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. 2017 Jul 5;8:59. doi: 10.1038/s41467-017-00050-4

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© The Author(s) 2017

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. 2 — Performance of different alignment schemes. a Overlap between the detected splice junctions by different schemes and their validation rate on reliable junctions in dbEST database⁷⁴. A reliable EST junction set consists of junctions supported by at least two ESTs. The sizes of the circles reflect the number of junctions called by each scheme. For each tool, the number of junctions called and the validation rates (in parentheses) are shown. Validation rates for each subset of junctions are also shown on the Venn diagram. b Read mapping analysis: distribution of mapping status of sequenced fragments (left) (for NA12878, MCF7, and SEQC samples, mapping status for paired-end reads are shown, while for hESC, the distribution reflects percentage of uniquely mapped (blue), multi-mapped (orange), and unmapped (red) single-end reads), distribution of number of soft-clipped bases in mapped fragments (middle), distribution of the number of mismatches in mapped fragments (right)