Only a small part of the changes in transcript structures can be explained by underlying genomic variation. (a) The overlap between splice junctions that are produced at different levels in SHR and BN-Lx and small genomic variants in essential splice sites. Only one of the splice junctions that is different in BN-Lx and SHR carries a variant in an essential splice site. (b) The single differential splice junction that overlaps with an SNV (arrow) results in exon skipping in Slc22A18C. The exons are indicated as black boxes. RNA-seq reads that mapped at this gene locus are shown as small horizontal bars. The red scale indicates the amount of times each read was found in the data set. The number of RNA-seq reads that mapped across the exon-exon junctions is represented in the numbers above the arcs. (c) Mapped RNA sequencing reads (small black bars) in D3ZCV5_RAT show a different transcript structure in BN-Lx versus SHR. The different transcripts in the current annotation are shown on top of the reads. The gene is duplicated in SHR (red bar) (d) A large deletion (red) in SHR covers the last exon of the RT1-Bp gene. The deleted exon shows little coverage in the RNA-seq data of SHR.