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. 2022 Nov 19;13:7115. doi: 10.1038/s41467-022-34810-8

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© The Author(s) 2022

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. 3 — a Median similarity between TEs at TEMR breakpoints differs by TE type and mechanism (TEMR-HR: 354 Alu and 36 LINE-1 and TEMR-NHE: 43 Alu and 60 LINE-1). A two-sided Welch’s t-test was used to calculate the p-value. HR, homologous recombination; NHE, non-homologous repair; TE, transposable element; SV, structural variant; MEI, mobile element insertion, TEMR, transposable element-mediated rearrangement; LINE; long interspersed nuclear element. b Distribution of the breakpoint microhomology along the Alu consensus sequence. Alu elements consist of a left monomer (indigo), right monomer (green), RNA polymerase III promoter regions (gray A-Box, B-Box and A′-Box) and Adenosine Rich region (AR, purple). c Example of a 988 bp TEMR inversion (INV) with additional complex breakpoints (38 bp and 56 bp deletion (DEL) indicated in pink shaded sections) implicating replication-based mechanisms of variant formation. REF, reference genome (GRCh38).