Fig. 2
Landscape of genetic-variant hotspots and hotspot clusters. a Tracks on chromosome 1-22 show from top to bottom, in successive and non-overlapping 500-kb windows: (i) coverage of genetic-variant hotspots in window (green bar) capped at 50% by the dark red rectangles in chromosomes 8, 12, and 16; (ii) Genic zones are colored in blue, Proximal in green, and Distal in red; (iii) ideogram; (iv) sequence windows displaying top coverage (top 10%) of positive selection hotspots (red), purifying selection hotspots (green), and both positive and purifying selections (purple); (v) sequence windows displaying top 10% coverage of balancing selection hotspots (pink); (vi) number of hotspots clusters (height of downward blue bars). Beige windows indicate where neither positive nor purifying selection hotspots reach top 10% level in track (iv), or where balancing selection hotspots do not reach top 10% level in track (v). b Tracks (i)–(vi) enlarged for red boxes I and II in (a) for the locations of MHC on chromosome 6, and a cluster of transcription factors on chromosome 16 [55], respectively. c Enrichment and selection-status of eight kinds of genetic-variant hotspots (x-axis) in immune system gene loci (y-axis). Fold of hotspot density inside each immunoprotein gene locus relative to autosomal average is represented by the area of the corresponding pie chart: hashed slices indicating proportion of GV hotspots overlapping, and gray slices indicating non-overlapping, with selection hotspots. Colored bars beside each pie chart show the relative abundance of different kinds of selection hotspots acting on these GV hotspots: “B” stands for GV hotspots overlapping with balancing selection hotspots, “P” with positive selection hotspots, “N” with negative selection hotspots. See Supplementary Table S9 for numerical data. MHC, major histocompatibility complex; IGH, IGK, and IGL, immunoglobulin heavy, kappa and lambda loci respectively; TRA, TRB, TRD, and TRG are the T cell receptor alpha, beta, delta and gamma loci. Since TRD is embedded in TRA, they are merged into a TRA/D locus. “H” stands for “hotspots”