Table 5.
MAF distribution for all SNPs after applying info score (0.7) and marker call rate filter (99%).
| Threshold | SNPs dropped at threshold | Proportion of SNPs dropped at threshold | SNPs remaining at threshold | Proportion of SNPs remaining at threshold |
|---|---|---|---|---|
| ADULT DNA SAMPLES | ||||
| 0.05 | 2803753 | 5.1615e-01 | 2628296 | 0.4838 |
| 0.01 | 995223 | 1.8321e-01 | 4436826 | 0.8168 |
| 0.005 | 466779 | 8.5930e-02 | 4965270 | 0.9141 |
| 0.001 | 13979 | 2.5734e-03 | 5418070 | 0.997 |
| 0.0005 | 624 | 1.1487e-04 | 5431425 | 0.9998 |
| 0.0001 | 1 | 1.8409e-07 | 5432048 | 0.9999 |
| PEDIATRIC DNA SAMPLES | ||||
| Threshold | #SNPs dropped at threshold | Proportion of SNPs dropped at threshold | #SNPs remaining at threshold | Proportion of SNPs remaining at threshold |
| 0.05 | 6523370 | 7.3938e-01 | 2299322 | 0.2606 |
| 0.01 | 4631783 | 5.2498e-01 | 4190909 | 0.4750 |
| 0.005 | 3141053 | 3.5601e-01 | 5681639 | 0.6440 |
| 0.001 | 240254 | 2.7231e-02 | 8582438 | 0.9728 |
| 0.0005 | 30674 | 3.4767e-03 | 8792018 | 0.9965 |
| 0.0001 | 19 | 2.1535e-06 | 8822673 | 0.9999 |