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PathoFact will generate a number of different reports within the PathoFact_report directory, dependent on which module has been run:
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PathoFact will generate a number of different reports within the **PathoFact_report** directory, dependent on which module has been run:
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1. AMR_MGE_prediction_{sample}_report.tsv **(AMR)**
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2. Virulence_prediction_{sample}_report.tsv **(Vir)**
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4. Toxin_gene_library_{sample}_report.tsv **(Tox)**
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5. PathoFact_{sample}_predictions.tsv **(complete)**
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For a detailed explanation of the reports please see below:
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## AMR
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The AMR report contains the prediction of antimicrobial resistance genes as well as mobile genetic elements (phage + plasmid) Within the report the first columns contain the Contig name, Contig ID (as given by PathoFact), ORF name and the ORF ID (as given by PathoFact).
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```markdown
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| Contig | Contig_ID | ORF | ORF_ID | ARG | ARG_SNPs | AMR_category | AMR_sub_class | Resistance_mechanism | Database | MGE_prediction |
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| contig_1 | 0000000001 | 1_1 | 00000000001 | vanRD | n/a | glycopeptide | glycopeptide antibiotic | antibiotic target alteration | DeepARG/RGI | plasmid |
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| contig_1 | 0000000001 | 1_2 | 00000000002 | - | - | - | - | - | - | chromosome |
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| contig_2 | 0000000002 | 2_1 | 00000000003 | gyrA | S81L | multidrug | fluoroquinolone antibiotic;nybomycin | antibiotic target alteration | RGI | chromosome | |
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\ No newline at end of file |