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. 2019 Jul 26;9:10846. doi: 10.1038/s41598-019-47318-x

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© The Author(s) 2019

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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Nucleotide diversity and selection analysis of all accessions and subgroups. (a) Nucleotide diversity of all accessions. A 500 bp window size was used in this analysis. (b) Nucleotide diversity of subgroups. The sorted values were plotted in each group. Ind: indica; Niv: O. nivara; Ruf: O. rufipogon; Te_J; temperate japonica; Tr_J; tropical japonica. (c) Nucleotide diversity of cultivated rice and wild rice. (d) The reduction in nucleotides was calculated based on previous diversity analysis. The threshold of the top 5 percentile is indicated as a red dotted circle for indica and blue circle for japonica. The regions within the 2.5 percentile are considered candidate regions under selection. The genome position unit is kb.