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_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/).
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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.
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## In the "tox_allele" column of the _diphtOscan_ table
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Notes:
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* _diphtOscan_ tries to report the closest matching allele if a precise match is not found.
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* Imprecise allele matches (representing potential novel alleles) are indicated with a `*`.
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## In the "TOXIN" column of the *diphtOscan* table
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Notes:
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* 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.
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* Annotations indicate aspects of the hit: `*` (inexact identity nucleotide but inexact length coverage).
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* 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).
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* For further information: `#` (truncated but is a CDS) and `$` (truncated by position at end of contig).
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## Examples
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| strain | tox_allele | TOXIN | Interpretation |
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|------------|--------------|-----------------------------------|----------------------------------------------------|
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| ---------- | ------------ | --------------------------------- | ----------------------------------------- |
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| strain A | - | - | tox absent |
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| strain B | 1 | tox_diphtheriae | Exact compared to the _C. diphtheriae_ tox reference |
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| strain A | 10 | tox_diphtheriae* | Incorrect compared to the reference tox |
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| strain B | 2 | tox_diphtheriae;tox_diphtheriae | two copies of tox |
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| strain A | 38* | tox_diphtheriae-NTTB?$-20% | Tox is truncated by 20% at the end of the contigs |
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| strain B | 24 | tox_diphtheriae-NTTB?-14% | Tox is truncated by 14%. |
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| strain B | 6* | tox_ulcerans | Exact compared to the reference tox of _C. ulcerans_ |
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