Root mean square of the mapping quality of reads across all samples (MQ)
Category Variant Annotations
OverviewRoot 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
The root mean square is equivalent to the mean of the mapping qualities plus the standard deviation of the mapping qualities.
- MappingQualityRankSumTest compares the mapping quality of reads supporting the REF and ALT alleles.
GATK version 220.127.116.11 built at Sat, 23 Nov 2019 17:12:18 -0500.