Fig. 3
From: Zea mays RNA-seq estimated transcript abundances are strongly affected by read mapping bias
For genes positively affected by B73 (A) and Mo17 (B) cis-eQTL, the number of genic SNPs and expression level differences of homozygous B73 and Mo17 lines were plotted. Exon sequence divergence was calculated as the number of SNPs matching exons in a gene divided by the total exon lengths and multiplied by 1000. The numbers in parenthesis represent the numbers of genes in each group. The y-axis is the absolute value of the allelic expression level difference of B73 minus Mo17 in FPKM, or two times the expected additive effect of the locus. a Expression differences between B73 and Mo17 were highly correlated with numbers of SNPs per 1 kb exon for the 5559 B73 positive cis-eQTL genes with SNP information. b Expression level differences between Mo17 and B73 were weakly correlated with numbers of SNPs per 1 kb exon for the 2561 Mo17 positive cis-eQTL genes