The transcriptomes of SHR and BN- Lx liver have differences in both expression levels and splicing events. (a) The amount of sequencing reads that could be mapped to the genome per RNA-seq library. Three animals were analyzed for each strain. (b) Twelve genes found to be differentially expressed between BN-Lx and SHR with RNA-seq were analyzed with qPCR. (c) Schematic representation of alternative splicing analyses. To analyze splicing events a novel reference was created by combining the sequences of the annotated exon ends. RNA-seq reads were mapped to this reference and junctions used differentially by BN-Lx and SHR were determined.