Number of significant genes at different p-value thresholds.

‘Total genes’ gives the number of genes analysed. This was lower for the summary statistics analyses because some genes contained no SNPs present in both CD data and reference data and because VEGAS does not analyse the X chromosome. As such, those genes effectively have a p-value of 1 by default. For permutation-based methods, p-values were based on up to 1,000,000 permutations. No stratification correction was used in the analyses except the three under the ‘Strat. Correction’ header.
Number of significant genes at different p-value thresholds.