Reproducibility materials accompanying "Beyond resistance-gene calling: a provenance-aware case study of ciprofloxacin genotype–phenotype discordance in African Escherichia coli"
This dataset contains the publication-facing reproducibility materials for a provenance-aware, bounded genomic case study of ciprofloxacin genotype–phenotype discordance in African Escherichia coli. The archive preserves public accession linkage, frozen analytical and reporting rules, software and database metadata, final evidence registries, machine-readable tables, figure sources and exports, and supplementary material. Raw sequencing data are not redistributed because the analysed genomes and reads are available through public sequence archives. The biological analysis was frozen before repository preparation; no candidate discovery, threshold optimisation, association testing or causal inference was introduced during repository assembly. The focal ciprofloxacin-resistant isolate remained mechanistically unresolved by sequence data alone. Four ompF-region noncoding substitutions and one coherent raw-read qnrB locus remained as sequence-level candidates without an established causal genomic explanation.