Mapping Quality of reads with mismatches in STAR

Question

[grant.hovhannisyan]

Dear All,

STAR mapper by default assigns MAPQ 255 for uniquely mapped reads. However, read can map uniquely, but have mismatches (due to SNVs and indels). I am wondering how mismatches influence the mapping quality in this case. In other words, does the uniquely mapped read with mismatches have MAPQ 255?

Thanks,

Answer 1

[Devon Ryan]

Any read that has a single "best" alignment will have a MAPQ of 255. Containing mismatches, be they SNVs or InDels, does not change that.

[grant.hovhannisyan]

Thank you, Devon! Very helpful.