Fig. 2

Identifying high and low expression alleles. Two genes with allele specific expression (ASE) are shown. ASE was detected as significant variation in the ratio of sequence reads from wild alleles sampled from natural populations and the reference allele across the different fly genotypes. The lines were divided into those with high and low expression alleles using a grouping approach with maximum likelihood (panels a and c in blue, high and green, low). The group with the mean log₂ ratio closest to 0 was assumed to have the cis-regulatory element (CRE) allele found in the reference genome. Note that in a the reference genome has the low expression allele (mean log₂ ratio of alternate group > 0), and in c it has the high expression allele (mean log₂ ratio of alternate group < 0). Panels b and d show the total expression of lines carrying the high and low expression alleles