Identifying where polymorphisms occur in bacterial genome

Question

[otterad]

Hi,

I'm a bit of a noob, but I've got a list of all polymorphisms (see below as an example) between two closely related bacteria taken from Mauve. Is there a quick way I can identify which genes these polymorphisms occur in? I'm not interested in polymorphisms that occur in intergenic regions but would be ideal to just know which ones are intergenic.

     SNP seq1     seq1pos   seq1_genomepos  seq2    seq2pos seq2_genomepos
    ag  Bacteria1   467     467     Bacteria1    467     467
    ga  Bacteria1   1057    1057    Bacteria2   1057    1057
    ag  Bacteria1   1977    1977    Bacteria2   1977    1977
    ag  Bacteria1   2347    2347    Bacterie2   2347    2347

For example, the first polymorphism 'ag' is A > G substitution in gene_001. I've tried googling and searching looking for some scripts, but can't find anything.

In addition, is there a way I can identify regions where deletion/insertions have occurred? Any perl or python scripts available?