Some mutations could have a chromatogram signal lesser than the reference one. This situation very often appears if the mix of cells (healthy and oncological) has been being analyzed. That means that the mutation signal could be different (due to a different concentration of oncological cells in a sample).
Look at the picture below. The signal of the "C" nucleotide (blue) is the highest. But there is a signal of the "T" nucleotide (red), which is high enough too. The second strongest signal is the thing we call Alternative mutation.
It's very important to make Alternative mutations clearly visible. To do this, you can use the Alternative mutations function. When the function is enabled and an alternative mutation fits to settings, the corresponding character will be replaced to the alternative one. The replacement cause the difference between the read and the reference character, that means, that the read character will be highlighted:
Alternative mutations settings are presented on the following picture:
Show alternative mutations - enable the Alternative mutations if checked, disable otherwise.
You can change font by Appearance–>Change characters font context menu item or by the main Actions–>Appearance menu item.