Expanded metadata for all samples presented in Fig 1.

Sample Statistics: “Input Genomes” refers to the number of copies of TP47 (tp0574) included in pre-capture library preparation. “Coverage” refers to the average deduplicated read depth at any position in the initial mapping of reads to the reference sequence NC_021508. “Length” is the length of the final consensus genome. “Number Ambiguities” and “Percent Ambiguities” refers to Ns in samples prior to masking. Sample Accessions: NCBI Biosample and assembly accessions per sample. Sample Metadata: “Tip Number” refers to sample position on the phylogenetic tree in Fig 1, with #1 at the bottom of the page. tp0136 MLST, tp0548 MLST, tp0705 MLST: Complete information on MLST alleles, including how novel sequences relate to the closest known match. (XLSX)