Analyzing the alignments of each rootstock genomic DNA against the reference genome, it is possible to infer the differences between the two. It has to be taken into account that the variability of the coverage across the whole genome – a normal behaviour of any shotgun sequencing experiment – will make each difference more or less probable (accurate).
There are two strategies to assemble a genome when a close relative is available.
First we can use the relative as a reference, and after mapping reads against it, to reconstruct the reference considering mismatches and indels in the alignment as hints pointing to differences in the two genomes. A second approach is to work as if no reference is available, and to assemble de novo the genomes. The two approaches are both useful and have been considered to yield different answers.