... | ... | @@ -11,9 +11,34 @@ 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 information regarding the Contig and ORF names and IDs, this is followed with the prediction of (if identified) the resistance gene (ARG) and if present any mutation contributing to this resistance (ARG_SNPs). If a resistance gene is identified, the resistance category (AMR_category), any sub classifications (AMR_sub_class) and the corresponding resistance mechanism (Resistance_mechanism) is given. Furthermore, it will report with which tool, rgi or deeparg, the resistance genes was identified with (Database). Finally the localization of the sequences will be reported (i.e plasmid, phage, chromosome, unclassified). If the result is ambiguous it will be reported as thus (i.e. ambiguous (plasmid/phage), ambiguous (phage/chromosome), ambiguous (plasmid/chromosome))
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** example report: **
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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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|:---:| :---:| :---:| :---:| :---:| :---:| :---:| :---:| :---: | :---:| :---:|
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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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## Virulence Factors
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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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|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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|4: Potential Non-secreted Virulence factor| +/-| +/-| - |
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** example report: **
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| ORF | ORF_ID | Virulence_HMM_prediction | Virulence_classified_prediction | Virulence_prediction | Signal_peptide | Virulence_confidence_level |
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|:---:| :---:| :---:| :---:| :---:| :---:| :---:|
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| 1_1 | 0000000001 | pathogenic | pathogenic | pathogenic | Y | 1: Secreted Virulence factor |
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| 1_2 | 0000000002 | negative | pathogenic | unclassified | N | 4: Potential Non-secreted Virulence factor |
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| 2_1 | 0000000003 | negative | negative | non_pathogenic | N | - |
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