Non-Uniquely Mapped Reads
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!
1 answer
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.
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