I have a few questions regarding snippy. I need to analyze around 20 genomes and compare them to reference genome. I used unicycler to assemble my reference genome from illumina short reads and Pacbio long reads and then I used snippy to find changes in genomes. I am getting very confusing results, for instance in some of the genomes I get exact same mutations in the same position. For instance indel on a gene for immunity protein caused same change in almost every analzyed genome. Then I used prokka to annotate some of the genomes and clustal omega to align genes of interest to reference genome and found out that they are identical 100 % to reference genome. So what could be the isssues ? Can anyone explain.
Have a nice day.