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ST data for Staphylococcus aureus genomes for clindamycin vignette

Source: R/data.R
ST_data_CLI.Rd

Used to investigate the distribution of clindamycin resistance determinants across lineages. Assemblies were generated by the AllTheBacteria project and STs were determined based one the PubMLST scheme for S. aureus https://pubmlst.org/bigsdb/page/schemes, using bactopia run by Robert Petit.

Usage

ST_data_CLI

Format

ST_data_CLI A data frame with 37934 rows and 10 columns:

  • id: Sample identifier, imported from the #BioSample column in the raw input.

  • schema: Typing scheme used to determine sequence type (ST), in this case pubmlst_saureus.

  • ST: Sequence type, determined by PubMLST scheme for S. aureus.

  • arc allele: Allele identifier for the arc locus in the PubMLST scheme.

  • aroE allele: Allele identifier for the aroE locus in the PubMLST scheme.

  • glpF allele: Allele identifier for the glpF locus in the PubMLST scheme.

  • gmk allele: Allele identifier for the gmk locus in the PubMLST scheme.

  • pta allele: Allele identifier for the pta locus in the PubMLST scheme.

  • tpi allele: Allele identifier for the tpi locus in the PubMLST scheme.

  • yqiL allele: Allele identifier for the yqiL locus in the PubMLST scheme.

Source

https://github.com/AllTheBacteria/AllTheBacteria