Pointfinder can't find gyrA mutation in campylobacter coli

[陳柏翰]

Hi, I used pointfinder search gyrA mutation of campylobacter coli in web, it didn’t find any mutation.

I extracted gyrA sequence from genome annotation and alignment with gyrA sequence of pointfinder, there is indeed mutation in postition T86I.

I tried to reduce threshold and coverage, but it’s no any change.

Do you have any idea?

Thanks

job id : 605D736B00004DEC6CFB3666

[CGE Helpdesk]

Dear Mr./Mrs.,

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Thank you for your interest in ResFinder.

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I checked your job output and noticed a premature stop codon mutation at position 62 (gyrA:p.S62*). After detecting such premature stop codon the software will skip searching for further downstream mutations as these will not be translated.
The reporting will be updated in the new major update.

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Best,
Karen, CGE Helpdesk

[陳柏翰]

Hello

Can the program ignore stop codon and scan all sequence?

Thanks

[CGE Helpdesk]

Dear User,

In the current version of Resfinder ignoring stop codons is not an option. This will be an enhancement in the up-coming version.

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Best,
Karen, CGE Helpdesk

[RolfKaas]

ResFinder is now able to ignore stop codons via the flag "--ignore_stop_codons"