Skip to main content

Table 4 Comparison of BovineHD chip heterozygous 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 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 %)
  1. 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