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. 2016 Mar;26(3):279–290. doi: 10.1101/gr.192971.115

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© 2016 Hsieh et al.; Published by Cold Spring Harbor Laboratory Press

This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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Figure 2. — Importance of using P-values to define candidates in the G2D analysis. Each point is a window of 500 single-nucleotide variants, and shading represents the density of points. The vertical dotted line and the horizontal dashed line are the top 0.5% significance cutoffs for the G2D and P-value distributions, respectively. Windows in Quadrant I are outliers in the G2D distribution but are not statistically significant when the effects of demography and genome architecture are controlled for. In Quadrant III are the many windows that are statistically significant even though their G2D values are modest.