Fig. 2.

Validating the sequence level IBD status of bulls predicted to be carriers of a BovineSNP50 lethal haplotype using sequence data. Homozygous inconsistency rates are calculated pairwise amongst predicted carriers, sire-son pairs and randomly sampled animals (not 1st degree relatives). Two different regions are compared: within the tested chromosome 29 haplotype and across the entirety of chromosome 29. The discordance rate among pairs (shown in red) that contain one animal with low coverage (<10X) is greatly elevated. Overall this suggests that there is IBD between inferred carriers in haplotype regions, as they appear similar to sire-son pairs that should share a single haplotype IBD. These carriers were not more related to each other than the population at large across the whole chromosome. The detection of IBD with our sequence data is sensitive to the average depth of sequence coverage of the reference assembly for both compared animals