E. coli genotype example data

Genotypes called using AMRfinderplus (v3.12.8, DB 2024-01-31.1), sourced from AllTheBacteria project

Usage

ecoli_geno_raw

Format

ecoli_geno_raw

A data frame with 53591 rows and 10 columns representing genotyping results from AMRfinderplus:

Name

sample identifier

Gene symbol

gene symbol in NCBI refgene

Hierarchy node

node in NCBI hierarchy

Class, Subclass

drug class/es associated with marker (in NCBI refgene)

% Coverage of reference sequence,% Identity to reference sequence, Accession of closest sequence`

sequence match information

...

Source

https://github.com/ncbi/amr/wiki/Interpreting-results