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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. 8 — a, Gene annotation of part of the RHCE gene. b, Genotyping performance in this region for three approaches (horizontal panels). The top panel, using the HPRC pangenome, shows the best performance with most variants being true positives (TP, blue points) based on the CMRG (v.1.0) truth set while more other methods have a higher number of false negatives (FN, red points). c, Allele frequency across 2,504 unrelated individuals of the 1KG. The HPRC-Giraffe-DeepVariant calls show higher frequencies. In particular, the gene-converted alleles, at about 25.406-25.410 Mbp, are observed at ~25% frequency, similar to estimates from the HPRC haplotypes (Fig. 5a–c). d,e, A pangenomic view of the gene-converted region showing 1 of 4 haplotypes in the HPRC pangenome supporting the non-reference alleles. The inclusion of this haplotype in the HPRC pangenome enables short sequencing reads, here from HG002, to map along this gene-converted haplotype.