I recently ran Prokka on a bacterial genome and the results showed 1 16S rRNA. I had moderately expected two 16S rRNA in this genome (just because a similar genome had two 16S rRNA). As a result, I want to double check that there really is only one copy in these genome (and not that there are two similar copies and Prokka could only find one).
What I have done:
1) Mapping the raw reads of my genome to the 16S rRNA sequence detected by Prokka as the reference genome. 2) I have resulting .sam, .bam, and .bed file. 3) It seems 893 reads in my genome mapped to the reference 16S rRNA.
What I would like to do now:
I would like to view these 893 reads against the reference genome and determine if there are any nucleotides that have "variants". If I see certain nucleotides in the reference rRNA genome having multiple bases aligning to it from the raw reads, then I will assume this is evidence that perhaps there are multiple (but similar) 16S rRNA in my genome and that perhaps only the consensus was picked up by Prokka.
1) Does my thinking about this process seem sound conceptually? (That variants in the mapped reads to the 16S rRNA reference sequence may be evidence for the presence of more than 1 16S rRNA in my genome sequence?)
2) What is a simple step for someone using MacOSX with only basic Linux skills to indeed view these 893 reads against the reference genome and check for possible variants?