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. 2023 May 10;617(7960):312–324. doi: 10.1038/s41586-023-05896-x

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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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 9 — A leave-one-out experiment was conducted by repeatedly removing one of the assembly-samples from the panel VCF and genotyping it based on the remaining samples. Plots show the resulting weighted genotype concordances for different variant allele classes. a, weighted genotype concordances are stratified by graph complexity: biallelic regions of the MC graph include only bubbles with two branches, and multiallelic regions include all bubbles with > 2 different alternative paths defined by the 88 haplotypes. b, results of the same experiment stratified by different genomic regions defined by the GIAB.