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MicroBIGG-E for E.coli containing all chloramphenicol resistance genes

Source: R/data.R
MICROBIGGE_Ecoli_CHLR.Rd

Data from NCBI Pathogen Detection Microbial Browser for Identification of Genetic and Genomic Elements (MicroBIGG-E), containing all chloramphenicol resistance gene hits in Escherichia coli genomes, imported using import_amrfp().

Usage

MICROBIGGE_Ecoli_CHLR

Format

MICROBIGGE_Ecoli_CHLR A data frame with 95,776 rows and 27 columns:

  • id: BioSample.

  • drug, drug_class: Antibiotic agent and class, determined by parsing AMRFinderPlus subclass field in the downloaded file.

  • gene, node, marker: gene identifiers.

  • mutation: mutation within gene, parsed into HGVS nomenclature format from amr_element_symbol field in the downloaded file.

  • % Coverage of reference: % Coverage of reference.

  • % Identity to reference: % Identity to reference.

  • ...: Additional data columns from AMRFinderPlus #' @source https://www.ncbi.nlm.nih.gov/pathogens/microbigge/#chloramphenicol%20AND%20Escherichia