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S. aureus Clindamycin Resistance Genotype Data

Source: R/data.R
afp_CLI_public.Rd

Processed and filtered output from AMRFinderPlus run on Staphylococcus aureus genome assemblies from AllTheBacteria. This object was processed by import_amrfp and is used to investigate the genetic basis of clindamycin resistance.

Usage

afp_CLI_public

Format

afp_CLI_public A data frame with 43,287 rows and 42 columns:

  • id: Sample identifier (ENA run accession).

  • Protein id: Protein identifier (all NA).

  • Contig id: Assembly contig identifier.

  • Start, Stop: Start and stop positions of the AMR element on the contig.

  • Strand: Strand orientation (+ or -).

  • Element symbol: AMRFinderPlus element symbol (e.g. rpsJ_V57M, tet(M)).

  • Element name: Full descriptive name of the AMR element.

  • Scope: AMRFinderPlus scope (core or plus).

  • Type: Type of AMR element (e.g. AMR).

  • Subtype: Subtype of AMR element (e.g. POINT, AMR, ALLELEX).

  • Class: Antibiotic class (e.g. TETRACYCLINE, BETA-LACTAM, RIFAMYCIN).

  • Subclass: Antibiotic subclass (e.g. TETRACYCLINE, CEPHALOSPORIN, RIFAMPIN).

  • Method: Detection method (e.g. POINTX, BLASTX, ALLELEX).

  • Target length, Reference sequence length, Alignment length: Sequence length metrics (bp).

  • % Coverage of reference, % Identity to reference: Alignment quality metrics.

  • Closest reference accession: NCBI accession of the closest reference sequence.

  • Closest reference name: Name of the closest reference sequence.

  • HMM accession, HMM description: HMM-based annotation fields (all NA).

  • Hierarchy node: Gene hierarchy node name required for import_amrfp.

  • variation type: Type of genetic variation interpreted by import_amrfp.

Source

https://github.com/AllTheBacteria/AllTheBacteria