Table 3 Genome-wide coverage estimates for all eight arrays, in AFR and AMR ancestry groups
Ancestry GroupAFR (n = 246)AMR (n = 181)
MAF bin0.4%<MAF≤ 1%1%<MAF≤ 5%MAF>1%MAF>5%0.6%<MAF≤1%1%<MAF≤5%MAF>1%MAF>5%
Number of variants5,567,5967,515,31316,995,3519,480,0383,783,5954,245,24711,211,3696,966,122
 ArrayMetric
 HumanCorer2 ≥ 0.8 (%)8.1%12.4%31.0%45.8%23.0%33.0%59.3%75.4%
r2 (mean)0.2750.4470.5880.6990.4460.5760.7410.842
MA conc (mean)0.2530.4450.5990.7210.4040.5630.7420.851
geno conc (mean)0.9890.9680.9340.9070.9900.9760.9580.946
 HumanCore + Exomer2 ≥ 0.8 (%)9.5%15.1%33.8%48.6%24.8%35.3%60.9%76.4%
r2 (mean)0.2960.4760.6100.7170.4630.5940.7520.849
MA conc (mean)0.2730.4730.6200.7360.4220.5810.7530.857
geno conc (mean)0.9890.9690.9380.9120.9900.9770.9590.949
 Axiom Biobankr2 ≥ 0.8 (%)9.9%15.0%33.5%48.2%26.5%38.4%64.7%80.8%
r2 (mean)0.2990.4820.6220.7330.4880.6330.7800.870
MA conc (mean)0.2760.4780.6290.7490.4450.6180.7780.876
geno conc (mean)0.9890.9700.9390.9140.9910.9800.9640.955
 OmniExpressr2 ≥ 0.8 (%)18.4%35.0%56.1%72.8%36.4%51.8%73.1%86.0%
r2 (mean)0.4150.6440.7540.8410.5690.7080.8300.904
MA conc (mean)0.3870.6320.7530.8480.5320.6970.8290.910
geno conc (mean)0.9910.9800.9640.9510.9920.9840.9740.967
 Axiom World Array 4r2 ≥ 0.8 (%)17.5%29.6%51.9%69.5%36.2%55.1%75.5%88.0%
r2 (mean)0.4010.6190.7350.8280.5770.7370.8450.910
MA conc (mean)0.3750.6070.7340.8340.5360.7240.8430.915
geno conc (mean)0.9910.9790.9610.9470.9930.9860.9750.968
 Omni2.5Mr2 ≥ 0.8 (%)27.6%57.6%74.4%87.7%42.6%62.7%79.9%90.3%
r2 (mean)0.5090.7690.8500.9140.6250.7810.8740.931
MA conc (mean)0.4810.7580.8470.9170.5900.7720.8740.936
geno conc (mean)0.9930.9880.9790.9730.9930.9890.9810.976
 Omni2.5M + Exomer2 ≥ 0.8 (%)27.8%57.5%74.2%87.5%42.7%62.7%79.8%90.2%
r2 (mean)0.5100.7690.8490.9120.6260.7800.8740.930
MA conc (mean)0.4820.7570.8460.9160.5920.7720.8730.935
geno conc (mean)0.9930.9880.9790.9720.9930.9890.9810.976
 Omni5Mr2 ≥ 0.8 (%)33.3%63.0%77.8%89.4%51.4%72.4%84.4%91.7%
r2 (mean)0.5530.7970.8690.9260.6900.8380.9020.941
MA conc (mean)0.5260.7870.8660.9290.6580.8330.9030.945
geno conc (mean)0.9930.9890.9820.9760.9950.9920.9840.980
  • Four metrics are presented for each array: fraction of variants with imputation r2 ≥ 0.8; mean imputation r2; mean minor allele concordance (“MA conc”); and mean genotype concordance (“geno conc”); separately by ancestry group (AFR, AMR) and MAF bin. Note the lower bound of MAF in the first MAF bin differs across ancestry groups. This is because we required at least two copies of the minor allele in each panel in order to contribute to these metrics summaries, and there are differing numbers of samples in each group. AFR, African, AMR, American, MAF, minor allele frequency.