Non-homozygous VINOtype call rates increase with divergence from the reference genome. A) Genetic distance from the mouse reference genome for 143 laboratory inbred strains (additional file 1). Each strain is shown as a vertical tick mark. Strains are grouped according to their origin are arranged left-to-right in increasing order of genetic distance from the reference. Genetic distance is computed as the fraction of non-reference (non-A allele) genotype calls. B) VINOtype calls for each strain. For each strain, the number of SNP probe sets assigned each of the five possible calls (A, B, H, V or N) are shown as five points of different colors that sum to 526363 SNP probe sets. The same analysis using only standard genotype calls (A, B, H, N) is shown in additional file 2.