At 95% of the CNPs the variation observed was explained by a simple biallelic model obeying Mendelian inheritance and Hardy–Weinberg equilibrium. The remaining 5% of loci showed multi-allelic patterns, somewhat lower than the 15% reported in a recent study7, which may reflect improved resolution of the assays and analyses used in this study. Among the biallelic loci, 92% were deletions (diploid copy numbers ≤2) and 8% were duplications (diploid copy numbers ≥2); the disparity reflects our higher power to detect small deletions than small insertions. The median size of CNPs genotyped in this study was 7.2 kb (Fig. 1a), with biallelic deletions significantly smaller on average than biallelic duplications because of this difference in power.
