Clear cases of non-recombinants

[szhan]

Discussion started with XN in #285 and then with these other Pango X.
XAU
XBQ
XBK (XBK.1)
XBE

Quoting Yan here in #285:
"No clear recombination, and no reversions etc on the nearby branches. Unless there is a deletion we are missing, I suppose."

[szhan]

XAU

Image from Yan copied from #285.

[szhan]

XBQ and XBK

Image from Yan copied from #285.

[szhan]

XBE

Image from Yan copied from #285.

[jeromekelleher]

I think XN should be here also?

[szhan]

I think XN should be here also?

Yes, but it has its own issue.

[szhan]

XN

Image from Yan copied from #285.

[jeromekelleher]

I see - I got confused when this was titled "Clear cases of non recombinant" and it was omitted though.

[jeromekelleher]

I was hoping that we could gather evidence for each of these cases in separate threads (optionally with some linking issues) so that we could easily find them and add to them. This is basically the same as #285 now.

[szhan]

I thought we separate the clear cases from the less clear cases, for which we have a separate issue each?

[szhan]

We could just close this and retitle #285?

[jeromekelleher]

We need to list out the evidence somewhere for why we think something is not a recombinant, all we have at the moment is a few pictures which are hard to collate. I want to have, for each thing which disagrees with pango ground truth:

• A picture from sc2ts summarising the topology
• Information about the original matches from the match file (along with follow-up matches with different params, if marginal)
• What recombinhunt and other methods think
• Links to any other relevant information, like Pango designation issue and analyses that Katherine might have done.

So we're using these issue to collate information in a way that's findable and extendable. We can then make qualitative judgements about things that are definitely one other or another later on.

I think #337, #338, #338 and #339 are are a great start on this.

[szhan]

Okay, closing this and starting issues for each non-recombinant.