Documentation

MappingQualityZero

Count of all reads with MAPQ = 0 across all samples

Category Variant Annotations

VCF Field INFO (variant-level)

Type StandardAnnotation, ActiveRegionBasedAnnotation

Header info
  • INFO=

  • 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.

    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).

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    See also Guide Index | Tool Documentation Index | Support Forum

    GATK version 3.3-0-g37228af built at 2014/10/24 14:40:51. GTD: NA