Table 1.
Derived significance thresholds for the Illumina 1M data.
| Chromo- some |
Number of SNPs |
Permutation | simpleM | Keff | Bonferroni | |||
|---|---|---|---|---|---|---|---|---|
| Meff | αp | Meff | αp | w=20 | αp | αp | ||
| 1 | 63560 | 30881 | 1.66E-06 | 31898 | 1.61E-06 | 41438 | 1.24E-06 | 7.87E-07 |
| 2 | 64367 | 31760 | 1.62E-06 | 33386 | 1.54E-06 | 43538 | 1.18E-06 | 7.77E-07 |
| 3 | 53622 | 26328 | 1.95E-06 | 27675 | 1.85E-06 | 36009 | 1.42E-06 | 9.32E-07 |
| 4 | 47096 | 24292 | 2.11E-06 | 24474 | 2.10E-06 | 31651 | 1.62E-06 | 1.06E-06 |
| 5 | 48758 | 24187 | 2.12E-06 | 25229 | 2.03E-06 | 32699 | 1.57E-06 | 1.03E-06 |
| 6 | 52870 | 25667 | 2.00E-06 | 26165 | 1.96E-06 | 34945 | 1.47E-06 | 9.46E-07 |
| 7 | 43084 | 23040 | 2.23E-06 | 23123 | 2.22E-06 | 29607 | 1.73E-06 | 1.16E-06 |
| 8 | 41932 | 23254 | 2.21E-06 | 22314 | 2.30E-06 | 28809 | 1.78E-06 | 1.19E-06 |
| 9 | 35591 | 20078 | 2.55E-06 | 20061 | 2.56E-06 | 25505 | 2.01E-06 | 1.40E-06 |
| 10 | 40195 | 21186 | 2.42E-06 | 21277 | 2.41E-06 | 27575 | 1.86E-06 | 1.24E-06 |
| 11 | 39420 | 21101 | 2.43E-06 | 20359 | 2.52E-06 | 26188 | 1.96E-06 | 1.27E-06 |
| 12 | 38787 | 20875 | 2.46E-06 | 21318 | 2.41E-06 | 26644 | 1.93E-06 | 1.29E-06 |
| 13 | 28656 | 14936 | 3.43E-06 | 15087 | 3.40E-06 | 19624 | 2.61E-06 | 1.74E-06 |
| 14 | 26026 | 14414 | 3.56E-06 | 13829 | 3.71E-06 | 17749 | 2.89E-06 | 1.92E-06 |
| 15 | 23896 | 12277 | 4.18E-06 | 13312 | 3.85E-06 | 16477 | 3.11E-06 | 2.09E-06 |
| 16 | 24517 | 14346 | 3.58E-06 | 14626 | 3.51E-06 | 17627 | 2.91E-06 | 2.04E-06 |
| 17 | 23054 | 11558 | 4.44E-06 | 12578 | 4.08E-06 | 15360 | 3.34E-06 | 2.17E-06 |
| 18 | 22885 | 11629 | 4.41E-06 | 12583 | 4.08E-06 | 15935 | 3.22E-06 | 2.18E-06 |
| 19 | 16918 | 9152 | 5.60E-06 | 9646 | 5.32E-06 | 11389 | 4.50E-06 | 2.96E-06 |
| 20 | 19995 | 10177 | 5.04E-06 | 11169 | 4.59E-06 | 13971 | 3.67E-06 | 2.50E-06 |
| 21 | 11012 | 6150 | 8.34E-06 | 6247 | 8.21E-06 | 7747 | 6.62E-06 | 4.54E-06 |
| 22 | 12388 | 6708 | 7.65E-06 | 7004 | 7.32E-06 | 8537 | 6.01E-06 | 4.04E-06 |
| genome- wide |
778629 | 378368 | 1.36E-07 | 413360 | 1.24E-07 | 529024 | 9.70E-08 | 6.42E-08 |
The permutation thresholds were calculated using 10,000 random shuffles.
The experiment-wise error rates for each chromosome and the genome-wide adjustment was set at αe = 0.05.
αp: point-wise error rate.
Meff: the effective number of independent tests.
w=20: window size is set equal to 20.