Deep sequencing of Danish Holstein dairy cattle for variant detection and insight into potential loss-of-function variants in protein coding genes

Table 4 Comparison of BovineHD chip heterozygous genotypes to sequencing calls

Animal ID	BovineHD	Sequencing calls	Concordant	Heterozygous > homozygous
44–6	223,103	215,822 (96.7 %)	215,348 (96.5 %)	474 (0.2 %)
46–25	225,985	214,607 (94.9 %)	214,065 (94.7 %)	542 (0.2 %)
49–25	215,929	204,225 (95.6 %)	203,639 (94.3 %)	586 (0.3 %)
50–38	222,315	208,328 (93.7 %)	207,498 (93.3 %)	830 (0.4 %)

Concordant, the same alleles at the same sites were detected by both the BovineHD chip and sequencing calls; Heterozygous > homozygous, heterozygous SNPs on the BovineHD chip that were under-called as homozygous in sequencing calls

ISSN: 1471-2164