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–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.