diff --git a/docs/commands/stats.md b/docs/commands/stats.md
index 4f84297..0d51792 100644
--- a/docs/commands/stats.md
+++ b/docs/commands/stats.md
@@ -18,8 +18,20 @@ If `--per-sequences` option is given, then prints statistics for all sequences i
 3. gapsstart: Number of consecutive gaps  at the beginning;
 4. gapsend: Number of consecutive gaps at the end;
 5. gapsuniques: Number of gaps unique to that sequence;
+
+	If --profile is given along, then the output will be : unique\tnew\tboth, with:
+	- 5a unique: # gaps that are unique in each sequence in the alignment
+	- 5b new: # gaps that are new in each sequence compared to the profile
+	- 5c both: # gaps that are unique in each sequence in the alignment and that are new compared the profile
+
 6. gapsopenning: Number of streches of gaps;
 7. mutuniques: Number of unique mutations;
+
+	If --profile is given along, then the output will be : unique\tnew\tboth, with:
+	- 7a unique: # mutations that are unique in each sequence in the alignment
+	- 7b new: # mutations that are new in each sequence compared to the profile
+	- 7c both: # mutations that are unique in each sequence in the alignment and that are new compared the profile
+
 7. (bis) mutref:  Number mutations compared to a reference sequence (only if `--ref-sequence`is given)
 8. length: Lenght of the unaligned sequence;
 9. A	C	G	T...: Number of occurence of each character.
diff --git a/docs/index.md b/docs/index.md
index 26476a7..00c3f43 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -55,7 +55,6 @@ Command                                                     | Subcommand |
 ------------------------------------------------------------|------------|-----------------------------------------------------------------------
 [addid](commands/addid.md) ([api](api/addid.md))            |            | Adds a string to each sequence identifier of the input alignment
 [append](commands/append.md) ([api](api/append.md))         |            | Concatenates several alignments by adding new alignments as new sequences of the first alignment
-
 [build](commands/build.md) ([api](api/build.md))            |            | Command to build output files : bootstrap for example
 --                                                          | distboot   | Builds bootstrap distances matrices from input alignment (nt only)
 --                                                          | seqboot    | Builds bootstrap alignments from input alignment