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. 2021 Apr 7;593(7857):101–107. doi: 10.1038/s41586-021-03420-7

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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. 1 — a, Gaps in the GRCh38 chromosome 8 reference sequence. b, Targeted assembly method to resolve complex repeat regions in the human genome. Ultra-long ONT reads (grey) are barcoded with SUNKs (coloured bars) and assembled into a sequence scaffold. Regions within the scaffold sharing high sequence identity with PacBio HiFi contigs (dark grey) are replaced, improving the base accuracy to greater than 99.99%. The PacBio HiFi assembly is integrated into an assembly of CHM13 chromosome 8 (ref. ⁵) and validated. c, Sequence, structure, methylation status and genetic composition of the CHM13 β-defensin locus. The locus contains three segmental duplications (dups) at chr8:7098892–7643091, chr8:11528114–12220905 and chr8:12233870–12878079. A 4,110,038-bp inversion (chr8:7500325–11610363) separates the first and second duplications. Iso-Seq data reveal that the third duplication (light blue) contains 12 new protein-coding genes, five of which are DEFB genes (Extended Data Fig. 3g). d, Copy number of the DEFB genes (chr8:7783837−7929198 in GRCh38) throughout the human population, determined from a collection of 1,105 high-coverage genomes (Methods). Data are median ± s.d.