SoftGenetics developed the Overall Mutation score to provide an empirical estimation of the likelihood that a given variant call is real and not an artifact of sequencing or alignment errors. This score is based on the concept of Phred scores, where quality scores are logarithmically linked to error probabilities as shown the figure below.

The Overall Mutation score is calculated according to the following equation:

The Overall Mutation score does not have a set maximum value; however, its value does depend on the coverage. For example, if all the optional scores are ignored for the calculation (value = 1), then the Overall Mutation score would be as shown below:

If any of the optional scores is less than one, then the Overall Mutation score is reduced. A low Overall Mutation score, however, does not mean that the variant is more than likely a false variant. The low score implies only that the variant cannot be called a true variant with absolute certainty. As a general guideline, if the coverage is high (500 to several thousand reads) and the data is bi-directional, then scores that are 5 and lower indicate that the variant is most likely false, while scores of 25 and higher indicate that the variant is most likely true. Even true variants that occur in a high percentage of reads can have low Overall Mutation scores if the coverage is low.

For detailed information about the scores that are used to calculate the Overall Mutation Score, see the following: