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. 2024 Mar 21;25:75. doi: 10.1186/s13059-024-03216-8

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© The Author(s) 2024

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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 5 — Comparison of virulence and antibiotic resistance genes between Escherichia coli reference genomes isolated from the bladder and gut. A Boxplots analysis showing the comparison of counts of virulence and antibiotic resistance genes in the bladder and gut E. coli genomes. Each data point represents the counts of virulence and antibiotic resistance genes in each E. coli genome. B Boxplot analysis showing the comparison of counts of virulence and antibiotic resistance genes in different E. coli phylogroups. Phylogroup G was not shown here due to the low sample size. *, **, ***, **** indicated FDR < 0.05, 0.01, 0.001, and 0.0001, respectively. C Virulence and antibiotic resistance genes that were enriched in bladder E. coli genomes. D Virulence and antibiotic resistance genes that were enriched in gut E. coli genomes. Virulence and antibiotic resistance genes with an FDR of < 0.01 were displayed here