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Hi there,

I might need a screenshot to provide a more concrete answer.

Depending on the zoom level, the height of the reads may start to become so small that the color appears darker. You can adjust the zoom in the vertical direction directly by togging the little zoom mode button in the top-right of the plot that has a letter like "A", "F", "H" or "M" on it.

When the view zooms out to show the precomputed coverage, the Pile-Up plot will show per-base mismatch data as black so it is easy to identify areas of mutation.