We examined the distribution of variant sites across the genome by counting variants across ordered 1-megabase (Mb) concatenations of contiguous sequence with a similar conservation level (indicated by combined annotation-dependent depletion (CADD score21), and in segments categorized by coding versus noncoding status (Fig. 1 and Extended Data Fig. 2). As expected, the vast majority of human genomic variation is rare (minor allele frequency (MAF) < 0.5%)10,11 and located in putatively neutral, noncoding regions of the genome (Fig. 1). Although coding regions have lower average levels of both common (MAF ≥ 0.5%) and rare variation, we identified some ultra-conserved noncoding regions with even lower levels of genetic variation22 (Fig. 1 and Supplementary Fig. 15).
