... | @@ -67,4 +67,11 @@ Since the prediction of toxin is based on the presence of identified toxin domai |
... | @@ -67,4 +67,11 @@ Since the prediction of toxin is based on the presence of identified toxin domai |
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| 0000000001 | 1_1 | PF13091.1 | 34.2 | 1.2e-08 | PLDc_2 | - | PFAM | PLD-like domain
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| 0000000001 | 1_1 | PF13091.1 | 34.2 | 1.2e-08 | PLDc_2 | - | PFAM | PLD-like domain
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| 0000000003 | 2_1 | TIGR01263 | 210.1 | 3.4e-62 | 4HPPD | - | TIGR | 4-hydroxyphenylpyruvate dioxygenase
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| 0000000003 | 2_1 | TIGR01263 | 210.1 | 3.4e-62 | 4HPPD | - | TIGR | 4-hydroxyphenylpyruvate dioxygenase
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## PathoFact report
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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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| 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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| 0000000010 | 3_2 | 0000000003 | contig_3 | - | - | N | - | - | evgS | n/a | multidrug | fluoroquinolone antibiotic;macrolide antibiotic;penam;tetracycline antibiotic | antibiotic efflux | unclassified | |
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