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. 2011 Sep 23;3(9):1777–1799. doi: 10.3390/v3091777

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© 2011 by the authors; licensee MDPI, Basel, Switzerland.

This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).

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Figure 3. — Recombination breakpoint distribution plot generated for IBV using the Recombination Detection Program 4 (RDP4) showing the detectable recombination breakpoints. The plot was constructed using a 200 bp window moved 1 nucleotide a a time along the length of the genome. Recombination breakpoint positions are shown as hash marks at the top of the figure. The dashed lines under the breakpoint positions represent 99% (upper) and 95% (lower) confidence thresholds for globally significant breakpoint clusters (defined as windows with more breakpoint positions than the maximum found in >95% of the permuted plots). The dark gray and white areas are 95% confidence and 99% confidence intervals, respectively, for local breakpoint clusters (defined as windows with more breakpoint positions than the maximum found in >99% of the windows at that location in permuted plots), and the black line indicates the breakpoint count within the 200 bp p window.