Table 3

Comparison of BovineHD array genotypes to sequencing SNPs

Detectable genotype


Sequencing calls


Homozygous variant


206,480 (91%)

203,812 (90%)



152,910 (81%)

149,550 (79%)

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.

Stothard et al. BMC Genomics 2011 12:559   doi:10.1186/1471-2164-12-559

Open Data