MAF>0.25 are captured extremely well (mean maximum r2 of 0.93 in YRI to 0.97 in CEU), whereas rarer SNPs with MAF<0.05 are less well covered (mean maximum r2 of 0.74 in CHB+JPT to 0.76 in YRI). The latter figure is probably an overestimate because it is based on lower frequency SNPs discovered via re-sequencing 48 HapMap individuals, and does not include a much larger number of very rare SNPs. We also assessed the increase in coverage provided by using two-SNP haplotypes as proxies for SNPs that are poorly captured by single SNPs16 (Table 2). These two-SNP haplotypes lead to a modest increase in mean maximum r2 of 0.01 to 0.03 across all allele frequencies. However, in some regions, particularly where marker density is low, gains from multi-marker and imputation approaches in practical situations can be substantial (see below).
