Sanger Reads Settings

Some mutations may have a chromatogram signal weaker than the reference one. This situation often arises when analyzing a mix of cells (healthy and oncological). This means that the mutation signal could vary due to the different concentration of oncological cells in a sample.

Look at the picture below. The signal of the “C” nucleotide (blue) is the highest. However, there is also a signal for the “T” nucleotide (red), which is significant. The second strongest signal is what we call an Alternative mutation.

An Alternative mutation example

It is very important to make Alternative mutations clearly visible. To accomplish this, you can use the function of the Alternative mutation. When this function is enabled and an alternative mutation meets the settings, the corresponding character will be replaced with the alternative one. This replacement causes a difference between the read and the reference character, meaning the read character will be highlighted:

A visible Alternative mutation

The settings for Alternative mutations are presented in the following picture:

Settings of the function

Show alternative mutations – Enable Alternative mutations to display them if checked; otherwise, disable and hide them.
Threshold – Determines how strong the second strongest signal (relative to the first strongest signal) should be to be visible. In the picture below, the height of the second signal is 75% of the height of the first signal. This means the threshold value should be set to 75% (or below) to make this alternative mutation visible.

Update – Click this button to update the alignment according to the set values.