Table 3.

Overview of parameters evaluated for filtering SNPs. Vcftools test settings and subsequent ranges of investigated specifications are displayed

Test setting	Parameter	Tested range	Description
1	minDP	2–16 (interval 2)	minimum read depth—allow only SNPs with given minimum read depth
1	max DP	30–100 (interval 5)	maximum read depth—allow only SNPs with given maximum read depth
2	max-missing-count	8–18 (interval 2)	maximum number of allowed missing genotypes—exclude SNPs with more than defined number of missing genotypes over all individuals
2	min-mean-DP	10–30 (interval 2)	minimum mean read depths—allow only SNPs with at least the given mean read depth values over all individuals