MouseDivGeno identifies VINOs as a cluster of low-intensity samples. Contrast plots of a SNP called by A) BRLMM-P 2D and B) MouseDivGeno. Probe intensities from 351 samples (additional file 1) are shown in MA-transformed space. The sample contrast is the normalized difference between A and B allele intensities [(A-B)/(A+B)]. The y-axis shows the log2 mean of A and B allele intensities. Dark blue: AA call; light blue: BB call; purple: AB call; red: V call; gray: N call. Circles represent strains with a homozygous haplotype in the region of the SNP, while squares represent strains with a heterozygous haplotype. F1 animals with parental alleles of AA and BB are true heterozygotes and are highlighted along with their parental strains. MouseDivGeno software is able to identify samples in the low intensity cluster as containing an OTV and assigns a VINO (V) call, whereas BRLMM-P 2D assigns several different genotype calls (AB, N) to samples in this cluster.