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It's very important to make Alternative mutations clearly visible. To do this, you can use the function of the Alternative mutations functionmutation. When the function is enabled and an alternative mutation fits to settings, the corresponding character will be replaced to replaced with the alternative one. The replacement cause replacement causes the difference between the read and the reference character, that which means, that the read character will be highlighted:
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Show alternative mutations - enable the Alternative mutations if Alternative mutations and show them if checked, disable otherwise.
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and hide otherwise.
Threshold - how high the second strongest signal (corresponding to the firsts strongest signal) should be to be visible. Look at the picture below. The height of the second signal is 75% of the height of the first signal. That means, that the threshold value should be set to 75% (or below) to make this alternative mutation visible.
Update - click on this button to update the alignment corresponding to the set values.