Although levels of common and rare variation within segments are significantly correlated (R2 = 0.462, P ≤ 2 × 10−16) (Supplementary Fig. 16), there are outliers. For example, segments overlapping the major histocompatibility complex (MHC) have the highest levels of common variation but no notable increase in levels of rare variation, consistent with balancing selection24–26. A detailed examination of the MHC shows peaks of increased variation and nucleotide diversity consistent with assembly-based analyses of the region27 (Supplementary Fig. 17). Segments with a high proportion of coding bases feature a strong depletion in the number of common variants but only a modest depletion in rare variants (Supplementary Fig. 18).
