Nonsynonymous changes in synonymous counts table

[ijhoskins]

Hello @afrubin,

I extracted the "/main/synonymous/counts" table from the HDF5 and I see the following:

                                         V1   count
   1:                                   _wt 1368724
   2:                                   _sy   63422
   3:                           p.Asn228Thr   19055
   4:                           p.Asp198Arg   15161
   5:                           p.Asp221Ala   13472

Why are nonsynonymous changes reported in the synonymous table? Also, the annotation does not contain the nucleotide change (c.X>X) so it is unclear what variants are causing the protein change. I do however see the nucleotide changes for variants in the "/main/variants/counts" table. Is there a configurable I need to turn on to get the nucleotide change?

My expectation is that this table would only contain silent/synonymous mutations. Is _sy just a summation of counts for all synonymous mutations?

I tried looking at the documentation (https://enrich2.readthedocs.io/en/latest/output.html#list-of-tables-by-object-type) but it is not clear what the synonymous counts table should contain.

Any help would be greatly appreciated! Thanks