Identifying Non Synonymous mutations in bacterial genomes
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6.4 years ago
mmart12 ▴ 30

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

SNP R next-gen genome sequence • 1.8k views
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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.....

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