WGS sample has lower mapping rate (92%), bimodal depth of coverage peak and aberrant synonymous/missense variation rate

Question

[Andrew]

Hi,

I am trying to determine if there is an artifact from sequencing or if there is something real happening with a sample that I sequenced alongside two other samples. Some basics

Mapping Rate --> S1 99.7%, S2 92.13%, S3 99.71%

SNPs --> S1 22K, S2 73K, S3 23K

Sequence depth - target 100X, average all around 100, but S2 has another peak about 10% the size of main peak at 100 at around 50 reads, the other two have almost no loci < 80 reads.

Best, Andrew

[Fabio Marroni]

Which species? How did you compute sequence depth? Via kmer counts? Could it be that S2 is simply highly heterozyogus compared to S1 and S3?