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. 2023 Jun 26;20(8):1213–1221. doi: 10.1038/s41592-023-01914-y

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© The Author(s), under exclusive licence to Springer Nature America, Inc. 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. 4 — a, MAP-graph principal bundle decomposition shows the repeat number changes of the OPN1LW, OPN1MW1/2/3 to FLNA loci. Auxiliary tracks are as follows: top OPN1LW, middle OPN1MW1/2/3 and bottom FLNA. b, The upper left image displays a dot plot comparing the HG002 assembly to GRCh38 over a 5 Mb region containing the DAZ1/2/3/4 loci, highlighting an inversion between DAZ1/2 and DAZ3/4. The image on the right provides a detailed view of the rearrangements at the gene scale level, with four tracks indicating the local matches to DAZ1/2/3/4 from top to bottom. Comparison to GRCh38’s DAZ2 reveals that the HG002 assembly is missing a segment (roughly 10 kb) of the darker green. The intergenic region between DAZ3 and DAZ4 also displays a rearrangement that can be described as an incomplete inversion or separate insertions and deletions. The bottom image shows a rearrangement at the whole locus, including all DAZ1/2/3/4 over a 5 Mb region. The principal bundle decomposition reveals the different inverted structure of the HG002 T2T assembly and the HG1258 assembly compared to GRCh38. c, MAP-graph diffusion entropy versus repetitiveness survey for the 385 GIAB challenge CMRGs.