Several variations from the reference sequence that occur very close together often indicates a region where variant calls are less reliable. The Mismatch score penalizes a specific variant call if other mismatched bases are found nearby. The software first looks for mismatches that occur in a minimum percentage of reads in the 10 bp region that is found on either of side of the variant that is being scored. The number of mismatches is used to calculate the score. If the number of nearby variations is < 3, then the Mismatch Score is set to one and no penalty is applied; otherwise, the score is calculated according to the following:

where N = the number of nearby mismatches.