Figure 5

Tagging pattern for HuRef SVs as a function of its minimum allele frequency (MAF). Linkage disequilibrium is depicted as the best r² between a SV and a HapMap SNP in 120 Europeans (CEU). There were a total of 405 bi-allelic polymorphic SV sites of overlap between GSV and HuRef loci; 24% of the SV loci have a HapMap SNP with r² < 0.8 in CEU, a cutoff below which HuRef CNVs would not be imputed simply by SNP detection. The line graph corresponds to the left y-axis, while the bar graph corresponds to the right y-axis. It should be noted that this analysis is performed on a small subset of bi-allelic SVs and that the ability to impute a larger fraction of SVs based on common SNPs would be even lower.