Fig. 3

Single-exon and ORF proportions in annotated and unannotated scaffolds. Many scaffolds align partially to the exome. A scaffold is said to be “annotated” when it has an alignment that exceeds an arbitrary fraction, i.e. annotation threshold, of either the scaffold length or of the reference transcript length. Annotated and unannotated SE refers to the proportion of annotated and unannotated transcripts that are single-exon. Unannotated SEI refers to the proportion of unannotated single-exon transcripts that are intronic. Annotated and Unannotated ORF refers to the proportion of scaffolds in each category that have ORFs of at least 100 amino acids in length, out of the scaffolds that are at least 300 bases long