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. 2014 Jul 3;9(7):e101127. doi: 10.1371/journal.pone.0101127

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.