Entering edit mode
6.7 years ago
grant.hovhannisyan
★
2.6k
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,
Thank you, Devon! Very helpful.