Figure 4.

Alignments against a 17-bp insertion present in a nonreference genome. (a) Alignments of Est-1 reads against the graph of Arabidopsis chromosome 1, reference positions 20,166,584 to 20,166,747. Alignments against both the Col-0 reference and the Bur-0 variant genomes are highlighted in dark gray; alignments of reads aligning best against a single genome are highlighted in light gray. Most reads align against the Bur-0 allele, suggesting that Est-1 is more similar to Bur-0 at this locus. In particular, the 17-bp insertion found in Bur-0 is supported by the Est-1 reads. Because of the alignment constraints (maximum of four edit operations), these alignments could not have been performed against the Col-0 sequence only. Within the second divergent region, indicated by a red arrow, Bur-0 has a complex change, ACC->T, relative to Col-0, with Est-1 featuring a third allele, ACC->TA. Because this change is near the 17-bp insertion, only a subset of the alignments would have been found with single reference alignments only. For simplicity, Tsu-1, which also is included in the graph target, is not shown here. (b) Annotation of this region with respect to the Col-0 reference genome.