Table 2.

SNP statistics reported by GATK and thresholds used for filtering

Abbreviation	Rel	Threshold	Full name
QD	<	2.0	Quality by Depth
MQ	<	40.0	Root mean square of Mapping Quality
MQRankSum	<	−12.5	Mapping Quality Rank Sum test
FS	>	60.0	Fisher’s exact test for Strand bias
SOR	>	4.0	Strand bias Odds Ratio
ReadPosRankSum	<	−8.0	Read Position Rank Sum test
DP	>	200.0	Depth of Coverage
GQ	<	20.0	Genotype Quality

SNPs with statistics above or below (Rel) the corresponding threshold were removed from consideration. For detailed description of these statistics and justification for the threshold selection, see Van der Auwera et al. [24] and GATK documentation at https://www.broadinstitute.org/gatk/