Table 4 Genome-wide coverage estimates for all eight arrays, in ASN and EUR ancestry groups
Ancestry groupASN (n = 286)EUR (n = 379)
MAF bin0.4%<MAF≤ 1%1%<MAF≤5%MAF>1%MAF>5%0.3%<MAF≤1%1%<MAF≤5%MAF>1%MAF>5%
Number of variants3,004,5242,385,0948,606,0856,220,9913,991,0912,944,2229,705,5856,761,363
ArrayMetric
 HumanCorer2 ≥ 0.8 (%)7.8%29.6%62.4%75.0%11.0%33.7%64.1%77.3%
r2 (mean)0.1930.4550.7260.8300.2690.5440.7580.851
MA conc (mean)0.1800.4600.7380.8450.2560.5450.7660.862
geno conc (mean)0.9880.9680.9480.9410.9910.9740.9570.950
 HumanCore + Exomer2 ≥ 0.8 (%)8.7%31.4%63.6%75.9%12.3%35.8%65.3%78.2%
r2 (mean)0.2050.4710.7350.8360.2850.5620.7670.857
MA conc (mean)0.1920.4760.7470.8510.2710.5620.7750.868
geno conc (mean)0.9880.9690.9500.9430.9910.9750.9590.952
 Axiom Biobankr2 ≥ 0.8 (%)9.5%32.8%63.1%74.8%12.0%37.1%70.5%85.0%
r2 (mean)0.2150.4920.7420.8390.3030.6030.8030.890
MA conc (mean)0.2030.4960.7530.8510.2880.5980.8060.897
geno conc (mean)0.9890.9700.9510.9430.9910.9780.9660.962
 OmniExpressr2 ≥ 0.8 (%)13.3%42.9%73.0%84.5%18.1%48.7%75.1%86.6%
r2 (mean)0.2670.5700.8020.8920.3590.6650.8340.908
MA conc (mean)0.2530.5740.8100.9010.3460.6630.8390.915
geno conc (mean)0.9900.9760.9660.9620.9920.9810.9730.969
 Axiom World Array 4r2 ≥ 0.8 (%)13.4%42.9%72.9%84.4%18.5%55.4%79.0%89.3%
r2 (mean)0.2690.5740.8020.8890.3800.7200.8590.920
MA conc (mean)0.2570.5780.8090.8980.3640.7160.8620.926
geno conc (mean)0.9890.9760.9650.9610.9920.9850.9760.971
 Omni2.5Mr2 ≥ 0.8 (%)17.8%50.8%78.5%89.1%23.9%60.6%81.5%90.5%
r2 (mean)0.3240.6430.8460.9230.4260.7520.8790.935
MA conc (mean)0.3100.6470.8520.9300.4120.7500.8830.940
geno conc (mean)0.9900.9800.9750.9740.9930.9860.9800.977
 Omni2.5M + Exomer2 ≥ 0.8 (%)18.0%50.8%78.4%89.0%24.2%60.6%81.4%90.4%
r2 (mean)0.3260.6430.8450.9230.4280.7520.8790.934
MA conc (mean)0.3130.6480.8510.9300.4140.7500.8820.940
geno conc (mean)0.9900.9800.9750.9730.9930.9860.9800.977
 Omni5Mr2 ≥ 0.8 (%)20.7%53.6%80.0%90.2%37.5%76.8%87.3%91.9%
r2 (mean)0.3570.6700.8590.9320.5450.8490.9160.944
MA conc (mean)0.3440.6740.8650.9380.5300.8490.9190.949
geno conc (mean)0.9910.9820.9780.9770.9950.9910.9840.980
  • 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 (ASN, EUR) 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 to contribute to these metrics summaries, and there are differing numbers of samples in each group. ASN, Asian, EUR, European, MAF, minimum allele frequency.