Fig. 3.

Insertion at locus AC225449_6.1 of M. truncatula. Shown are length of depicted region (in base pairs), contig ID, location of mapped EPTs, the Mt3.5v4 gene model and 3-frame translation, and depth of RNA-Seq coverage (scale in reads per bp shown at left). An apparent 1-bp insertion in the genomic sequence causes the gene caller to insert an erroneous intron to correct for the frameshift. EPT_046967 (8 PSMs) overlapping the intron justified a closer look at the genomic locus, and RNA-Seq data of ∼1700-fold coverage clearly showed an insertion in the genomic sequence at the location of the intron (black arrow). Such indels were observed numerous times in both BAC-based pseudomolecule constructs as well as short read contigs.