Predicting antimicrobial resistance phenotypes across 7,000 E. coli genomes

This dataset builds on previous work that collected 7,000 Escherichia coli genomes and associated phenotypes, published here. In this current pub we use this previously published dataset to explore the population genetics/phylogenomics captured in this dataset and perform linear genomic prediction on several antimicrobial resistance phenotypes. New files generated in this study extend presence/absence information to all loci in all 7,000 samples and are captured in subdirectory 'presence_absence'. All other files are copied from the previously published dataset, which are included here for ease of use.