Question: What Does The Zero Mapping Quality Mean For The Bwa Mapper?
2
gravatar for lyz10302012
6.2 years ago by
lyz10302012320
China
lyz10302012320 wrote:

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.

calling variant mapping bwa • 9.5k views
ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by lyz10302012320

Variant callers ignore reads with mapping quality zero

ADD REPLYlink written 6.2 years ago by Irsan6.8k

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

ADD REPLYlink written 6.2 years ago by lyz10302012320
1

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

ADD REPLYlink written 6.2 years ago by Istvan Albert ♦♦ 79k
14
gravatar for Istvan Albert
6.2 years ago by
Istvan Albert ♦♦ 79k
University Park, USA
Istvan Albert ♦♦ 79k wrote:

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

ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by Istvan Albert ♦♦ 79k

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"

ADD REPLYlink written 3.8 years ago by zju.whw40

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"

ADD REPLYlink written 3.8 years ago by zju.whw40

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

ADD REPLYlink written 3.8 years ago by zju.whw40
5
gravatar for Jeremy Leipzig
6.2 years ago by
Philadelphia, PA
Jeremy Leipzig18k wrote:

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

ADD COMMENTlink written 6.2 years ago by Jeremy Leipzig18k

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

ADD REPLYlink written 2.5 years ago by wjidea50
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