The array includes 296,038 markers for genome-wide coverage of common genetic variations. The relationship between genome-wide array coverage and the observed correlation of imputed and actual genotypes (obsRSQ) in 1000 Genomes Phase 1 YRI, ASN, and EUR populations is shown in Fig. 1 (left panel). As the threshold on obsRSQ increases (x-axis), fewer variants exceed the threshold, and the coverage decreases (y-axis). The array design achieves good coverage of common variants (MAF ≥ 0.05, obsRSQ > 0.8): 65.67, 82.37, and 90.72 % in YRI, ASN, and EUR populations respectively, and covers 52.71, 71.68, and 78.17 % respectively of variants with MAF ≥ 0.01. The average obsRSQ for variants with MAF ≥ 0.05 were 0.82, 0.89 and 0.93 for YRI, ASN, and EUR respectively, and 0.72, 0.80, and 0.85 for variants with MAF ≥ 0.01. These metrics demonstrate the array’s suitability for genome-wide analyses and meta analyses based on genotype imputation using 1000 Genomes Project Phase 1 data.
