What Does The Zero Mapping Quality Mean For The Bwa Mapper?
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.
• 24,467 views
•
link
written
by
lyz10302012
2 answers
Zero mapping quality indicates that the read maps to multiple locations. Note that this behavior is BWA specific.
• 0 views
•
link
written
by
Istvan Albert
It has zero chance of being a uniquely mapped read, because it actually was mapped elsewhere.
• 0 views
•
link
written
by
Jeremy Leipzig
Log in to answer this question.
More posts like this
-
what does it mean to cap mapping quality of poorly mapped reads
written by Repo1 •
-
Get rid of multimapped and unmapped reads for snp calling improvement
written by Denis
-
Alignment of reads to gene and pseudogene
written by nkausthu •
-
Command line explain
written by f1978hp •
-
-C 50 parameter MPILEUP
written by f1978hp •
-
Hard filtering results of vcf file for multiple samps
written by seta
-
Does The Mapping Of A Read'S Pair Affect Its Own Mapping Score In Bwa?
written by jhrf •
-
Skipping The Local Realignment Around The Indels And Rather Aligning The Mapped Reads On The Exonic…
written by ivivek_ngs
-
Tophat Rna-Seq Mapping Quality
written by siyu •
-
Variant Calling For Ultra High Coverage Region Of Whole Exome Sequencing Data
written by lyz10302012
Variant callers ignore reads with mapping quality zero
Can anyone explain why there are a lot of MQ0 reads in some particular regions (almost all reads are MQ0)?
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
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?