Rank Sum Test of REF versus ALT base quality scores
INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
This variant-level annotation compares the base qualities of the data supporting the reference allele with those supporting any 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.
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.
GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.