Fig. 7

Evaluation of whether each pair of contigs was connected because of the existence of an underlying gene. The top row of each panel shows a single sequence that will be assembled into two contigs. The site where the split in the assembly occurs is indicated by ‘cut’. The bottom row of each panel shows, for the two contigs, whether they are brought together because of exons of the same gene. Blue and green boxes represent genes, with the red boxes inside them representing exons; arrows in purple represent joining-pairs of reads. a Case 1. Two contigs are connected by AGOUTI because they carry exons of the same gene. Approximately 95 % of the contig pairs scaffolded by AGOUTI fell into this category. b Case 2. Only one end of a joining-pair overlaps a predicted gene on either contig. This suggests the existence of a new exon in one of the predicted genes. c Case 3. The joining-pairs are mapped to two different annotated genes in the C. elegans genome. This suggests that the two genes should be merged into one, or that there was a failure of transcriptional termination such that reads connected two adjacent genes. d Case 4. The joining-pairs are not mapped to any predicted genes, which may indicate the existence of a novel gene