pheno_table.txt Genetic background

[Former user]

I've been trying to figure out how to interpret the genetic background column of the pheno_table.txt output, and I'm wondering if there is an issue. From what I understand, it is supposed to mean the number of genes which contribute to a particular phenotype.

However, I've noticed that the number in the genetic background seems to be only 2 or 3 (and I assume when it is blank it indicates 1 ARG), even if there seems to be more than 3 genes with a phenotype implying resistance to a particular antibiotic. Is this normal, is this a bug, or should I interpret the data from this in another way?

A good example is Erythromycin, which appears in the ResFinder_results.txt output as a phenotype appearing in seven different genes. However, the pheno_table doesn't have any number in the genetic background column, only a 3 in the match column, which I believe only indicates the quality of the best match according to match ID and coverage.

Any help would be appreciated.

[CGE Helpdesk]

Dear Mr./Mrs.

Thank you for your message and interest in ResFinder.

There is currently an error regarding the genetic background causing it to output just a number, so I understand the confusion. When working properly it will output the name and accession number of the gene found causing the listed phenotype.

We will of course work on fixing the error, and thank you for brining our attention to this.

Best regards,

Maja, CGE Helpdesk

[RolfKaas]

Fix issue #93

→ <<cset 5bc5d59e8567>>