Sample size and effect size. a) Power and FDR for an idealized phenotype. Simulations in which a single random SNP explaining 5%, 10% or 20% of the phenotypic variance (with heritability ~0.75) were performed in either 200, 400 or 800 individuals . Simulations are based on the available SNP data for Arabidopsis, with structure added by giving 10,000 random SNPs a tiny effects size. The star indicates power (the ability to find true positives) and FDR (false positives) at the 5% bonferroni-corrected threshold for 220,000 markers. b) An example of one particular simulation in which the causative SNP (red diamond) is not the most significant SNP in the local window. Remaining SNPs are colored according to their linkage to the causative SNP. Dashed line denotes the 5% bonferroni-corrected threshold for 220,000 markers.