From: A joint use of pooling and imputation for genotyping SNPs
MAF | 0.00–0.02 | 0.02–0.04 | 0.04–0.06 | 0.06–0.10 | 0.10–0.20 | 0.20–0.40 | 0.40–0.50 |
---|---|---|---|---|---|---|---|
Scenario: LD + HD | |||||||
Number before imputation | 520.000 | 779.000 | 673.000 | 1537.000 | 3969.000 | 6561.000 | 2976.000 |
Number after imputation | |||||||
Beagle | 12699.362 | 5167.613 | 2776.687 | 4673.658 | 8804.892 | 12301.371 | 5337.921 |
Prophaser | 12727.142 | 5193.438 | 2793.221 | 4705.346 | 8870.104 | 12396.258 | 5379.408 |
Proportion before imputation | 0.041 | 0.149 | 0.238 | 0.322 | 0.441 | 0.520 | 0.543 |
Proportion after imputation | |||||||
Beagle | 0.994 | 0.987 | 0.984 | 0.981 | 0.977 | 0.975 | 0.975 |
Prophaser | 0.996 | 0.992 | 0.989 | 0.987 | 0.985 | 0.983 | 0.982 |
Scenario: pooled HD | |||||||
Number before imputation | 12534.608 | 4826.542 | 2396.671 | 3481.896 | 4249.592 | 1853.529 | 159.575 |
Number after imputation | |||||||
Beagle | 12565.650 | 4892.246 | 2478.292 | 3778.296 | 5637.525 | 5407.479 | 1941.162 |
Prophaser | 12755.854 | 5184.621 | 2758.079 | 4532.467 | 7964.742 | 9858.467 | 4012.725 |
Proportion before imputation | 0.981 | 0.922 | 0.849 | 0.731 | 0.472 | 0.147 | 0.029 |
Proportion after imputation | |||||||
Beagle | 0.984 | 0.935 | 0.878 | 0.793 | 0.626 | 0.429 | 0.354 |
Prophaser | 0.999 | 0.990 | 0.977 | 0.951 | 0.884 | 0.782 | 0.733 |