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. 2016 May 11;6(7):2103–2111. doi: 10.1534/g3.116.030452

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Copyright © 2016 Johnson et al.

This is an open-access article 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 the original work is properly cited.

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Strand-biased selection of MMAP alignment positions by bowtie. Bias is shown as the overall ratio of top-strand aligned reads to bottom, based on simulated libraries from A. thaliana (n = 15). Boxplots show medians (horizontal bars), the 1st to 3rd quartile range (boxes), data out to 1.5 times the interquartile range (whiskers), and outliers (dots). Treatments sharing a common letter indicate groups that are not significantly different by nonparametric analysis (Kruskal-Wallis ANOVA with Dunn multiple comparison test, α = 0.05).