Differential expression analysis compared the expression of each variant to its respective reference allele for all SNPs. To account for differences in the concentrations of the variant and reference plasmids that were used for the transfections, a plasmid input correction factor for each target site was calculated as the average of the number of reads from the variant plasmid divided by the number of reads from the reference plasmid across four replicates of the plasmids. The reads from the variant alleles for all biological replicates were divided by the input correction factor. The corrected read counts were fit into a generalized linear model using EdgeR (Robinson et al., 2010) assuming a negative binomial distribution. Biological replicates and the genotype were used as covariates. p-Values and log2 fold-change of the variant alleles compared to the respective reference alleles were derived using a likelihood ratio test on the genotype variable in the generalized linear model. The p-values were corrected for a false discovery rate (FDR) using the Benjamini and Hochberg algorithm (Benjamini and Hochberg, 1995). The EdgeR script can be found in Supplementary File 1.
