... | ... | @@ -25,7 +25,7 @@ Within the report of the virulence factors the first columns contain information |
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**confidence levels:**
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| Virulence confidence level | HMM prediction | classifier prediction | SignalP |
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|:---:| :---:| :---:| :---:|
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|:---| :---:| :---:| :---:|
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|1: Secreted Virulence factor| +| +| + |
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|2: Non-secreted Virulence factor| +| +| - |
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|3: Potential Secreted Virulence factor| +/-| +/-| + |
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... | ... | @@ -46,11 +46,11 @@ For the prediction of toxins in particular two different reports are generated, |
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**confidence levels:**
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| Toxin confidence level | HMM prediction | SignalP |
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|:---:| :---:| :---:|
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|:---| :---:| :---:|
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|1: Secreted Toxin| +| +|
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|2: Non-secreted Toxin| +| - |
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**prediction report:**
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**example prediction report:**
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| ORF | ORF_ID | Number_of_hits | Toxin_prediction | Signal_peptide | Toxin_confidence_level |
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|:---:| :---:| :---:| :---:| :---:| :---:|
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... | ... | @@ -60,7 +60,7 @@ For the prediction of toxins in particular two different reports are generated, |
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Since the prediction of toxin is based on the presence of identified toxin domains, a second "library" report is generated containing information regarding the identified domains. As well as the ORF ID, the identified domain is reported (HMM_Name) with it's score and significance_evalue, it's full name, the database it is identified with, and a description of the domain.
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**library:**
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**example library:**
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| ORF_ID | ORF | HMM_Name | Score | Significance_evalue | NAME | Alternative_name | Database | Description |
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|:---:| :---:| :---:| :---:| :---:| :---:|:---:|:---:|:---:|
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... | ... | @@ -71,6 +71,8 @@ Since the prediction of toxin is based on the presence of identified toxin domai |
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If the complete pipeline is run a final master reports will be generated from the previously mentioned sub-reports. The PathoFact report will give for each sequence the Toxin prediction and confidence level, signal peptide prediction and Virulence prediction and confidence level, followed by the AMR prediction (resistance genes, categories and mechanisms) and finally the prediction of mobile genetic elements.
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**example report:**
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| ORF_ID | ORF | Contig_ID | Contig | Toxin_prediction | Toxin_confidence_level | Signal_peptide | Virulence_prediction | Virulence_confidence_level | ARG | ARG_SNPs | AMR_category | AMR_sub_class | Resistance_mechanism | MGE_prediction |
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|:---:| :---:| :---:| :---:| :---:| :---:|:---:|:---:|:---:|:---:|:---:|:---:|:---:|:---:|:---:|
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| 0000000007 | 2_4 | 0000000002 | contig_2 | pathogenic | 2: Non-secreted Toxin | N | pathogenic | 2: Non-secreted Virulence factor | - | - | - | - | - | chromosome |
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