Assessing impact of reference genome on variant calling accuracy

45 variants within 32 genes were identified as potentially embryonic lethal on the basis on missing homozygosity in the studied population (n = 675). These variants were then examined in a separate cohort of 39 dogs. Sequence reads from this cohort mapped to CanFam3.1 were compared to other publicly available canine reference genomes; this comparison revealed that the variants were called erroneously and instead indicated sequence gaps in CanFam3.1. We demonstrate the importance of using multiple newer reference genomes for accurate variant identification.