variance. Further, the three parameters, π1, σβ2, σ02, are fitted by direct maximization of the likelihood function. The optimization is based on a set of approximately 600,000 SNPs, obtained by selecting a random set of 2,000,000 SNPs with minor allele frequency of 5% or higher, followed by LD pruning procedure at LD r2 = 0.8 threshold. The random SNP selection and full optimization procedure are repeated 20 times to obtain mean and standard errors of model parameters. The log-likelihood figures show individual curves for each of the 20 runs, each shifted vertically so that best log-likelihood point is shown at zero ordinate.
