|1||1|insertion||Clone_based_ensembl_gene||YES|1|P2|CCDS86973.1|ENSP00000485129|||||||PANTHER:PTHR24100&PANTHER:PTHR24100|10|||||HC||PHYLOCSF_WEAK|PERCENTILE:0.790979097909791,GERP_DIST:-372.525567065179,BP_DIST:197,DIST_FROM_LAST_EXON:187,50_BP_RULE:PASS,ANN_ORF:-698.745,MAX_ORF:-698.745,GA|frameshift_variant|HIGH|LOC102723996|102723996|Transcript|NM_001363770.2|protein_coding|5/7||NM_001363770.2:c.718_719dup|NP_001350699.1:p.Asp240GlufsTer35|858-859|709-710|237|G/GX|gga/gGAga|1||1|insertion||EntrezGene||YES||||NP_001350699.1||||||||10|||||HC|||PERCENTILE:0.790979097909791,GERP_DIST:-372.525567065179,BP_DIST:197,DIST_FROM_LAST_EXON:187,50_BP_RULE:PASS,PHYLOCSF_TOO_SHORT,GA|frameshift_variant|HIGH|LOC102723996|102723996|Transcript|XM_006723899.2|protein_coding|5/6||XM_006723899.2:c.718_719dup|XP_006723962.1:p.Asp240GlufsTer35|1345-1346|709-710|237|G/GX|gga/gGAga|1||1|insertion||EntrezGene||||||XP_006723962.1||||||||10|||||HC|||PERCENTILE:0.463571889103804,GERP_DIST:-1141.14512844086,BP_DIST:840,DIST_FROM_LAST_EXON:152,50_BP_RULE:PASS,PHYLOCSF_TOO_SHORT,GA|frameshift_variant|HIGH|LOC102723996|102723996|Transcript|XM_011546078.2|protein_coding|5/7||XM_011546078.2:c.718_719dup|XP_011544380.1:p.Asp240GlufsTer35|1345-1346|709-710|237|G/GX|gga/gGAga|1||1|insertion||EntrezGene||||||XP_011544380.1||||||||10|||||HC|||PERCENTILE:0.662062615101289,GERP_DIST:-354.294564935565,BP_DIST:374,DIST_FROM_LAST_EXON:187,50_BP_RULE:PASS,PHYLOCSF_TOO_SHORT,GA|frameshift_variant|HIGH|LOC102723996|102723996|Transcript|XM_011546079.1|protein_coding|5/7||XM_011546079.1:c.718_719dup|XP_011544381.1:p.Asp240GlufsTer35|1345-1346|709-710|237|G/GX|gga/gGAga|1||1|insertion||EntrezGene||||||XP_011544381.1||||||||10|||||HC|||PERCENTILE:0.785792349726776,GERP_DIST:-391.862466733158,BP_DIST:203,DIST_FROM_LAST_EXON:187,50_BP_RULE:PASS,PHYLOCSF_TOO_SHORT diff --git a/test/test.pl b/test/test.pl index 4ef961c1a..32e4563b5 100755 --- a/test/test.pl +++ b/test/test.pl @@ -659,6 +659,7 @@ run_test(\&test_vcf_plugin,$opts,in=>'split-vep.gene-list',out=>'split-vep.gene-list.1.out',cmd=>'+split-vep',args=>qq[-d -f '%CHROM:%POS %Gene %Consequence\\n']); run_test(\&test_vcf_plugin,$opts,in=>'split-vep.gene-list',out=>'split-vep.gene-list.2.out',cmd=>'+split-vep',args=>qq[-d -f '%CHROM:%POS %Gene %Consequence\\n' -g {PATH}/split-vep.gene-list.txt]); run_test(\&test_vcf_plugin,$opts,in=>'split-vep.gene-list',out=>'split-vep.gene-list.3.out',cmd=>'+split-vep',args=>qq[-d -f '%CHROM:%POS %Gene %Consequence\\n' -g +{PATH}/split-vep.gene-list.txt]); +run_test(\&test_vcf_plugin,$opts,in=>'split-vep.broken-LoF',out=>'split-vep.broken-LoF.out',cmd=>'+split-vep',args=>qq[-d -f '%CHROM:%POS %Consequence %LoF_info\\n' -a vep]); run_test(\&test_vcf_plugin,$opts,in=>'parental-origin',out=>'parental-origin.1.out',cmd=>'+parental-origin',args=>qq[-r 20:100 -p proband,father,mother -t del | grep -v ^#]); run_test(\&test_vcf_plugin,$opts,in=>'parental-origin',out=>'parental-origin.2.out',cmd=>'+parental-origin',args=>qq[-r 20:101 -p proband,father,mother -t del | grep -v ^#]); run_test(\&test_vcf_plugin,$opts,in=>'parental-origin',out=>'parental-origin.3.out',cmd=>'+parental-origin',args=>qq[-r 20:102 -p proband,father,mother -t del | grep -v ^#]); From 2191405e8afd9b123d18dc7084459d409afc4ea4 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Fri, 10 Feb 2023 18:37:08 +0100 Subject: [PATCH 82/84] The -c option can be omitted when a VEP subfield is used in filtering expressions Note that this is an experimental feature. --- NEWS | 4 + filter.c | 53 +++- filter.h | 21 +- plugins/split-vep.c | 430 ++++++++++++++++++-------------- test/split-vep.broken-LoF.2.out | 8 + test/test.pl | 1 + 6 files changed, 328 insertions(+), 189 deletions(-) create mode 100644 test/split-vep.broken-LoF.2.out diff --git a/NEWS b/NEWS index 7d03c1eff..9ef29c06a 100644 --- a/NEWS +++ b/NEWS @@ -133,6 +133,10 @@ Changes affecting specific commands: VEP subfields. The +split-vep plugin can now work with such files, replacing the offending commas with slash (/) characters. See also https://github.com/Ensembl/ensembl-vep/issues/1351 + - Newly the `-c, --columns` option can be omitted when a subfield is used in `-i/-e` filtering + expression. Note that `-c` may still have to be given when it is not possible to infer the + type of the subfield. Note that this is an experimental feature. + * bcftools stats - The per-sample stats (PSC) would not be computed when `-i/-e` filtering options and diff --git a/filter.c b/filter.c index b9174c3a0..3925475b7 100644 --- a/filter.c +++ b/filter.c @@ -109,6 +109,9 @@ struct _filter_t #if ENABLE_PERL_FILTERS PerlInterpreter *perl; #endif + char **undef_tag; + int nundef_tag; + int status, exit_on_error; }; @@ -304,6 +307,28 @@ static int filters_next_token(char **str, int *len) return TOK_VAL; } +#define FILTER_OK 0 +#define FILTER_ERR_UNKN_TAGS 1 +#define FILTER_ERR_OTHER 2 + +static void filter_add_undef_tag(filter_t *filter, char *str) +{ + int i; + for (i=0; inundef_tag; i++) + if ( !strcmp(str,filter->undef_tag[i]) ) break; + if ( inundef_tag ) return; + filter->nundef_tag++; + filter->undef_tag = (char**)realloc(filter->undef_tag,sizeof(*filter->undef_tag)*filter->nundef_tag); + if ( !filter->undef_tag ) error("Could not allocate memory\n"); + filter->undef_tag[filter->nundef_tag-1] = strdup(str); + if ( !filter->undef_tag[filter->nundef_tag-1] ) error("Could not allocate memory\n"); +} +const char **filter_list_undef_tags(filter_t *filter, int *ntags) +{ + *ntags = filter->nundef_tag; + return (const char**)filter->undef_tag; +} + /* Simple path expansion, expands ~/, ~user, $var. The result must be freed by the caller. @@ -3063,7 +3088,13 @@ static int filters_init1(filter_t *filter, char *str, int len, token_t *tok) { errno = 0; tok->threshold = strtod(tmp.s, &end); // float? - if ( errno!=0 || end!=tmp.s+len ) error("[%s:%d %s] Error: the tag \"%s\" is not defined in the VCF header\n", __FILE__,__LINE__,__FUNCTION__,tmp.s); + if ( errno!=0 || end!=tmp.s+len ) + { + if ( filter->exit_on_error ) + error("[%s:%d %s] Error: the tag \"%s\" is not defined in the VCF header\n", __FILE__,__LINE__,__FUNCTION__,tmp.s); + filter->status |= FILTER_ERR_UNKN_TAGS; + filter_add_undef_tag(filter,tmp.s); + } } tok->is_constant = 1; @@ -3071,7 +3102,6 @@ static int filters_init1(filter_t *filter, char *str, int len, token_t *tok) return 0; } - static void filter_debug_print(token_t *toks, token_t **tok_ptrs, int ntoks) { int i; @@ -3221,12 +3251,13 @@ static void perl_destroy(filter_t *filter) // Parse filter expression and convert to reverse polish notation. Dijkstra's shunting-yard algorithm -filter_t *filter_init(bcf_hdr_t *hdr, const char *str) +static filter_t *filter_init_(bcf_hdr_t *hdr, const char *str, int exit_on_error) { filter_t *filter = (filter_t *) calloc(1,sizeof(filter_t)); filter->str = strdup(str); filter->hdr = hdr; filter->max_unpack |= BCF_UN_STR; + filter->exit_on_error = exit_on_error; int nops = 0, mops = 0; // operators stack int nout = 0, mout = 0; // filter tokens, RPN @@ -3608,6 +3639,14 @@ filter_t *filter_init(bcf_hdr_t *hdr, const char *str) filter->flt_stack = (token_t **)malloc(sizeof(token_t*)*nout); return filter; } +filter_t *filter_parse(bcf_hdr_t *hdr, const char *str) +{ + return filter_init_(hdr, str, 0); +} +filter_t *filter_init(bcf_hdr_t *hdr, const char *str) +{ + return filter_init_(hdr, str, 1); +} void filter_destroy(filter_t *filter) { @@ -3629,6 +3668,8 @@ void filter_destroy(filter_t *filter) free(filter->filters[i].regex); } } + for (i=0; inundef_tag; i++) free(filter->undef_tag[i]); + free(filter->undef_tag); free(filter->cached_GT.buf); free(filter->cached_GT.mask); free(filter->filters); @@ -3642,6 +3683,7 @@ void filter_destroy(filter_t *filter) int filter_test(filter_t *filter, bcf1_t *line, const uint8_t **samples) { + if ( filter->status != FILTER_OK ) error("Error: the caller did not check the filter status\n"); bcf_unpack(line, filter->max_unpack); int i, nstack = 0; @@ -3804,3 +3846,8 @@ void filter_set_samples(filter_t *filter, const uint8_t *samples) } } +int filter_status(filter_t *filter) +{ + return filter->status; +} + diff --git a/filter.h b/filter.h index 243e3b69e..7be842a3a 100644 --- a/filter.h +++ b/filter.h @@ -1,6 +1,6 @@ /* filter.h -- filter expressions. - Copyright (C) 2013-2021 Genome Research Ltd. + Copyright (C) 2013-2023 Genome Research Ltd. Author: Petr Danecek @@ -32,6 +32,8 @@ typedef struct _filter_t filter_t; /** * @hdr: BCF header file * @str: see the bcftools filter command help for description + * + * Same as filter_parse() but exits on errors */ filter_t *filter_init(bcf_hdr_t *hdr, const char *str); @@ -61,4 +63,21 @@ const double *filter_get_doubles(filter_t *filter, int *nval, int *nval1); void filter_expression_info(FILE *fp); int filter_max_unpack(filter_t *filter); +/** + * Same as filter_init() but may not exit on some type of errors. The caller + * must check if the returned value is not NULL and if the consequent call + * of filter_status() returns FILTER_OK before the filter_pass() can be called. + */ +filter_t *filter_parse(bcf_hdr_t *hdr, const char *str); + +#define FILTER_OK 0 +#define FILTER_ERR_UNKN_TAGS 1 +#define FILTER_ERR_OTHER 2 + +/** + * Check if filter_parse() was successful + */ +int filter_status(filter_t *filter); +const char **filter_list_undef_tags(filter_t *filter, int *nundef); + #endif diff --git a/plugins/split-vep.c b/plugins/split-vep.c index 387ebc8ee..e5dfeb14a 100644 --- a/plugins/split-vep.c +++ b/plugins/split-vep.c @@ -268,6 +268,21 @@ static const char *usage_text(void) "\n"; } +static void destroy_annot(args_t *args) +{ + int i; + for (i=0; inannot; i++) + { + annot_t *ann = &args->annot[i]; + free(ann->field); + free(ann->tag); + free(ann->str.s); + } + free(args->annot); + args->annot = NULL; + args->nannot = 0; +} + static void expand_csq_expression(args_t *args, kstring_t *str) { if ( !args->all_fields_delim ) return; @@ -361,11 +376,13 @@ static void destroy_column2type(args_t *args) int i; for (i=0; incolumn2type; i++) { - regfree(args->column2type[i].regex); + if ( args->column2type[i].regex ) regfree(args->column2type[i].regex); free(args->column2type[i].regex); free(args->column2type[i].type); } free(args->column2type); + args->ncolumn2type = 0; + args->column2type = NULL; } static const char *get_column_type(args_t *args, char *field) { @@ -378,6 +395,8 @@ static const char *get_column_type(args_t *args, char *field) } return "String"; } + +// Is the tag "field" present in the -f query string, such as '%CHROM %POS %field\n'? static int query_has_field(char *fmt, char *field, kstring_t *str) { str->l = 0; @@ -489,6 +508,225 @@ static void init_gene_list(args_t *args) args->ngene_fields = j; if ( !args->ngene_fields ) error("None of the \"%s\" fields is present in INFO/%s\n",args->gene_fields_str,args->vep_tag); } + +// The program was requested to create a text output as with `bcftools query -f`. For this we need to +// determine the fields to be extracted from the formatting expression. Any subfields not listed in the +// header will be added to column_str so that they can be added to the header +static void parse_format_str(args_t *args) +{ + int i; + kstring_t str = {0,0,0}; + + // Special case: -A was given, extract all fields, for this the -a tag (%CSQ) must be present + if ( args->all_fields_delim ) expand_csq_expression(args, &str); + + for (i=0; infield; i++) + { + if ( !query_has_field(args->format_str,args->field[i],&str) ) continue; + + int