Within-transcript variations in RNA-seq coverage. (A) Simulated RNA-seq coverage for a representative IVT transcript (BC015891). RNA-seq coverage plot (black) is displayed according to the gene model (green), as it is mapped to the reference genome. Blocks correspond to exons and lines indicate introns. The chevrons within the intronic lines indicate the direction of transcription. Numbers on y-axis refer to RNA-seq read-depth at a given nucleotide position. (B) The actual RNA-seq coverage plot for BC015891 in the IVT-only sample. Representative coverage plots for the IVT transcripts (C) BC009037 and (D) BC016283 are displayed according to the same conventions used above. All transcripts are displayed in the 5ʹ to 3ʹ direction.