Table 4.
Whole-exome variable threshold results
| Minor allele load | |||||
|---|---|---|---|---|---|
| Procedure | MAF threshold | Number of SNPs | Odds ratio | Observed p-value | Empirical p-value |
| All SNPs | 0.0065 | 17,207 | 1.350 | 7.51 × 10−4 | 0.002 |
| Nonsynonymous | 0.023 | 11,647 | 1.401 | 3.45 × 10−4 | 0.001 |
| Synonymous | 0.405 | 9,951 | 1.321 | 1.49 × 10−3 | 0.004 |
| BLOSUM weighting | 0.144 | 22,759 | 1.355 | 8.10 × 10−4 | 0.002 |
The variable threshold procedure examines all MAF thresholds to find the most significant threshold. Empirical p-values are derived from 1,000 permutations of affection status.