Table 1.
Estimation of true positive and false positive rates under varying significance thresholds using 1X to 5X samples and 90 normal test samples.
| Sample and Data | Stage | p-value < 10-2 | p-value < 10-4 | p-value < 10-6 | Total | |||
| Count | Percent | Count | Percent | Count | Percent | Count | ||
| 90 normal samples (autosomes) | SP | 409049 | 5.05% | 42182 | 0.52% | 11154 | 0.14% | 8095770 |
| KS | 40247 | 0.497% | 3302 | 0.041% | 770 | 0.009% | 8095770 | |
| TR | 5417 | 0.067% | 506 | 0.006% | 167 | 0.002% | 8095770 | |
| 1X | SP | 1441 | 73.71% | 694 | 35.50% | 286 | 14.63% | 1955 |
| KS | 1780 | 91.05% | 714 | 36.52% | 111 | 5.68% | 1955 | |
| TR | p-value = 1.99 × 10-4 | 1955 | ||||||
| 3X | SP | 1271 | 65.01% | 879 | 44.96% | 603 | 30.84% | 1955 |
| KS | 1707 | 87.31% | 1136 | 58.11% | 547 | 27.98% | 1955 | |
| TR | p-value = 8.13 × 10-6 | 1955 | ||||||
| 4X | SP | 1726 | 88.29% | 1523 | 77.90% | 1343 | 68.70% | 1955 |
| KS | 1929 | 98.67% | 1861 | 95.19% | 1697 | 86.80% | 1955 | |
| TR | p-value = 6.15 × 10-12 | 1955 | ||||||
| 5X | SP | 1884 | 96.37% | 1801 | 92.12% | 1724 | 88.18% | 1955 |
| KS | 1950 | 99.74% | 1933 | 98.87% | 1907 | 97.54% | 1955 | |
| TR | p-value = 1.50 × 10-16 | 1955 | ||||||
Notes:
1 SP: Single point analysis
2 KS: Kernel smoothing with 100 kb window after single point analysis
3 TR: Tree partitioning of the genome on the kernel smoothed result.