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. 2019 Dec 13;9:19123. doi: 10.1038/s41598-019-55636-3

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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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Intra- and inter-platform comparison of somatic variants. (A) Comparison of SNVs, Indels and structural variants between two replicates COLO-829 NovaSeq data (created using reads from mutually exclusive lanes) and between HiSeqX and NovaSeq data for the three cell lines. Orange bars (resp. purple) represent the number of variants called uniquely in the NovaSeq runs (resp. HiSeqX) and the grey bars correspond to the variants called in both samples. The numbers in the grey bars represent the concordance between the two samples, calculated as percentage of the (number of variants in the intersect)/(number of variants in the union). (B) Allele frequency of the variants called only in HiSeqX in purple, and for reference the allele frequency of variants called in both platforms in grey. (C) The decomposition in trinucleotide contexts of the SNVs called uniquely by each platform. Substitutions are represented by the pyrimidine of the mutated Watson-Crick base pair. (D) Similar to panel B but for variants uniquely called in NovaSeq. The AllSomatic callsets were used for panels B, C and D.