Neutral expectations, statistical power, and probability of detection. A) Unweighted probability density of derived allele frequencies under the neutral theory. Calculations use Equation 1 and are represented by a black line. MATLAB simulation data is represented by grey circles. B) Statistical power of GWAS plotted as a function of odds ratio and allele frequency. Darker shading indicates greater statistical power. Parameter values: 2500 cases and controls, a p-value of 5 × 10-8, complete linkage, multiplicative dominance. C) Probability of detecting a disease-associated allele. Three distributions of odds ratios are considered: uniform (evenly distributed odds ratios between 1.0 and 1.5, dashed grey line), Dirac delta (every allele has an odds ratio of 1.25, solid grey line), and normal (mean 1.25, standard deviation = 0.1, dashed black line). Equation 6 is plotted as a solid black line.