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Count of reads with mapping quality zero for each sample

Category Annotation Modules

VCF Field FORMAT (sample genotype-level)

Header definition line
  • FORMAT=<ID=MQ0,Number=1,Type=Integer,Description="Number of Mapping Quality Zero Reads per sample">

  • Overview

    This annotation gives you the count of all reads that have MAPQ = 0 for each sample. The count of reads with MAPQ0 can be used for quality control; high counts typically indicate regions where it is difficult to make confident calls.


    It is not useful to apply this annotation with HaplotypeCaller because HC filters out all reads with MQ0 upfront, so the annotation will always return a value of 0.

    Related annotations

    • MappingQualityZero gives the count of reads with MAPQ=0 across all samples.
    • LowMQ gives the proportion of reads with low mapping quality (MAPQ below 10, including 0).

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    GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.