Behaviour of the different methods under the null.

This table relates to the simulation study to test the type 1 error rates of MultiPhen, CCA, and the univariate approach, described in the text. The elements of the table show the number of results with P<1e–5 in the scenario described by the corresponding row and column (which give the minor allele frequencies) headers. Since 100000 replicates of SNP-phenotype associations were simulated under the null hypothesis of no association, the expectation for all elements of the table is 1; those with >1 indicating inflation of the type 1 error rate. Simulations with MAF = 30%, 0.5% were performed on a sample size of N = 5000. For the full results see Figures S1–S8 and Table S1–S3.