Non-Uniquely Mapped Reads

Question

[Wen.Huang]

Hi everybody,

I know bwa always reports one alignment only (randomly) for non-unique alignments. But I got this impression at one point that all non-unique alignments by bwa will have MAPQ 0 or some small value. Is this true or not?

Thank you!

Answer 1

[Pablo]

I understand that you can have non-zero quality for multiple hits. You should check the XA and XT flags

XT  Type: Unique/Repeat/N/Mate-sw
XA  Alternative hits; format: (chr,pos,CIGAR,NM;)*

E.g.: "XT:A:R" or "XA:Z:Group7.5,-109717,51M,1;Group7.5,-110184,51M,2;" denote multiple hits.