Fig. 1: Approach to bacterial GWAS power calculations.

Four steps were implemented to conduct power calculations. First, known or randomly sampled causal variants are chosen from existing genotypes, in the sub-sampling or phenotype simulation approach, respectively. In the latter, causal variants meeting a range of selected MAF and degree of homoplasy are selected. Second, phenotypes are either modified from existing ones (sub-sampling approach) or simulated from randomly selected genotypes (phenotype simulation approach) to achieve the range of chosen sample sizes and effect sizes (or heritability values). Third, a genome-wide association study (GWAS) is conducted for each combination of parameters and p-values of causal variant extracted. And forth, power is calculated as the proportion of GWAS replicates in which the causal variant is above the Bonferroni-corrected genome-wide significance threshold.