tag_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, args->field[i]); + if ( bcf_hdr_idinfo_exists(args->hdr,BCF_HL_INFO,tag_id) ) + fprintf(stderr,"Note: ambiguous key %%%s; using the %s subfield of %s, not the INFO/%s tag\n", args->field[i],args->field[i],args->vep_tag,args->field[i]); + + int olen = args->column_str ? strlen(args->column_str) : 0; + int nlen = strlen(args->field[i]); + args->column_str = (char*)realloc(args->column_str, olen + nlen + 2); + if ( olen ) + { + memcpy(args->column_str+olen,",",1); + olen++; + } + memcpy(args->column_str+olen,args->field[i],nlen); + args->column_str[olen+nlen] = 0; + } + if ( query_has_field(args->format_str,args->vep_tag,&str) ) args->raw_vep_request = 1; + free(str.s); +} + +// The program was requested to extract one or more columns via -c. It can contain names, 0-based indexes or ranges of indexes +static void parse_column_str(args_t *args) +{ + int i,j; + int *column = NULL; + int *types = NULL; + if ( !strcmp("-",args->column_str) ) // all subfields + { + free(args->column_str); + kstring_t str = {0,0,0}; + ksprintf(&str,"0-%d",args->nfield-1); + args->column_str = str.s; + } + char *ep = args->column_str; + while ( *ep ) + { + char *tp, *bp = ep; + while ( *ep && *ep!=',' ) ep++; + char keep = *ep; + *ep = 0; + int type = -1; + int idx_beg, idx_end; + if ( !strcmp("-",bp) ) + { + kstring_t str = {0,0,0}; + ksprintf(&str,"0-%d",args->nfield-1); + if ( keep ) ksprintf(&str,",%s",ep+1); + free(args->column_str); + args->column_str = str.s; + ep = str.s; + continue; + } + char *tmp = strdup_annot_prefix(args, bp); + if ( khash_str2int_get(args->field2idx, bp, &idx_beg)==0 || khash_str2int_get(args->field2idx, tmp, &idx_beg)==0 ) + idx_end = idx_beg; + else if ( (tp=strrchr(bp,':')) ) + { + *tp = 0; + if ( khash_str2int_get(args->field2idx, bp, &idx_beg)!=0 ) + { + *tp = ':'; + tp = strrchr(tmp,':'); + *tp = 0; + if ( khash_str2int_get(args->field2idx, tmp, &idx_beg)!=0 ) error("No such column: \"%s\"\n", bp); + } + idx_end = idx_beg; + *tp = ':'; + if ( !strcasecmp(tp+1,"string") ) type = BCF_HT_STR; + else if ( !strcasecmp(tp+1,"float") || !strcasecmp(tp+1,"real") ) type = BCF_HT_REAL; + else if ( !strcasecmp(tp+1,"integer") || !strcasecmp(tp+1,"int") ) type = BCF_HT_INT; + else if ( !strcasecmp(tp+1,"flag") ) type = BCF_HT_FLAG; + else error("The type \"%s\" (or column \"%s\"?) not recognised\n", tp+1,bp); + } + else + { + char *mp; + idx_beg = strtol(bp,&mp,10); + if ( !*mp ) idx_end = idx_beg; + else if ( *mp=='-' ) + idx_end = strtol(mp+1,&mp,10); + if ( *mp ) + { + if ( *mp==':' ) + { + idx_end = idx_beg; + if ( !strcasecmp(mp+1,"string") ) type = BCF_HT_STR; + else if ( !strcasecmp(mp+1,"float") || !strcasecmp(mp+1,"real") ) type = BCF_HT_REAL; + else if ( !strcasecmp(mp+1,"integer") || !strcasecmp(mp+1,"int") ) type = BCF_HT_INT; + else if ( !strcasecmp(mp+1,"flag") ) type = BCF_HT_FLAG; + else error("The type \"%s\" (or column \"%s\"?) not recognised\n", mp+1,bp); + } + else if ( !strcmp(bp,args->vep_tag) ) + { + free(tmp); + args->raw_vep_request = 1; + if ( !keep ) break; + ep++; + continue; + } + else + error("No such column: \"%s\"\n", bp); + } + } + free(tmp); + + i = args->nannot; + args->nannot += idx_end - idx_beg + 1; + column = (int*)realloc(column,args->nannot*sizeof(*column)); + types = (int*)realloc(types,args->nannot*sizeof(*types)); + for (j=idx_beg; j<=idx_end; j++) + { + if ( j >= args->nfield ) error("The index is too big: %d\n", j); + column[i] = j; + types[i] = type; + i++; + } + if ( !keep ) break; + ep++; + } + + // Now add each column to the VCF header and reconstruct the column_str in case it will be needed later + free(args->column_str); + kstring_t str = {0,0,0}; + args->annot = (annot_t*)calloc(args->nannot,sizeof(*args->annot)); + for (i=0; inannot; i++) + { + annot_t *ann = &args->annot[i]; + ann->type = types[i]; + ann->idx = j = column[i]; + ann->field = strdup(args->field[j]); + ann->tag = strdup(args->field[j]); + args->kstr.l = 0; + const char *type = "String"; + if ( ann->type==BCF_HT_REAL ) type = "Float"; + else if ( ann->type==BCF_HT_INT ) type = "Integer"; + else if ( ann->type==BCF_HT_FLAG ) type = "Flag"; + else if ( ann->type==BCF_HT_STR ) type = "String"; + else if ( ann->type==-1 ) type = get_column_type(args, args->field[j]); + ksprintf(&args->kstr,"##INFO=",type); + bcf_hdr_printf(args->hdr_out, args->kstr.s, ann->tag,ann->field,args->vep_tag); + if ( str.l ) kputc(',',&str); + kputs(ann->tag,&str); + } + args->column_str = str.s; + if ( args->raw_vep_request && args->select_tr==SELECT_TR_ALL ) args->raw_vep_request = 0; + if ( args->raw_vep_request ) + { + args->nannot++; + args->annot = (annot_t*)realloc(args->annot,args->nannot*sizeof(*args->annot)); + annot_t *ann = &args->annot[args->nannot-1]; + ann->type = BCF_HT_STR; + ann->idx = -1; + ann->field = strdup(args->vep_tag); + ann->tag = strdup(args->vep_tag); + memset(&ann->str,0,sizeof(ann->str)); + } + free(column); + free(types); + destroy_column2type(args); + + if ( bcf_hdr_sync(args->hdr_out)<0 ) + error_errno("[%s] Failed to update header", __func__); +} + +// Init filters. When neither -c,--columns nor -f,--format contains a VEP subfield used in the +// filtering expression, and the subfield is not defined in the VCF header, then the filtering +// will throw an error. We can be smart, detect these failures and such undefined subfields +// as if the user passed them via the -c option. +static void parse_filter_str(args_t *args) +{ + int max_unpack = args->convert ? convert_max_unpack(args->convert) : 0; + args->filter = filter_parse(args->hdr_out, args->filter_str); + if ( !args->filter ) error(NULL); // this type of error would have been reported + int ret = filter_status(args->filter); + if ( ret!=FILTER_OK ) + { + if ( ret!=FILTER_ERR_UNKN_TAGS ) error(NULL); // this type of error would have been reported + + // add the undefined tags to the -c string + int ntags, i,j; + const char **tags = filter_list_undef_tags(args->filter, &ntags); + kstring_t str; + str.s = args->column_str; + str.l = str.m = strlen(str.s); + destroy_annot(args); + destroy_column2type(args); + for (i=0; ifield2idx,tags[i],&j)!=0 ) + error("Error: the tag \"%s\" is not defined in the VCF header or in INFO/%s\n",tags[i],args->vep_tag); + if ( str.l ) kputc(',',&str); + kputs(tags[i],&str); + } + args->column_str = str.s; + parse_column_str(args); + filter_destroy(args->filter); + args->filter = filter_init(args->hdr_out, args->filter_str); + } + max_unpack |= filter_max_unpack(args->filter); + if ( !args->format_str ) max_unpack |= BCF_UN_FMT; // don't drop FMT fields on VCF input when VCF/BCF is output + args->sr->max_unpack = max_unpack; + if ( args->convert && (max_unpack & BCF_UN_FMT) ) + convert_set_option(args->convert, subset_samples, &args->smpl_pass); +} static void init_data(args_t *args) { args->sr = bcf_sr_init(); @@ -532,7 +770,7 @@ static void init_data(args_t *args) } if ( !args->nfield ) error("Could not parse Description of INFO/%s: %s\n", args->vep_tag,hrec->vals[ret]); args->field2idx = khash_str2int_init(); - int i,j; + int i; for (i=0; infield; i++) { if ( khash_str2int_has_key(args->field2idx, args->field[i]) ) @@ -619,176 +857,14 @@ static void init_data(args_t *args) free(tmp); } - // Create a text output as with `bcftools query -f`. For this we need to determine the fields to be extracted - // from the formatting expression - if ( args->format_str && !args->column_str ) - { - // Special case: -A was given, extract all fields, for this the -a tag (%CSQ) must be present - if ( args->all_fields_delim ) expand_csq_expression(args, &str); - - for (i=0; infield; i++) - { - if ( !query_has_field(args->format_str,args->field[i],&str) ) continue; - - int tag_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, args->field[i]); - if ( bcf_hdr_idinfo_exists(args->hdr,BCF_HL_INFO,tag_id) ) - fprintf(stderr,"Note: ambiguous key %%%s; using the %s subfield of %s, not the INFO/%s tag\n", args->field[i],args->field[i],args->vep_tag,args->field[i]); - - int olen = args->column_str ? strlen(args->column_str) : 0; - int nlen = strlen(args->field[i]); - args->column_str = (char*)realloc(args->column_str, olen + nlen + 2); - if ( olen ) - { - memcpy(args->column_str+olen,",",1); - olen++; - } - memcpy(args->column_str+olen,args->field[i],nlen); - args->column_str[olen+nlen] = 0; - } - if ( query_has_field(args->format_str,args->vep_tag,&str) ) args->raw_vep_request = 1; - } - - // The "Consequence" column to look up severity, its name is hardwired for now + // The "Consequence" column to determine severity for filtering. The name of this column is hardwired for now, both VEP and bt/csq use the same name char *tmp = strdup_annot_prefix(args,"Consequence"); if ( khash_str2int_get(args->field2idx,tmp,&args->csq_idx)!=0 ) error("The field \"Consequence\" is not present in INFO/%s: %s\n", args->vep_tag,hrec->vals[ret]); free(tmp); - // Columns to extract: given as names, 0-based indexes or ranges of indexes - if ( args->column_str ) - { - int *column = NULL; - int *types = NULL; - if ( !strcmp("-",args->column_str) ) // all subfields - { - free(args->column_str); - kstring_t str = {0,0,0}; - ksprintf(&str,"0-%d",args->nfield-1); - args->column_str = str.s; - } - ep = args->column_str; - while ( *ep ) - { - char *tp, *bp = ep; - while ( *ep && *ep!=',' ) ep++; - char keep = *ep; - *ep = 0; - int type = -1; - int idx_beg, idx_end; - if ( !strcmp("-",bp) ) - { - kstring_t str = {0,0,0}; - ksprintf(&str,"0-%d",args->nfield-1); - if ( keep ) ksprintf(&str,",%s",ep+1); - free(args->column_str); - args->column_str = str.s; - ep = str.s; - continue; - } - char *tmp = strdup_annot_prefix(args, bp); - if ( khash_str2int_get(args->field2idx, bp, &idx_beg)==0 || khash_str2int_get(args->field2idx, tmp, &idx_beg)==0 ) - idx_end = idx_beg; - else if ( (tp=strrchr(bp,':')) ) - { - *tp = 0; - if ( khash_str2int_get(args->field2idx, bp, &idx_beg)!=0 ) - { - *tp = ':'; - tp = strrchr(tmp,':'); - *tp = 0; - if ( khash_str2int_get(args->field2idx, tmp, &idx_beg)!=0 ) error("No such column: \"%s\"\n", bp); - } - idx_end = idx_beg; - *tp = ':'; - if ( !strcasecmp(tp+1,"string") ) type = BCF_HT_STR; - else if ( !strcasecmp(tp+1,"float") || !strcasecmp(tp+1,"real") ) type = BCF_HT_REAL; - else if ( !strcasecmp(tp+1,"integer") || !strcasecmp(tp+1,"int") ) type = BCF_HT_INT; - else if ( !strcasecmp(tp+1,"flag") ) type = BCF_HT_FLAG; - else error("The type \"%s\" (or column \"%s\"?) not recognised\n", tp+1,bp); - } - else - { - char *mp; - idx_beg = strtol(bp,&mp,10); - if ( !*mp ) idx_end = idx_beg; - else if ( *mp=='-' ) - idx_end = strtol(mp+1,&mp,10); - if ( *mp ) - { - if ( *mp==':' ) - { - idx_end = idx_beg; - if ( !strcasecmp(mp+1,"string") ) type = BCF_HT_STR; - else if ( !strcasecmp(mp+1,"float") || !strcasecmp(mp+1,"real") ) type = BCF_HT_REAL; - else if ( !strcasecmp(mp+1,"integer") || !strcasecmp(mp+1,"int") ) type = BCF_HT_INT; - else if ( !strcasecmp(mp+1,"flag") ) type = BCF_HT_FLAG; - else error("The type \"%s\" (or column \"%s\"?) not recognised\n", mp+1,bp); - } - else if ( !strcmp(bp,args->vep_tag) ) - { - free(tmp); - args->raw_vep_request = 1; - if ( !keep ) break; - ep++; - continue; - } - else - error("No such column: \"%s\"\n", bp); - } - } - free(tmp); - - i = args->nannot; - args->nannot += idx_end - idx_beg + 1; - column = (int*)realloc(column,args->nannot*sizeof(*column)); - types = (int*)realloc(types,args->nannot*sizeof(*types)); - for (j=idx_beg; j<=idx_end; j++) - { - if ( j >= args->nfield ) error("The index is too big: %d\n", j); - column[i] = j; - types[i] = type; - i++; - } - if ( !keep ) break; - ep++; - } - args->annot = (annot_t*)calloc(args->nannot,sizeof(*args->annot)); - for (i=0; inannot; i++) - { - annot_t *ann = &args->annot[i]; - ann->type = types[i]; - ann->idx = j = column[i]; - ann->field = strdup(args->field[j]); - ann->tag = strdup(args->field[j]); - args->kstr.l = 0; - const char *type = "String"; - if ( ann->type==BCF_HT_REAL ) type = "Float"; - else if ( ann->type==BCF_HT_INT ) type = "Integer"; - else if ( ann->type==BCF_HT_FLAG ) type = "Flag"; - else if ( ann->type==BCF_HT_STR ) type = "String"; - else if ( ann->type==-1 ) type = get_column_type(args, args->field[j]); - ksprintf(&args->kstr,"##INFO=",type); - bcf_hdr_printf(args->hdr_out, args->kstr.s, ann->tag,ann->field,args->vep_tag); - } - if ( args->raw_vep_request && args->select_tr==SELECT_TR_ALL ) args->raw_vep_request = 0; - if ( args->raw_vep_request ) - { - args->nannot++; - args->annot = (annot_t*)realloc(args->annot,args->nannot*sizeof(*args->annot)); - annot_t *ann = &args->annot[args->nannot-1]; - ann->type = BCF_HT_STR; - ann->idx = -1; - ann->field = strdup(args->vep_tag); - ann->tag = strdup(args->vep_tag); - memset(&ann->str,0,sizeof(ann->str)); - } - free(column); - free(types); - destroy_column2type(args); - - if ( bcf_hdr_sync(args->hdr_out)<0 ) - error_errno("[%s] Failed to update header", __func__); - } + if ( args->format_str ) parse_format_str(args); // Text output, e.g. bcftools +split-vep -f '%Consequence\n' + if ( args->column_str ) parse_column_str(args); // The --columns option was given, update the header if ( args->format_str ) { if ( !args->column_str && !args->select ) error("Error: No %s field selected in the formatting expression and -s not given: a typo?\n",args->vep_tag); @@ -796,16 +872,7 @@ static void init_data(args_t *args) if ( !args->convert ) error("Could not parse the expression: %s\n", args->format_str); if ( args->allow_undef_tags ) convert_set_option(args->convert, allow_undef_tags, 1); } - if ( args->filter_str ) - { - int max_unpack = args->convert ? convert_max_unpack(args->convert) : 0; - args->filter = filter_init(args->hdr_out, args->filter_str); - max_unpack |= filter_max_unpack(args->filter); - if ( !args->format_str ) max_unpack |= BCF_UN_FMT; // don't drop FMT fields on VCF input when VCF/BCF is output - args->sr->max_unpack = max_unpack; - if ( args->convert && (max_unpack & BCF_UN_FMT) ) - convert_set_option(args->convert, subset_samples, &args->smpl_pass); - } + if ( args->filter_str ) parse_filter_str(args); if ( args->genes_fname ) init_gene_list(args); free(str.s); @@ -826,14 +893,7 @@ static void destroy_data(args_t *args) free(args->scale); for (i=0; infield; i++) free(args->field[i]); free(args->field); - for (i=0; inannot; i++) - { - annot_t *ann = &args->annot[i]; - free(ann->field); - free(ann->tag); - free(ann->str.s); - } - free(args->annot); + destroy_annot(args); free(args->gene_fields); if ( args->genes ) khash_str2int_destroy_free(args->genes); if ( args->field2idx ) khash_str2int_destroy(args->field2idx); diff --git a/test/split-vep.broken-LoF.2.out b/test/split-vep.broken-LoF.2.out new file mode 100644 index 000000000..7ccb3d34d --- /dev/null +++ b/test/split-vep.broken-LoF.2.out @@ -0,0 +1,8 @@ +chr21:5032064 PERCENTILE:0.773118279569892/GERP_DIST:-366.377766615897/BP_DIST:218/DIST_FROM_LAST_EXON:187/50_BP_RULE:PASS/ANN_ORF:-698.745/MAX_ORF:-698.745 +chr21:5032064 PERCENTILE:0.635578583765112/GERP_DIST:-366.377766615897/BP_DIST:218/DIST_FROM_LAST_EXON:187/50_BP_RULE:PASS/ANN_ORF:-698.745/MAX_ORF:-698.745 +chr21:5032064 PERCENTILE:0.659498207885305/GERP_DIST:-372.525567065179/BP_DIST:197/DIST_FROM_LAST_EXON:187/50_BP_RULE:PASS/ANN_ORF:-698.745/MAX_ORF:-698.745 +chr21:5032064 