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. 2019 Sep 24;9:13775. doi: 10.1038/s41598-019-50302-0

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© The Author(s) 2019

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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Assembly of λgt10-lacZ transgene integration site using PacBio read data and NGS coverage data. There are approximately 29 copies of the λgt10 ori replication site³⁵. However, we show here that at least one copy (at the right breakpoint, downstream of the integration site) is non-functional. There are 18 SNVs that are constitutional in every copy of the transgene (shown by blue arrows in the top panel for one transgene monomer, and listed in Table 5). The breakpoints near the integration site were resolved by the use of long PacBio reads that map to both the λgt10 transgene sequence and mouse genomic sequence (bottom panel, colored text). The integration of the transgene comprised an unusual event involving (1) the deletion of ~465 Kbp of mouse genomic sequence, (2) the inversion of 370 bp of mouse genomic sequence from the downstream breakpoint to the upstream breakpoint, (3) the insertion of two partial truncated transgene monomers at either breakpoint, and (4) the insertion of shuffled transgene sequence at the downstream breakpoint as well as the insertion of several random nucleotides at the upstream breakpoint.