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DASSIM genotype data (AMRFinderPlus)

Source: R/data.R
DASSIM_geno.Rd

The DASSIM dataset screened for Antimicrobial resistance genes (ARGs) using AMRFinderPlus v4.0.23

Usage

DASSIM_geno

Format

DASSIM_geno A data frame with 12414 rows and 31 columns:

  • id: Name.

  • gene: gene.

  • mutation: mutation.

  • node: node.

  • marker: marker.

  • marker.label: marker.label.

  • drug: drug.

  • drug_class: drug_class.

  • Protein id: Protein id.

  • Contig id: Contig id.

  • Start: Start.

  • Stop: Stop.

  • Strand: Strand.

  • Gene symbol: Gene symbol.

  • Element name: Element name.

  • Scope: Scope.

  • Type: Type.

  • Subtype: Subtype.

  • Class: Class.

  • Subclass: Subclass.

  • Method: Method.

  • Target length: Target length.

  • Reference sequence length: Reference sequence length.

  • % Coverage of reference: % Coverage of reference.

  • % Identity to reference: % Identity to reference.

  • Alignment length: Alignment length.

  • Closest reference accession: Closest reference accession.

  • Closest reference name: Closest reference name.

  • HMM accession: HMM accession.

  • HMM description: HMM description.

  • variation type: variation type.

Source

https://www.ebi.ac.uk/ena/browser/view/PRJEB26677

https://www.ebi.ac.uk/ena/browser/view/PRJEB36486