Using intermediate genomes to identify correlations between SNPs and gene model events.

<p>Comparison of exon models from vdB (red), vdB* (yellow), and intermediate (orange) genomes. All SNPs in the region are shown, with the SNP that perfectly correlates with the event in bold. A) A “shift” event. A SNP in a <i>TGA</i> stop codon in vdB* is associated with a shift in exon length on contig 16: 3577500–3576100. B) Two “shift” events. A novel splice donor in vdB* affects the length of its exon and a neighboring exon on contig 20: 2945150–2945750. C) An “intron gain/loss” event. An intronic SNP affects the presence/absence of an intron on contig 12: 69800–70950.