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. 2018 Dec 18;9:36. doi: 10.1186/s13100-018-0142-3

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© The Author(s). 2018

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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 Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Fig. 4 — Flowchart of findsoloLTR pipeline. The first step indexes the coordinates of proviruses of a HERV family in the reference genome. Average of read depth (of mapping quality score (MAPQ) equal or greater than 30 and base call accuracy equal to or greater than 20) at the HERV locus and at the flanking window extending ±250-bp from both LTRs are calculated. Percentage of the average read depth at each HERV locus to the average of the read depths at the two flanking 250-bp window is assessed. An estimated percentage equal to or greater than 50% is used to infer the presence of a provirus and the percentage lower than 50% infer the presence of a solo LTR allele