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

Table 3 Comparison of BovineHD chip homozygous alternative genotypes to sequencing calls

Animal ID	BovineHD	Sequencing calls	Concordant	Inconsistent	Homozygous > heterozygous
44–6	247,562	247,519 (99.9 %)	247,237 (99.8 %)	17	265 (0.1 %)
46–25	255,886	255,296 (99.8 %)	254,826 (99.6 %)	3	467 (0.2 %)
49–25	259,773	259,240 (99.8 %)	259,001 (99.7 %)	4	235 (0.1 %)
50–38	255,427	254,729 (99.7 %)	254,407 (99.6 %)	4	318 (0.1 %)

Concordant, the same alleles at the same sites were detected by both the BovineHD chip and sequencing calls; Inconsistent, homozygous calls by both the Bovine HD chip and sequencing calls but with different alleles; Homozygous > heterozygous, homozygous SNPs on the BovineHD chip that were over-called as heterozygous in sequencing calls

ISSN: 1471-2164