Between-sample variations in RNA-seq coverage. RNA-seq coverage plots across all samples for exons 4 to 11 of the IVT transcript BC003355. The black rectangles identify exon six, which shows extreme variability in coverage relative to the rest of the transcript when viewed across all of the samples. The ratio of IVT RNA to mouse RNA is listed to the left of each sample’s coverage plots. Coverage plots (red for first replicate; blue for second replicate) are displayed according to the gene model (black), as it is mapped to the reference genome. Blocks in the gene model correspond to exons and lines indicate introns. The chevrons within the intronic lines indicated the direction of transcription. Numbers on y-axes refer to RNA-seq read-depth at a given nucleotide position.