Skip to main content

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

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

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 %)
  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