We are working with whole genome sequence data of a Pseudomonas fluorescence strain. The de-novo assembly of the same was performed using abyss software. After that, contigs from denovo assembly was submitted in RAST server for annotation. From RAST, the closely related species to this strain was identified. When we did the alignment between our strain and the related strain using Bowtie2, it shows 71% overall alignment rate. So I want to know whether this alignment rate is good or not.
Just feel that the alignment should be a bit more between two strains of the same species. Not sure if this question is a blunder as we are new to NGS data analysis.
Also Could someone suggest any tool to find out a reference genome other than by BLAST?
Thanks in advance