Divergence is not a uniform value across the genome: coding regions are restricted by stronger selection force against fast and big changes over time, while non-coding regions are less constrained. Given you could map reads from one species to reference genome from another species, your comparison seems to be between two relatively related species. I'd suggest you to start with coding regions, following the standard practices in what is called phylogenomics, comparing gene sequences across species at a whole genome levels, and calculate divergences at the nucleotide level. Non-coding regions are a whole different ball game, you would need much more effort to find differences in non-coding regions, especially for structural variations.

Thanks for your answer ! I will try to do that :D