I have a reference strain that has undergone successive passages on agar plates. I sequenced and analyzed its genome and multiple SNPs, MNPs, indels have appeared.
What is the "threshold" in terms of mutations, ANI, etc. to be able to say: "this variant is different from the reference strain" or "this variant can be considered as a new strain" ?
I would like to have your opinion on this, please.
Have a nice day,