Identifying Non Synonymous mutations in bacterial genomes

Question

[mmart12]

Hello, I would like to discriminate non-synonymous mutations from synonymous mutations in bacterial genome sequences. In particular, I have got a list of mutations between a query and the reference genome obtained through the software breseq. I have used snpeff but I got problem because the software listed some mutations as "upstream gene variant" where in fact the mutation occurred in a gene. So i guess I can't really trust snpeff.
Do you know other software or script I can use?
And also, once I got the non synonymous mutations do you know how I can assess if they are deleterious or not?

Thank you very much

[alok.helix]

I too work on bacterial WGS. Did you try silencing that option in snpEFF? I have used freebayes to call my variants and have never tried breseq. Sometimes even if the gff3 file does have a proper formatting it might spring up many messages on the screen. Try using Polyphen,snpgo,predprotein,SIFT. I know still more but not able to recall.