The q-values for SNPs in the randomly selected genes were calculated based on the GWAS data. For simplicity of comparison, we compared the number of SNPs in each q-value range (e.g., < 0.9, < 0.8, etc.). The proportion of the q-value number for each q-value range in randomly selected genes was then calculated. If the proportion was larger than our ranked alcohol genes at the same q-value range, we counted this permutation as a "significant permutation" for the specific score range s and q-value range. After 100 permutations, the proportion of "significant permutation" was set as the p-value of our permutation result at the corresponding score and q-value range. For the weighting score matrix with the best performance, permutation testing was repeated 1000 times again to check the significance.
