Allele Balance Score
The Allele Balance score penalizes variations that occur at different frequencies in the forward and reverse directions because such variations are more likely to be the result of sequencing errors or alignment errors. The score is based on a Yate's chi-square test which is less likely than normal chi-square tests to reject the null hypothesis because of a lack of data, which, in this case, would be low coverage. The following value is calculated first:
where:
• #F = the number of forward reads
• #R = the number of reverse reads
• C = coverage
If this value is negative, then the value for Allele Balance score is set to one and no penalty is applied to the Overall Mutation score; otherwise, the score is calculated according to the following:
where:
• #F = the number of forward reads
• #R = the number of reverse reads