Observed vs expected less common alleles transmitted in 38 sire-son duos(left) and confidence interval of unrelated duos at different MAF (right) in the Bos Taurus autosome 1 (BTA1).

Almost 35% of sequence variants had MAF<0.01 (green dashed line in left plot), however 50% of these variants were not observed in the expected proportions in the parent offspring duos (red solid line in left plot). The proportion of transmitted alleles to the progeny was modeled according to the MAF (right plot). Green lines represent each of the duos, and the solid green line is the local weighted regression for the 38 duos. Red shadow represent the confident interval for the same regression when 10 pairs of unrelated animals were evaluated, with the red solid line being the local weighted regression. The dashed black line represents the expected theoretical proportion of transmission for the less frequent allele from sire to son under random mating. At MAF<0.10 we observed that observed proportions of transmission deviated from the theory, which implies that up to 50% of the uncommon and rare variants (at MAF<0.01) are sequencing errors.