The simulation was also repeated including information about stratification of the six phenotypes (described above) over genotyping waves. The genotyping wave was assumed to have no effect on the various probability parameters of the simulation and this time simulations were repeated only 10,000 times. The largest P-value encountered was 4.0x10−4 and the variance of this estimator is less than 1/(4x10000) = 0.000025, thus rejecting the null hypothesis.
