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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. 7 — Performance of different variant calling (a–c) RNA editing (d, e) and RNA fusion (f) detection approaches. a Accuracy of detecting NA12878 high-confidence calls in NIST gold standard. The analysis is restricted to the expressed exons identified by Cufflinks or StringTie. b Overlap between variants predicted by GATK and SAMtools. c Distribution of the predicted mismatch types by GATK that are missed in NIST HC calls (in StringTie’s expressed exons) in different genomic regions. d Distribution of RNA editing events detected in different genomic regions for NA12878. For multiple-samples scheme, final editing sites include the rare variants in NA12878 that are supported by at least 3 out of 12 short-read samples in our analysis. For pooled-samples scheme, final editing sites include the rare variants in NA12878 that are supported by at least 20 reads in the pooled alignment. e Measurement of RNA editing detection accuracy when some portion of SNPs are hidden from GIREMI. FDR represent proportion of predicted edits that are among high-confidence genomic variants in NA12878. f Performance of different RNA fusion detection schemes on MCF-7 sample