Filter

Symbol

T.

Definition

QualByDepth

QD

2.0

The variant confidence (from the QUAL field) divided by the unfiltered depth of non-reference samples.

FisherStrand

FS

60.0

Phred-scaled p-value using Fisher's Exact Test to detect strand bias (the variation being seen on only the forward or only the reverse strand) in the reads.

RMSMappingQuality

MQ

40.0

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

HaplotypeScore

HS

13.0

The consistency of the site with two (and only two) segregating haplotypes.

MappingQualityRankSumTest

MQRankSum

12.5

The U-based z-approximation from the Mann-Whitney Rank Sum Test for mapping qualities (reads with ref bases vs. those with the alternate allele).

ReadPosRankSumTest

ReadPosRankSum

8.0

The U-based z-approximation from the Mann-Whitney Rank Sum Test for the distance from the end of the read for reads with the alternate allele.