Figure 7
Co-localization of SNP and CNV hotspots.
(a) Distributions of SNPdb, SNP1K and CNVG features in windows of Genic, Proximal and Distal zones. SNPdb (from dbSNP build 138) features are shown in red in the left hand side panels, SNP1K (from SNP1K phase 1, release v3) in orange in the right hand side panels and the germline CNVG breakpoints in blue. Eliminating gaps in the genome devoid of known sequence, each of the three kinds of features are spread out at a fairly even basal occurrence level over the 500-kb non-overlapping windows along the lengths of the 22 autosomes on the x-axis. However, there are distinct red, orange and blue spikes indicative of sharply enhanced, or hotspot, occurrences. Some of the spikes are double red-blue or orange-blue hotspots where top-5% occurrence levels in both SNPs and CNVs are detected within the same 500-kb window. (b) Recombination rates for all 500-kb windows in the genome (left) and in SNP-CNV double hotspot windows with triple top-5% levels with respect to SNPdb, SNP1K and CNVG (right). The rates, obtained from RecH based on HapMap data, are compared using two-tailed t-test. (c) Venn diagrams of hotspots (viz. with top-5% level) in SNPdb (red area, >6,250 per window), SNP1K (orange area, >8,450 per window) and CNVG (blue area, >200 per window) in the three types of genomic zones. In each diagram, each segment size is proportional to the number of hotspots in the segment as indicated in the segment, e.g. top left diagram shows the presence of 79 + 44 = 123 SNPdb hotspots, 80 + 44 = 124 CNVG hotspots and 44 double SNPdb-CNVG hotspots in the Genic zones of the 22 autosomes. The locations of individual SNPdb, SNP1K and CNVG hotspots and their overlapped hotspots, are given in Supplementary Tables S6.
