Alternative Splicing in Next Generation Sequencing Data of <i>Saccharomyces cerevisiae - Fig 2 </i>

<p><b>(A)</b> Classification and filtering of reads and potential introns for further analysis. Long: the potential intron is longer than 1002 bases. Short: it is shorter than 40 bases. Signal: the potential intron is not flanked by a canonical splice signal. Support: the potential intron is supported by only one or two reads. After applying all filters, 94.2% of all reads (corresponding to 8.8% of all potential introns) pass this pipeline. <b>(B)</b> Read support for potential and annotated introns. The dashed line marks the longest known intron in S. cerevisiae. The high read support for annotated introns is clearly visible. There are cases of unknown potential introns with comparable read support, possibly representing novel introns. Evidence of longer introns (right of the dashed line) is not as strong, distinguishing them clearly from known introns. The two length classes of introns are visible, clustering around length 100 and 400. <b>(C)</b> Junction quality reports how well an intron junction is defined by split reads. Values close to 100 indicate long regions before and after the junction that are supported by split reads (anchor), lower values indicate shorter regions. Values also become lower if the exact split is not clearly defined, i.e. it would also map <i>n</i> bases upstream or downstream. For details refer to the methods section. <b>(D)</b> The distribution of read support for all unfiltered potential introns (total, grey background) is skewed with a median of 3 and an average of 171.1 reads. Read support for unfiltered potential introns is compared to that of filtered ones (white background): the highest read support is found among annotated introns in protein coding genes (Annotated Introns) with a median of 787 and mean of 2843.0 reads. Different classes of alternative splicing (3’, 5’, both alternative splice sites, single introns) exhibit different read support, with the lowest median (13) for combined 3’ & 5’ (both) alternative splice site usage.