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Note that it is possible to achieve a similar effect by increasing a threshold of "Lowest maximal coverage", "Minimum coverage", or any similar filtering option (Figure 6). However, using "Average coverage" is the most straightforward: the shrinkage procedure uses log2(Average coverage) as an independent variable to fit the trend, so the x axis in the shrinkage plot is always log2(Average coverage) regardless of the filtering option chosen in Figure 6.

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