Fig. 3
Strand-specific coverage plots. (A) Blue and red traces show transcription in the plus and minus strand, respectively. Similarly, blue and red arrows on the top indicates the annotated genes in the plus and minus direction. The x-axes record the position on the genome and the y-axes record the number of reads mapped at the location (average coverage depth = 658). Highlighted regions on the top show neighbouring or/and overlapping genes. Examples of gene annotated and transcribed in the minus strand (tp0813, left), intergenic region (tp0813-tp0814, middle), and gene annotated and transcribed in the plus strand (tp0814, right). (B) Example of a convergent 3’−3’ gene pair with overlapping transcripts. Transcription of the gene tp0114 (left), intergenic region (tp0114 - tp0115, middle) ad transcription of the gene tp0115 (right). (C) Example of transcripts that conflicted with existing annotations. Antisense transcript originating within annotated gene (tp0143, left), example of a region transcribed exclusively in the opposite orientation to the original annotated gene tp0694 (middle), and example of transcripts arising from intergenic regions (tp0129-tp0131, right). The complete set of 1775 strand-specific coverage plots are accessible from https://tpa-coverage-plots.pam.sanger.ac.uk/ and read coverage details can be found in the S6 Table.
