Question: Non-Uniquely Mapped Reads
1
gravatar for Wen.Huang
6.8 years ago by
Wen.Huang1.1k
Wen.Huang1.1k wrote:

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!

alignment bwa • 2.3k views
ADD COMMENTlink modified 6.8 years ago by Pablo1.9k • written 6.8 years ago by Wen.Huang1.1k
2
gravatar for Pablo
6.8 years ago by
Pablo1.9k
Canada
Pablo1.9k wrote:

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.

ADD COMMENTlink modified 6.8 years ago • written 6.8 years ago by Pablo1.9k
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