Differential expression of genes beneath QTL mapped in pA.

a Fragments Per Kilobase of transcript per Million mapped reads (values from Cuffdiff output files) for each of the four line/treatment combinations (Con = control food, Caff = caffeine food). b The log2 fold change (second sample divided by first sample) in gene expression for each of the four contrasts. ** indicates the test survives a per-contrast FDR of 5% (i.e., q < 0.05). * indicates the test is significant at p < 0.05. No asterisk indicates the test is not significant at a nominal 5% level. c These genes are also within the Q2 interval mapped in pB. d These genes are not within the Q3 interval mapped in pB. e This is the expression measured at the annotated Cyp12d1-p gene, with the annotation for the nearly identical gene Cyp12d1-d removed from the reference prior to RNAseq analysis. Similar results are seen using the Cyp12d1-d annotation, and masking the Cyp12d1-p gene. Differential expression of genes beneath QTL mapped in pA.