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. 2021 May 11;12:2684. doi: 10.1038/s41467-021-22700-4

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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. 2 — a Histogram of pairwise SNV distances between all discovery genomes, coloured by lineage comparison as per legend. Red lines mark SNV cut-offs used to define lineage, clade and subclade levels in genotyping scheme. b Boxplots of pairwise SNV distances (log scale, n = 1,873,081 pairwise distances) between discovery genomes at different hierarchical levels of the defined genotyping scheme. Boxes indicate the median (bold line), 25th to 75th percentiles (box), and the 5th and 95th percentile (whiskers), with outliers shown as points. Lineage, Clade and Subclade refer to the first three levels of the scheme. ‘4’ indicates the fourth level of the scheme (i.e., the final ‘1’ in 3.6.1.1), ‘5’ the fifth level (i.e., the ‘1’ in 3.7.30.4.1), and ‘6’ the sixth level (i.e., the final ‘1’ in 3.6.1.1.3.1).