slvrshot
commented
3 years ago From the wiki:
3. gene | 1=gene, 0=non-coding (same as metadata column 2) 4. var_only | 1=variant only, 0=presence/absence (same as metadata column 3)From my understanding, if the 'gene' column = 0, then it's non-coding, so it means it does not code for a transcript, which means it cannot be expressed and has no antimicrobial resistance functionality. If that is indeed the case, then under what circumstances would we be interested in detecting these non-functional ARGs?
According to the paper:
Further, each reference sequence is classified as ‘presence/absence’ where the existence of a sequence within a sample confers antimicrobial resistance, or ‘variant only’ where a known variant is required for antimicrobial resistance.
So it would seem that:
- gene = 1 & var_only = 1: a coding gene but is a variant that does not cause antiobiotic resistance
- gene = 1 & var_only = 0: a coding gene that can cause antiobiotic resistance
- gene = 0 & var_only = 0: a non-coding gene that can cause antibiotic resistance (This one makes no sense to me since you'd need to express a product to produce antimicrobial resistance effect? Please help me understand this one)
Where is this even listed in the wiki? I don't see it anymore.
From the wiki:
From my understanding, if the 'gene' column = 0, then it's non-coding, so it means it does not code for a transcript, which means it cannot be expressed and has no antimicrobial resistance functionality. If that is indeed the case, then under what circumstances would we be interested in detecting these non-functional ARGs?
According to the paper:
So it would seem that: