Rank sum test of REF versus ALT base quality scores (BaseQRankSum)

Category Variant Annotations

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Overview

Rank Sum Test of REF versus ALT base quality scores

This variant-level annotation tests compares the base qualities of the data supporting the reference allele with those supporting the alternate allele. The ideal result is a value close to zero, which indicates there is little to no difference. A negative value indicates that the bases supporting the alternate allele have lower quality scores than those supporting the reference allele. Conversely, a positive value indicates that the bases supporting the alternate allele have higher quality scores than those supporting the reference allele. Finding a statistically significant difference either way suggests that the sequencing process may have been biased or affected by an artifact.

Statistical notes

The value output for this annotation is the u-based z-approximation from the Mann-Whitney-Wilcoxon Rank Sum Test for base qualities (bases supporting REF vs. bases supporting ALT). See the method document on statistical tests for a more detailed explanation of the ranksum test.

Caveat

The base quality rank sum test can not be calculated for sites without a mixture of reads showing both the reference and alternate alleles.

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GATK version 4.0.3.0 built at 02-29-2019 02:29:33.