Showing docs for version 3.7-0

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RMSMappingQuality

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

Category Annotation Modules

VCF Field INFO (variant-level)

Type StandardAnnotation, ActiveRegionBasedAnnotation, ReducibleAnnotation

Header definition line

INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">

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Overview

This annotation provides an estimation of the overall mapping quality of reads supporting a variant call. It produce both raw data (sum of square and num of total reads) and 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.

Caveat

Uninformative reads are not used in this annotation.

Related annotations

• AS_RMSMappingQuality outputs an allele-specific version of this annotation.
• MappingQualityRankSumTest compares the mapping quality of reads supporting the REF and ALT alleles.

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