Empirical significance — Percentage of genome-wide transmission test false positives in 10,000 datasets with LD.

Proportion of 10,000 datasets simulated under the null hypothesis of no genotyping error and in the presence of 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.