Table 3.
Overlap analysis between DIAGRAM and PGC summary statistics
| Pt value | Variants | χ 2 | P value | Pperm value |
|---|---|---|---|---|
| 0.5 | 58504 | 1.4 | 2.30E-01 | 2.32E-01 |
| 0.1 | 6247 | 39.7 | 3.00E-10 | 0.00E + 00 |
| 0.05 | 2324 | 40.9 | 1.60E-10 | 0.00E + 00 |
| 0.04 | 1749 | 53.5 | 2.50E-13 | 0.00E + 00 |
| 0.03 | 1180 | 49 | 2.50E-12 | 0.00E + 00 |
| 0.02 | 658 | 32.4 | 1.30E-08 | 0.00E + 00 |
| 0.01 | 287 | 41.4 | 1.30E-10 | 0.00E + 00 |
| 0.005 | 125 | 37.7 | 8.10E-10 | 0.00E + 00 |
| 0.001 | 19 | 14.2 | 1.70E-04 | 8.30E-04 |
| 5.00E-04 | 10 | 13.8 | 2.00E-04 | 2.00E-03 |
For each p value threshold (Pt) the number of independent variants overlapping at this threshold is given, along with the resulting chi-squared statistic (χ2), p value (P) and empirical p value obtained by permutations (Pperm).