Table 5. Proportion of well-imputed variants in NCS imputation results.
| MAF |
0 < MAF ≤ 0.01% |
0.01% < MAF ≤ 0.5% |
0.5% < MAF ≤ 1% |
1% < MAF ≤ 5% |
MAF > 5% |
||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Reference panel | 1000 G | 1000 G + UK10K | 1000 G | 1000 G + UK10K | 1000 G | 1000 G + UK10K | 1000 G | 1000 G + UK10K | 1000 G | 1000 G + UK10K | |
| Total imputed variants | 8,111,504 | 13,485,420 | 10,354,147 | 12,236,827 | 1,386,886 | 1,450,070 | 2,299,157 | 2,464,567 | 5,404,143 | 6,183,666 | |
| INFO | ≥0.4 | 0.2% | 0.9% | 49.8% | 61.8% | 87.4% | 94.0% | 96.1% | 98.3% | 99.5% | 99.8% |
| ≥0.5 | 0.0% | 0.2% | 33.8% | 47.8% | 67.9% | 80.6% | 86.3% | 93.0% | 98.3% | 99.4% | |
| ≥0.6 | 0.0% | 0.0% | 21.1% | 33.2% | 47.6% | 60.3% | 72.9% | 81.7% | 96.3% | 98.3% | |
| ≥0.7 | 0.0% | 0.0% | 12.3% | 20.8% | 31.4% | 40.4% | 59.8% | 67.5% | 93.8% | 96.5% | |
| ≥0.8 | 0.0% | 0.0% | 6.2% | 11.5% | 19.1% | 24.5% | 47.4% | 53.2% | 90.3% | 93.6% | |
| ≥0.9 | 0.0% | 0.0% | 2.2% | 4.9% | 9.3% | 11.9% | 33.8% | 37.8% | 83.3% | 88.0% | |
The imputations were performed with 1000 G and 1000 G + UK10K reference panels.