Alleles-of-the-diphtheria-toxin-gene.md

@@ -2,30 +2,27 @@ _diphtOscan_ identifies the alleles of the _tox_ gene in case of presence of the
 
 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
+## _diphtOscan_ output: "tox_allele" column 
 
-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 `*`.
+* _diphtOscan_ will report the allele number of the tox gene, whenever an exact match is found.
+* _diphtOscan_ will 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
+## _diphtOscan_ output: "TOXIN" column
 
-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 `$` (truncated by position at end of contig).
+* Three references are used as queries for the tox gene: _C. diphtheriae_(), _C. ulcerans_() and _C. pseudotuberculosis_ (). The best query found will be reported in the column.
+* Annotations indicate aspects of the hit: `*` (inexact nucleotide identity but exact length coverage).
+* For any hit with inexact length coverage, the mention '_NTTB?' is noted. In addition of 'NTTB': `-X%` (% length corresponding to the missing amino acid sequence). 
+* Further, additionnal information may be provided: `#` (truncated but is a CDS) and `$` (truncated by position at end of contig).
 
 ## Examples
 
 | strain     |  tox_allele  |  TOXIN                            |  Interpretation                                                    |
-|------------|--------------|-----------------------------------|----------------------------------------------------|
 | ---------- | ------------ | --------------------------------- | -----------------------------------------                          |
-|  strain A  |  -           |  -                                | tox absent                                         |
-|  strain B  | 1            |  tox_diphtheriae                  | Exact compared to the _C. diphtheriae_ tox reference |
-|  strain A  | 10           |  tox_diphtheriae*                 | Incorrect compared to the reference tox            |
-|  strain B  | 2            |  tox_diphtheriae;tox_diphtheriae  | two copies of tox                                  |
-|  strain A  |  38*         |  tox_diphtheriae-NTTB?$-20%       | Tox is truncated by 20% at the end of the contigs  |
-|  strain B  | 24           |  tox_diphtheriae-NTTB?-14%        | Tox is truncated by 14%.                           |
-|  strain B  | 6*           |  tox_ulcerans                     | Exact compared to the reference tox of _C. ulcerans_ |
+|  strain A  |  -           |  -                                |  the tox gene is absent or less than 50% of its length is detected |
+|  strain B  | 1            |  tox_diphtheriae                  | Exact match compared to the _C. diphtheriae_ tox reference         |
+|  strain C  | 10           |  tox_diphtheriae*                 | Inexact match compared to the reference                            |
+|  strain D  | 2            |  tox_diphtheriae;tox_diphtheriae  | two copies of tox                                                  |
+|  strain E  |  38*         |  tox_diphtheriae-NTTB?$-20%       | tox is truncated by 20% and is located at the end of a contig      |
+|  strain F  | 24           |  tox_diphtheriae-NTTB?-14%        | Tox is truncated by 14%                                            |
+|  strain G  | 6*           |  tox_ulcerans                     | Exact match compared to the reference of _C. ulcerans_             |