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. 2023 Jul 8;14:4054. doi: 10.1038/s41467-023-39784-9

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© The Author(s) 2023

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 The number of CpGs in autosomes and sex chromosomes detected by using difference coverage of HG002 CCS reads. Values for 5×–70× are the average of 5 repeated tests. b Comparison of the number of CpGs detected by the total HG002 BS-seq (117.5×), ONT (65.8×), and CCS (71.0×) reads in repeats annotated by RepeatMasker, segmental duplications, and peri/centromeric regions of autosomes and sex chromosomes. CpGs covered by at least 5 reads are analyzed. c The number of CpGs in autosomes phased by using difference coverage of HG002 CCS reads. Values for 5×-70× are the average of 5 repeated tests. d Comparison of the number of CpGs phased by using the total HG002 BS-seq (117.5×), ONT (65.8×), and CCS (71.0×) reads in repeats annotated by RepeatMasker, segmental duplications, and peri/centromeric regions of autosomes. CpGs covered by at least 5 phased reads are analyzed. The standard deviation values of the multiple repeated tests of figures a and c are in Supplementary Tables 14–15. Values in the titles of Venn graphs in sub-figures b and d are the total number of CpGs in corresponding regions of the T2T-CHM13 genome. cov. coverage, SDs segmental duplications, cenSats peri/centromeric satellites. Source data underlying a and c are provided as a Source Data file.