Figure 3

Graphical illustration of how a posterior probability is calculated for a SNP. Graphs of the mixture prior p(g _j ), conditional likelihood h(g _j |G _j , σ²) and conditional posterior distribution p(g _j |g _-j, y) as given in equations (A1) and (A2) of Additional file 1 for $\gamma =0.05,\lambda =\mathit{10},{\sigma }_e^{\mathit{2}}=\mathit{1}$ and n = 500. The Dirac Delta function is replaced by a DE with λ _s = 1000 i.e. a Spike at 0. The posterior probability γ _j of SNP j being in LD with QTL is calculated from equation (A3) by numerical integration. Figures A and B show the distributions when G _j is 0.19 and 0.11 respectively, where G _j is the conditional maximum likelihood estimate of g _j .