I have fixation index statistics (FST) for approximately 4 million loci, genome-wide. I would like to calculate a 5% FDR threshold in order to select the top loci in terms of highest FST statistics. Population genetics papers often take the top x% FDR for FST and PBS stats, but do not state in methods how they calculate the FDR threshold.
I have tried calculating P-values, then calculating q values using fdrtool in R, but these FDR thresholds seem to be falling very low (not stringent at all). Can someone explain what it means to take a top x% FDR?