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. 2018 Oct 4;19:366. doi: 10.1186/s12859-018-2353-5

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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. 3 — The effect of mouse reads in PDX samples. a: Integrative Genome Viewer (IGV) image of exon 5 of PTEN. Top panel shows mouse DNA mapped to the human reference genome, middle panel melanoma PDX sample M005.X1 with 25% mouse stroma and bottom panel melanoma PDX sample M029.X1 with 1% of mouse stroma. Each grey horizontal line represents a single sequence read. Base pair differences between human reference genome and sequence reads (SNV) are indicated with a color (depending on the base pair change). b: Overlap between somatic SNVs detected in PDX, with high percentage mouse stroma (M005.X1), and low percentage of mouse stroma (M029.X1). c. The edit distance of sequence reads from mouse DNA aligned to a human reference genome (top panel) and from human DNA mapped to a human reference genome (bottom panel)