I have UV mutagenized microorganisms and screened for improved phenotypes. Now I want to identify the causative variants. I've sequenced (200x coverage) a cultivar (mixed population with improved phenotype) and have vcfs with thousands of variants. I was wanting to do GWAS and make some Manhattan Plots (treating each sequencing read like and individual) but it doesn't seem like that will work here. Maybe I should just plot allele frequencies? Is that calculated by doing AF = AD (allele depth) / DP (read depth) from the VCFs? Or what is the best way to find the dominant variants in this mixed population? Any suggestions on how to move forward? Thanks!