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Count of all reads with MAPQ = 0 across all samples (MQ0)

Category Variant Annotations


Count of all reads with MAPQ = 0 across all samples

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.


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).

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GATK version built at Wed, 9 Oct 2019 15:19:59 -0400.