A second major use of the 1000 Genomes Project data in medical genetics is imputing genotypes in existing genome-wide association studies (GWAS)26. For common variants, the accuracy of using the Phase 1 data to impute genotypes at sites not on the original GWAS chip is typically 90-95% in non-African and approximately 90% in African-ancestry genomes (Figs. 5a, S14a), which is comparable to the accuracy achieved with high quality benchmark haplotypes (Fig. S14b). Imputation accuracy is similar for intergenic SNPs, exome SNPs, indels and large deletions (see also Fig. S14c), despite the different amounts of information about such variants and accuracy of genotypes. For low-frequency variants (1-5%), imputed genotypes have between 60% and 90% accuracy in all populations, including those with admixed ancestry (also comparable to the accuracy from trio-phased haplotypes; Fig. S14b).
