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. 2023 Oct 26;8(11):2130–2141. doi: 10.1038/s41564-023-01494-9

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — a, k-mer genome containment scores of Illumina sequencing reads against the Pt76 (19ACT06) haplotypes. Identity is the percentage of bases that are shared between the genome and the sequencing reads. Shared k-mers is the percentage of k-mers shared between the genome and the sequencing reads. Two red lines indicate thresholds above which we consider a haplotype genome to be fully contained in the sequencing reads of an isolate (identity ≥99.99%, shared k-mers ≥99.5%). The A haplotype is fully contained in the sequencing reads of two isolates (19ACT06, 19QLD08) and the B haplotype is fully contained in the sequencing reads of 6 isolates (19ACT06, 19QLD08, 19ACT07, 19NSW04, 20QLD91, 20ACT90). The 20QLD87 isolate contains neither A nor B haplotypes. b, The phylogenetic tree against the combined haplotypes 19ACT06 A and B indicate three lineages. c, The phylogenetic tree against the 19ACT06 haplotype A shows that two isolates share the A haplotype. d, The phylogenetic tree against the 19ACT06 haplotype B shows that six isolates share the B haplotype. Bootstrap values of over 80% are indicated with blue circles.