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Allele-specific root-mean-square of the mapping quality of reads across all samples (AS_MQ)

Category Variant Annotations


Allele-specific Root Mean Square of the mapping quality of reads across all samples.

This annotation provides an estimation of the mapping quality of reads supporting each alternate allele in a variant call. Depending on the tool it is called from, it produces either raw data (sum of squared MQs) or the calculated root mean square.

The raw data is used to accurately calculate the root mean square when combining more than one sample.

Statistical notes

The root mean square is equivalent to the mean of the mapping qualities plus the standard deviation of the mapping qualities.

Related annotations


Uninformative reads are not used in this annotation.

Related annotations

  • RMSMappingQuality outputs a version of this annotation that includes all alternate alleles in a single calculation.
  • MappingQualityRankSumTest compares the mapping quality of reads supporting the REF and ALT alleles.

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