MappingQualityZero

Count of all reads with MAPQ = 0 across all samples

Category Annotation Modules

VCF Field INFO (variant-level)

Type StandardUGAnnotation, ActiveRegionBasedAnnotation

Header definition line
  • INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">

  • Overview

    This anotation gives you the count of all reads that have MAPQ = 0 across all samples. 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.

    Caveat

    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

    • MappingQualityZeroBySample gives the count of reads with MAPQ=0 for each individual sample.
    • LowMQ gives the proportion of reads with low mapping quality (MAPQ below 10, including 0).

    Return to top


    See also GATK Documentation Index | Tool Docs Index | Support Forum

    GATK version 3.8-0-ge9d806836 built at 2017/07/29 01:40:22.