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Table 3 Comparison of BovineHD array genotypes to sequencing SNPs

From: Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery

Detectable genotype BovineHD Sequencing calls Concordant
Homozygous variant 226,854 206,480 (91%) 203,812 (90%)
Heterozygous 189,784 152,910 (81%) 149,550 (79%)
  1. The sequenced Holstein animal was genotyped so that the ability of the sequencing to identify detectable SNPs (homozygous variant and heterozygote) could be quantified (false negative rate). The "Sequencing Calls" column gives the number of detectable array SNPs that were identified as SNPs through sequencing, regardless of whether the sequencing genotype matched the array genotype. The "Concordant" column gives the number of sequencing calls with a sequencing genotype that matched the array genotype.