Detected and undetected VINOs in homozygosity may lead to inaccurate genotyping in heterozygosity. Circles represent parental strains: C57BL/6J (dark blue), which have the AA allele; CAST/EiJ, which has the BB genotype at its target position and also an OTV within the probe and is called either BB (light blue) or V (red) by MouseDivGeno; squares: (C57BL/6JxCAST/EiJ)F1 samples, which have an OTV in heterozygosity and are called AA (dark blue) or N (black) by MouseDivGeno. A) MouseDivGeno calls CAST/EiJ as V; the F1 samples are called AA due to stronger hybridization intensity for the AA allele and thus the OTV goes unrecognized. B) MouseDivGeno calls CAST/EiJ as BB due to the absence of a true BB cluster; the F1 samples are again called AA. C) MouseDivGeno calls CAST/EiJ as V but calls the F1 samples as N due to poor discrimination between genotype clusters.