TABLE 3.

Total number of concordant and non-concordant SNPs between the variant callers and bead array data for all the animals genotyped.

	Freebayes and bead array	GATK-HC a and bead array	Freebayes and GATK-HC a
Concordant genotypes	5,542,493	5,508,868	5,814,822
Non-concordant genotypes	231,970	260,018	39,549
Het b vs. Hom c (A/B vs. A/A or B/B)	164,188	188,861	36,431
Hom c A vs. Hom c B (A/A vs. B/B)	67,782	71,157	3,118

^a Concordance was calculated using 40,426 SNPs, from both the Illumina and Affymetrix bead arrays and called by both variant callers.

^b Heterozygous.

^c Homozygous.