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. 2022 Apr 19;13:2047. doi: 10.1038/s41467-022-29584-y

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© The Author(s) 2022

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. 5 — A–C Average methylation levels (100 bp windows, introns included) with respect to PCGs (normalized to 5 kbp long) for the three sampled tissues (bud, catkin, and young leaf) by methylation context: A CG, B CHG, and C CHH. Dotted lines show genome-wide backgrounds, and TSS/TES = transcription start/end site. Supplementary Fig. 18 shows plots with introns excluded. D mCG for genes in deciles by gene length. E Average bud mCHH (20 bp windows) across representative repeat SFs (normalized to 400 bp long) in selected RepeatClassifier minor classes. F Relative density of representative repeat SFs around genes (100 bp windows). G Distribution of mCHH for representative repeat SFs (100 bp sliding disjoint windows). Genic = gene spans enlarged by 1 kbp on each end. H Partitioning of whole-genome base pairs into nine types of regions vs. mCHH coverage. Lower horizontal bars reflect relative size. Vertical bars show the percent of each genomic context covered by 100 bp windows with mCHH >25% or >90% in bud or young leaf. I mCHH by 3 nt subcontext (queried cytosine is underlined, and is the first nt of the three): left side 1 Mbp windows across all of chr. 2, right side across genes (normalized to 5 kbp length) in bud tissue.