Uniqueness in the transcriptome.

<p>(<b>A, B</b>) We calculated the proportion of unique positions for each transcript, both for single reads and paired-end fragments (mean 500 nt), and then plotted how many transcripts have a certain proportion of unique positions. The y-axis represents the proportion of all transcripts that satisfies the given condition. (<b>A</b>) Gene-level uniqueness of all RefSeq transcripts. (<b>B</b>) Transcript-level uniqueness for all transcripts from multi-isoform genes. (<b>C</b>) Positional plot of the uniqueness proportion across all coding transcripts. We calculated the number of reads of a specific length that passes through each position, and determined what proportion of these were unique. Since transcripts differ in length, we binned positions together so that each region (upstream, downstream, coding sequence, 5′ and 3′UTR) had the same number of bins for each transcript. The x-axis represents coordinate bins across transcripts.