I'm fairly new to bioinformatics and I am a little stuck. Essentially, I am trying to visualize really large deletions in mutant bacterial genomes (~300,000 base pairs) compared to a reference. I have confirmed the presence of these deletions using the program breseq. After doing so, I have used SPAdes to assemble contigs for each of my mutants, and then uploaded this data to RAST. I then attempted to use the BRIG software, which should align the mutants to the reference genome and show a large blank gap of 300,000 base pairs where the deletion occurred. However, I am getting regions of similarity within the section that should be blank. I was wondering if something sounds wrong with my process, or if anyone has any recommendations for software that could be used to create figures illustrating large genomic deletions instead of BRIG? Thank you in advance for the help.