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

Category Annotation Modules

VCF Field INFO (variant-level)

Type ActiveRegionBasedAnnotation, ReducibleAnnotation, AS_StandardAnnotation

Header definition line
  • INFO=<ID=AS_MQ,Number=A,Type=Float,Description="Allele-specific RMS Mapping Quality">

  • Overview

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

    GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.