Fig. 3.

Effect on total expression and population frequency of cis-regulatory polymorphisms. a ASE, measured as the imbalance in expression of high versus low alleles, has a phenotypic effect on total expression. The relative total expression of each gene in lines containing the high versus low ASE alleles was estimated as the log₂ ratio of the mean cpm (counts per million) of the high and low allele groups. ASE was estimated as the difference between the high and low expression groups in the mean log₂ wild-allele-read-count/reference-allele-read-count ratio (see Fig. 2). b The major ASE allele tends to have higher total expression than the minor allele (mean log₂ major/minor cpm = 0.311, t-test μ ≠ 0 P < 10⁻¹⁵). In b only genes where the minor allele had a frequency of less than 30% are analysed. In all cases, genes were considered to have ASE at an FDR < 0.20