_diphtOscan_ identifies the alleles of the _tox_ gene in case of presence of the gene in the genomes. The source of allele nomenclature is the [BIGSdb-Pasteur _C. diphtheriae_ database](https://bigsdb.pasteur.fr/diphtheria/).
A copy of the _tox_ alleles definitions is stored in the [data directory](https://gitlab.pasteur.fr/BEBP/diphtoscan/data) of this repository. The update can be executed with the `-u` option.
## In the "tox_allele" column of the _diphtOscan_ table
Notes:
* _diphtOscan_ tries to report the closest matching allele if a precise match is not found.
* Imprecise allele matches (representing potential novel alleles) are indicated with a `*`.
## In the "TOXIN" column of the *diphtOscan* table
Notes:
* Three references are used as queries for the gene tox: _C. diphtheriae_(), _C. ulcerans_() and _C. pseudotuberculosis_ (). The best query found is noted in the column.
* Annotations indicate aspects of the hit: `*` (inexact identity nucleotide but inexact length coverage).
* For any hit found inexact length coverage from the reference, the mention '_NTTB?' is noted. In addition of 'NTTB': `-X%` (% length of truncated amino acid sequence).
* For further information: `#` (truncated but is a CDS) and `$` (truncated by position at end of contig).
