Count of reads with mapping quality zero for each sample

Category Variant Annotations

VCF Field FORMAT (sample genotype-level)

Header info

  • 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.

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