119 Genome-wide analysis in E. coli unravels homoplasy associated with cefotaxime resistance coli genome to antibiotics. Thereby, this study grants insights into how chromosomeencoded antibiotic resistance evolves and, by combining genome-wide association studies with homoplasy analyses, provides potential strategies for future association studies into the causes of antibiotics resistance. Keywords: ampC, bioinformatics, Escherichia coli, genomics, whole-genome sequencing Data summary All data is available from the National Center for Biotechnology Information (NCBI) under BioProject number PRJNA592140. Raw Illumina sequencing data and metadata for all 171 Escherichia coli isolates used in this study is available from the NCBI Sequence Read Archive database under accession numbers SAMN15052485 to SAMN15052655. The full reference chromosome of ampC_0069 is available via GenBank accession number CP046396.1 and NCBI Reference Sequence NZ_CP046396.1. The scripts used to calculate homoplasy-based association analysis are available from GitHub (https:// github.com/JordyCoolen/hombaampC) under MIT license. 7
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