Different result with ClermonTyping

[iaposto]

Hello again @nickp60,

I caught an inconsistency between EzClermont (CLI) and ClermonTyping (webapp: http://clermontyping.iame-research.center/index.php).

[arpA, chuA, yjaA, TspE4.C2]
EzClermont: [- - + -] cryptic
ClermonTyping: [+ - + -] A

I am trying to figure out why is this happening.
Attached the genome in question.
3817_AV78.zip

Thanks!

[nickp60]

Hi @iaposto ,
Thanks for your message. It looks like the arpA allele present in this sample is unlike the ones the model is trained on. When in doubt its best to look at whole genome phylogeny. Here is where your strain (labeled AV78) falls in the cladogram: solidly with the A's (around the 5 o'clock position).

[iaposto]

Many thanks for your reply @nickp60!