Table 4. Genome-wide coverage estimates for all eight arrays, in ASN and EUR ancestry groups.
| Ancestry group | ASN (n = 286) |
EUR (n = 379) |
|||||||
|---|---|---|---|---|---|---|---|---|---|
| MAF bin | 0.4%<MAF≤ 1% | 1%<MAF≤5% | MAF>1% | MAF>5% | 0.3%<MAF≤1% | 1%<MAF≤5% | MAF>1% | MAF>5% | |
| Number of variants | 3,004,524 | 2,385,094 | 8,606,085 | 6,220,991 | 3,991,091 | 2,944,222 | 9,705,585 | 6,761,363 | |
| Array | Metric | ||||||||
| HumanCore | r2 ≥ 0.8 (%) | 7.8% | 29.6% | 62.4% | 75.0% | 11.0% | 33.7% | 64.1% | 77.3% |
| r2 (mean) | 0.193 | 0.455 | 0.726 | 0.830 | 0.269 | 0.544 | 0.758 | 0.851 | |
| MA conc (mean) | 0.180 | 0.460 | 0.738 | 0.845 | 0.256 | 0.545 | 0.766 | 0.862 | |
| geno conc (mean) | 0.988 | 0.968 | 0.948 | 0.941 | 0.991 | 0.974 | 0.957 | 0.950 | |
| HumanCore + Exome | r2 ≥ 0.8 (%) | 8.7% | 31.4% | 63.6% | 75.9% | 12.3% | 35.8% | 65.3% | 78.2% |
| r2 (mean) | 0.205 | 0.471 | 0.735 | 0.836 | 0.285 | 0.562 | 0.767 | 0.857 | |
| MA conc (mean) | 0.192 | 0.476 | 0.747 | 0.851 | 0.271 | 0.562 | 0.775 | 0.868 | |
| geno conc (mean) | 0.988 | 0.969 | 0.950 | 0.943 | 0.991 | 0.975 | 0.959 | 0.952 | |
| Axiom Biobank | r2 ≥ 0.8 (%) | 9.5% | 32.8% | 63.1% | 74.8% | 12.0% | 37.1% | 70.5% | 85.0% |
| r2 (mean) | 0.215 | 0.492 | 0.742 | 0.839 | 0.303 | 0.603 | 0.803 | 0.890 | |
| MA conc (mean) | 0.203 | 0.496 | 0.753 | 0.851 | 0.288 | 0.598 | 0.806 | 0.897 | |
| geno conc (mean) | 0.989 | 0.970 | 0.951 | 0.943 | 0.991 | 0.978 | 0.966 | 0.962 | |
| OmniExpress | r2 ≥ 0.8 (%) | 13.3% | 42.9% | 73.0% | 84.5% | 18.1% | 48.7% | 75.1% | 86.6% |
| r2 (mean) | 0.267 | 0.570 | 0.802 | 0.892 | 0.359 | 0.665 | 0.834 | 0.908 | |
| MA conc (mean) | 0.253 | 0.574 | 0.810 | 0.901 | 0.346 | 0.663 | 0.839 | 0.915 | |
| geno conc (mean) | 0.990 | 0.976 | 0.966 | 0.962 | 0.992 | 0.981 | 0.973 | 0.969 | |
| Axiom World Array 4 | r2 ≥ 0.8 (%) | 13.4% | 42.9% | 72.9% | 84.4% | 18.5% | 55.4% | 79.0% | 89.3% |
| r2 (mean) | 0.269 | 0.574 | 0.802 | 0.889 | 0.380 | 0.720 | 0.859 | 0.920 | |
| MA conc (mean) | 0.257 | 0.578 | 0.809 | 0.898 | 0.364 | 0.716 | 0.862 | 0.926 | |
| geno conc (mean) | 0.989 | 0.976 | 0.965 | 0.961 | 0.992 | 0.985 | 0.976 | 0.971 | |
| Omni2.5M | r2 ≥ 0.8 (%) | 17.8% | 50.8% | 78.5% | 89.1% | 23.9% | 60.6% | 81.5% | 90.5% |
| r2 (mean) | 0.324 | 0.643 | 0.846 | 0.923 | 0.426 | 0.752 | 0.879 | 0.935 | |
| MA conc (mean) | 0.310 | 0.647 | 0.852 | 0.930 | 0.412 | 0.750 | 0.883 | 0.940 | |
| geno conc (mean) | 0.990 | 0.980 | 0.975 | 0.974 | 0.993 | 0.986 | 0.980 | 0.977 | |
| Omni2.5M + Exome | r2 ≥ 0.8 (%) | 18.0% | 50.8% | 78.4% | 89.0% | 24.2% | 60.6% | 81.4% | 90.4% |
| r2 (mean) | 0.326 | 0.643 | 0.845 | 0.923 | 0.428 | 0.752 | 0.879 | 0.934 | |
| MA conc (mean) | 0.313 | 0.648 | 0.851 | 0.930 | 0.414 | 0.750 | 0.882 | 0.940 | |
| geno conc (mean) | 0.990 | 0.980 | 0.975 | 0.973 | 0.993 | 0.986 | 0.980 | 0.977 | |
| Omni5M | r2 ≥ 0.8 (%) | 20.7% | 53.6% | 80.0% | 90.2% | 37.5% | 76.8% | 87.3% | 91.9% |
| r2 (mean) | 0.357 | 0.670 | 0.859 | 0.932 | 0.545 | 0.849 | 0.916 | 0.944 | |
| MA conc (mean) | 0.344 | 0.674 | 0.865 | 0.938 | 0.530 | 0.849 | 0.919 | 0.949 | |
| geno conc (mean) | 0.991 | 0.982 | 0.978 | 0.977 | 0.995 | 0.991 | 0.984 | 0.980 | |
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.