The effect of allele frequency on false-positive rates.
L = 60 SNPs with minor allele frequency as given on the
x-axis were simulated and α was computed for the eight relationships listed in the inset. The
y-axis is the negative log to the base 10 of the ratio between α at
q = 0.5 (the minimum value of α) and α with
q as given on the
x-axis. For example, for the

relationship, the false-positive rate for 60 loci is almost 100 times larger when all loci have
q = 0.2 than when they have
q = 0.5.