Hi,
In my genomic analysis, I found a new mutation for antibiotic resistance, which is among the sequence conflict in Uniprot. What is the implication for that? Can I still trust my new found mutation?
Regards
You are reporting a new variation which is not in the reference gene
Can I still trust my new found mutation?
Depends how are you detecting this mutation, how much coverage do you have? what is the mutation base qualities? what was the alignment quality?
Besides, you will need to validate this on the Lab to publish or report.
JC, thanks a lot for your reply
First, it may be good to mention that I am working in E. Coli, and this mutation appears in 5 samples out of my 92 samples.
I am quite sure about the quality of my variants as it passes all the quality control criteria.
But, my main question is, for my new mutation, being among sequence conflict in UniProt is something positive or negative?
It is neutral, a variant in any species is common because genes are dynamic things that change all the time, so it is really possible you have a new one detected.
JC, thanks a lot for your reply First, it may be good to mention that I am working in E. Coli, and this mutation appears in 5 samples out of my 92 samples. I am quite sure about the quality of my variants as it passes all the quality control criteria. But, my main question is, for my new mutation, being among sequence conflict in UniProt is something positive or negative?
It is neutral, a variant in any species is common because genes are dynamic things that change all the time, so it is really possible you have a new one detected.