SNPs and 27,511 Indels from set C. We defined as isolated, an indel with no other indel in the 50bp flanking regions. We found 23,641 (85.9%) isolated indels and 3,870 (14.1%) non isolated indels. All these variants were then classified into frequency bins that were derived from the official release of haplotypes on a per continental group basis as defined in Supplementary Table 2. Then, for each continental group and frequency bin separately, we measured the squared Pearson correlation coefficient between the true (CG derived) and the imputed dosages, ranging from 0 in case of completely wrong imputation to 1 in the case of a perfect imputation. Note that a genotype dosage is the expected number of copies of non-reference alleles; being 0, 1 or 2 in the case of a known genotype and ranging from 0 to 2 in the case of an imputed genotype. Indels in the Phase 1 1000GP haplotypes were filtered at 1% which explains why there are no results for very low frequency Indels in Figure 2d.
