Empirical significance – Percentage of genome-wide transmission test false positives in 10,000 datasets with no LD.

Proportion of 10,000 datasets simulated under the null hypothesis of no genotyping error and without LD such that . Columns 2 through 5 display results for various chip sizes when generating minor allele frequencies from a Uniform (0.1,0.5) distribution. Columns 6 through 9 display analogous results when generating minor allele frequencies from a Beta (2,8) distribution. Each row depicts results corresponding to a distinct genotyping error model from Figure 1.