What Does The Zero Mapping Quality Mean For The Bwa Mapper?

Question

[lyz10302012]

In which condition, a read's mapping quality can be zero? (BWA) How can this kind of reads being used in variant calling or just be filtered out.

Thanks.

[Irsan]

Variant callers ignore reads with mapping quality zero

[lyz10302012]

Can anyone explain why there are a lot of MQ0 reads in some particular regions (almost all reads are MQ0)?

[Istvan Albert]

if a region is duplicated then all the reads mapping there will also map elsewhere - In general please ask questions as a new standalone question rather than adding them as an answer

[O.rka]

In the case of being mappable in multiple places, if it mapped slightly better to one region then would it have a mapping quality > 0?

Answer 1

[Istvan Albert]

Zero mapping quality indicates that the read maps to multiple locations. Note that this behavior is BWA specific.

[zju.whw]

I have add the same comment twice, how can I delete one of them?

[zju.whw]

Would you please tell me which did know this? Is there a website link or manual about "0 mapping quality means that the read maps to multiple locations"

[zju.whw]

Would you please tell me which did know this? Is there a website link or manual about "0 mapping quality means that the read maps to multiple locations"

Answer 2

[Jeremy Leipzig]

It has zero chance of being a uniquely mapped read, because it actually was mapped elsewhere.

[wjidea]

I agree, if the read mapped to a different chromosome, for example, the mapping quality could be 0 as well.