Problem interpreting 'gene' + 'var_only' columns

[ghost]

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)

[slvrshot]

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.