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. 2023 Aug 25;14:5183. doi: 10.1038/s41467-023-40901-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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Fig. 3 — The phased BAM format was performed with the Integrative Genomics Viewer (IGV_2.7.2)^48–50 sorted with 10x Genomics linked-read haplotype tag (HP; haplotype of the molecule that generated the read). The region of large SVs in the parental (NC01) and B2M^-/-−2 can be phased into two strands with an HP tag (left panel). Agarose gel electrophoresis images of the PCR products amplified from NC01 genomic DNA and B2M knockouts (right panel). Primers a and b are designed to target the breakpoint junctions and primers a and b for the intact genomic region. The base coverage of large SVs in B2M^-/-−2 was visualized by Loupe. M is the size marker. Primers are listed in Supplementary Table 12. n = 3 replicates for PCR analysis. Source data are provided as a Source Data file.