... | ... | @@ -20,6 +20,7 @@ The AMR report contains the prediction of antimicrobial resistance genes as well |
|
|
| contig_2 | 0000000002 | 2_1 | 00000000003 | gyrA | S81L | multidrug | fluoroquinolone antibiotic;nybomycin | antibiotic target alteration | RGI | chromosome |
|
|
|
|
|
|
## Virulence Factors
|
|
|
Within the report of the virulence factors the first columns contain information regarding the ORF ids, followed by (if identified) the prediction of the sequence as virulence factor. Since the prediction tool for virulence factors consist of two different parts, a HMM model and random forest classifier, the prediction of each are given within the report (Virulence_HMM_prediction, Virulence_classifier_prediction, respectively), followed by the final prediction (Virulence_prediction), prediction of signal peptides (Signal_peptide). Lastly the final prediction is given as the virulence confidence level. This confidence level is given depending on the prediction of the tool and the prediction as signal peptide (secreted or non-secreted). It should be noted that the confidence level of 3/4 is annotated as **potential** since only one part of the tools predicts the sequence as a virulence factor. Therefore, a confidence level of 1 and 2 should be taken above level 3 and 4.
|
|
|
|
|
|
**confidence levels:**
|
|
|
|
... | ... | @@ -32,7 +33,7 @@ The AMR report contains the prediction of antimicrobial resistance genes as well |
|
|
|
|
|
**example report:**
|
|
|
|
|
|
| ORF | ORF_ID | Virulence_HMM_prediction | Virulence_classified_prediction | Virulence_prediction | Signal_peptide | Virulence_confidence_level |
|
|
|
| ORF | ORF_ID | Virulence_HMM_prediction | Virulence_classifier_prediction | Virulence_prediction | Signal_peptide | Virulence_confidence_level |
|
|
|
|:---:| :---:| :---:| :---:| :---:| :---:| :---:|
|
|
|
| 1_1 | 0000000001 | pathogenic | pathogenic | pathogenic | Y | 1: Secreted Virulence factor |
|
|
|
| 1_2 | 0000000002 | negative | pathogenic | unclassified | N | 4: Potential Non-secreted Virulence factor |
|
... | ... | |