Fig. 4

Linkage disequilibrium between SNPs and CNVs

(A) Mean r² obtained from deletion-SNP pairs discovered in WGS data is displayed as a function of inter-marker distances. SNPs paired with common deletions (MAF ≥ 0.05) are marked with a solid line, whereas SNPs paired with rare deletions (MAF < 0.05) are marked with a dotted line. (B) Mean r² obtained from duplication-SNP pairs discovered in WGS data is shown. The legend is the same as panel (A). (C) Mean r² obtained from 50 K SNP genotyping array is displayed for common variants only (MAF ≥ 0.05). The SNP-SNP pairs are marked with a solid magenta line, and DEL-SNP pairs are marked with a solid grey line. The SNP-SNP pairs outnumbered the DEL-SNP pairs. To keep the comparison not influenced by the difference in the number of pairs, a subset of SNP-SNP pairs, equivalent to the number of DEL-SNP pairs, was made 1,000 times, and the mean and the standard deviation are displayed in the figure. (D) Mean r² obtained from 50 K SNP genotyping array is displayed for rare variants only (MAF < 0.05). Legends are identical to the panel (C)