Table 2.

Number of autosomal SNPs excluded during the quality control procedure of autosomal SNPs

Breed	Excluded SNPs			Remaining SNPsb
	MAF < 0.05	SNP CR < 0.90	HWE p-value < 0.00001
Duroc	16,815	2,849	4,503	34,927
Landrace	10,136	2,849	1,251	42,164
Yorkshire	10,260	2,837	1,905	42,121
Crossbreda	10,934	2,593	1,756	42,325

MAF minor allele frequency, CR call rate, HWE χ²-test for Hardy-Weinberg equilibrium, ^a: Landrace x Yorkshire, ^b: after exclusion of 608 possible misplaced SNPs