The positive rate of Fisher test (before/), mid-P test (between/), and our methodology (after/) under various simulated relative probability ratios.

The rows show a variety of different statistical cutoffs, and columns show a variety of relative probability ratios. The rejection frequency of our method is closer to the cutoff under the null hypothesis, and is more frequently able to find a difference when one exists. These simulations were based on simulated sequences of 1200 bp, with 1/16 of sequence positions in the focus context, and 3/16 in a control context, and with a background (control context) G to A mutation probability of 0.008.