PERCENTILE:0.790979097909791/GERP_DIST:-372.525567065179/BP_DIST:197/DIST_FROM_LAST_EXON:187/50_BP_RULE:PASS/ANN_ORF:-698.745/MAX_ORF:-698.745 +chr21:5032064 PERCENTILE:0.790979097909791/GERP_DIST:-372.525567065179/BP_DIST:197/DIST_FROM_LAST_EXON:187/50_BP_RULE:PASS/PHYLOCSF_TOO_SHORT +chr21:5032064 PERCENTILE:0.463571889103804/GERP_DIST:-1141.14512844086/BP_DIST:840/DIST_FROM_LAST_EXON:152/50_BP_RULE:PASS/PHYLOCSF_TOO_SHORT +chr21:5032064 PERCENTILE:0.662062615101289/GERP_DIST:-354.294564935565/BP_DIST:374/DIST_FROM_LAST_EXON:187/50_BP_RULE:PASS/PHYLOCSF_TOO_SHORT +chr21:5032064 PERCENTILE:0.785792349726776/GERP_DIST:-391.862466733158/BP_DIST:203/DIST_FROM_LAST_EXON:187/50_BP_RULE:PASS/PHYLOCSF_TOO_SHORT diff --git a/test/test.pl b/test/test.pl index 32e4563b5..37cb1a8d3 100755 --- a/test/test.pl +++ b/test/test.pl @@ -660,6 +660,7 @@ run_test(\&test_vcf_plugin,$opts,in=>'split-vep.gene-list',out=>'split-vep.gene-list.2.out',cmd=>'+split-vep',args=>qq[-d -f '%CHROM:%POS %Gene %Consequence\\n' -g {PATH}/split-vep.gene-list.txt]); run_test(\&test_vcf_plugin,$opts,in=>'split-vep.gene-list',out=>'split-vep.gene-list.3.out',cmd=>'+split-vep',args=>qq[-d -f '%CHROM:%POS %Gene %Consequence\\n' -g +{PATH}/split-vep.gene-list.txt]); run_test(\&test_vcf_plugin,$opts,in=>'split-vep.broken-LoF',out=>'split-vep.broken-LoF.out',cmd=>'+split-vep',args=>qq[-d -f '%CHROM:%POS %Consequence %LoF_info\\n' -a vep]); +run_test(\&test_vcf_plugin,$opts,in=>'split-vep.broken-LoF',out=>'split-vep.broken-LoF.2.out',cmd=>'+split-vep',args=>qq[-d -f '%CHROM:%POS %LoF_info\\n' -a vep -i 'Consequence=="frameshift_variant"']); run_test(\&test_vcf_plugin,$opts,in=>'parental-origin',out=>'parental-origin.1.out',cmd=>'+parental-origin',args=>qq[-r 20:100 -p proband,father,mother -t del | grep -v ^#]); run_test(\&test_vcf_plugin,$opts,in=>'parental-origin',out=>'parental-origin.2.out',cmd=>'+parental-origin',args=>qq[-r 20:101 -p proband,father,mother -t del | grep -v ^#]); run_test(\&test_vcf_plugin,$opts,in=>'parental-origin',out=>'parental-origin.3.out',cmd=>'+parental-origin',args=>qq[-r 20:102 -p proband,father,mother -t del | grep -v ^#]); From eed79571a3b445a336100381be4dfbfa05faf8a9 Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Mon, 20 Feb 2023 08:31:08 +0000 Subject: [PATCH 83/84] [minor] NEWS update --- NEWS | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/NEWS b/NEWS index 9ef29c06a..1457e3630 100644 --- a/NEWS +++ b/NEWS @@ -66,11 +66,11 @@ Changes affecting specific commands: - New gff2gff perl script to fix GFF formatting differences -* bcftools +* bcftools +fill-tags - More of the available annotations are now added by the `-t all` option -* bcftools fixref +* bcftools +fixref - New INFO/FIXREF annotation From fac806b985a71d8c4cbb4853e9fa5c93826e2d5c Mon Sep 17 00:00:00 2001 From: Petr Danecek Date: Mon, 20 Feb 2023 08:55:45 +0000 Subject: [PATCH 84/84] Clarify -R/-T format to prevent confusion such as #1862 --- doc/bcftools.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/bcftools.txt b/doc/bcftools.txt index 755d67262..b1a5f07c4 100644 --- a/doc/bcftools.txt +++ b/doc/bcftools.txt @@ -192,8 +192,8 @@ specific commands to see if they apply. *-R, --regions-file* 'FILE':: Regions can be specified either on command line or in a VCF, BED, or tab-delimited file (the default). The columns of the tab-delimited file - can contain either positions (two-column format) or intervals (three-column - format): CHROM, POS, and, optionally, END, where positions are 1-based + can contain either positions (two-column format: CHROM, POS) or intervals + (three-column format: CHROM, BEG, END), but not both. Positions are 1-based and inclusive. The columns of the tab-delimited BED file are also CHROM, POS and END (trailing columns are ignored), but coordinates are 0-based, half-open. To indicate that a file be treated as BED rather