ML tree of 456 mapped 7PET genomes

For variant calling, Illumina short reads were mapped against the novel reference strain CNRVC190243 genome. We mapped all 242 short read sets from 2018-2019 Yemeni V. cholerae isolates, provided read mapping were mapped at a sufficient depth (see below); we also mapped read sets from 218 contextual V. cholerae isolates linked to 7PET-T13 sublineage. Reads were trimmed with Trimmomatic, mapped to both CNRVC190243 reference chromosomes with BWA-MEM. Mapped genomes with an average read depth below 5x over the two chromosomes (n = 4, all from the novel Yemen read sets) were deemed of insufficient read depth and were excluded, for a final set of 456 mapped V. cholerae 7PET genomes. We used the software suite samtools/bcftools v1.9 to call variants with a minimum coverage of 10x read depth, excluding indels. Resulting consensus sequences were combined and processed with snp-sites (Page et al., 2016) to produce a single nucleotide polymorphism (SNP) alignment featuring 2,092 positions.