Table 4. Concordance between single nucleotide polymorphism (SNP) genotypes derived from the BovineSNP50 BeadChip and genotypes from whole-genome sequencing (WGS).

Chip Genotype	No. of chip SNPs			WGS genotype
	Hanwoo	Jeju Heugu	Korean Holstein	Hanwoo		Jeju Heugu		Korean Holstein
				A/B	B/B	A/B	B/B	A/B	B/B
A/A	26,330	26,503	24,925	37 (0.3%)	2 (0%)	38 (0.3%)	2 (0%)	42 (0.3%)	1 (0%)
A/B	13,562	13,119	15,340	13,129 (99.2%)	22 (0.2%)	12,763 (99.2%)	7 (0.1%)	14,840 (99.2%)	20 (0.2%)
B/B	13,840	14,063	13,462	41 (0.3%)	13,367 (99.7%)	31 (0.2%)	13,578 (99.6%)	46 (0.3%)	13,022 (99.6%)
./.	143	190	143	27 (0.2%)	21 (0.2%)	34 (0.3%)	42 (0.3%)	32 (0.2%)	32 (0.2%)
Total	53,875	53,875	53,870	13,234	13,412	12,866	13,629	14,960	13,075

‘A’, reference allele; ‘B’, non-reference (alternative) allele; ‘.’, no call. Dark gray cells indicate the concordant non-reference genotypes. Light gray cells indicate the discordant non-reference genotypes.