Root mean square of the mapping quality of reads across all samples (MQ)

Category Variant Annotations

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Overview

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

This annotation provides an estimation of the overall mapping quality of reads supporting a variant call, averaged over all samples in a cohort.

The raw data format for this annotation consists of a list of two entries: the sum of the squared mapping qualities and the number of reads across variant (not homRef) genotypes

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

• MappingQualityRankSumTest compares the mapping quality of reads supporting the REF and ALT alleles.

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GATK version 4.0.11.0 built at 25-15-2019 03:15:29.