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. 2021 May 24;12:3032. doi: 10.1038/s41467-021-23289-4

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© The Author(s) 2021

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. 4 — a The accuracy on PacBio Bordetella spp. data. b The accuracy on PacBio E. coli data. c The accuracy on ONT K. pneumoniae data. d The accuracy on ONT K. pneumoniae data with DNA methylation masked. e The legend of subfigures a–d RSM Random Subspace Maximization algorithm, SL single-locus algorithm, SLC single-locus algorithm with correcting sequence-context effect, and QV quality value. True positive rate = number of correctly detected SNVs/number of real SNVs. False discovery rate = 1 − number of correctly detected SNVs/number of detected SNVs. Source data are provided as a Source Data file.