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. 2019 Feb 6;9:1504. doi: 10.1038/s41598-018-37871-2

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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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Chimeric reads from mapping against viral reference are next mapped again human reference. The reads that aligned are in solid colour and the unaligned part is faded. If those chimeric reads mapped concordantly on the same human chromosome, then an integration event was called for this chromosome. Therefore the detection of integration events is based on chineric reads, mapped concordantly on viral reference, associated with low coverage and mapping on a single human chromosome.