The mutation rate in this simulation is the probability per offspring for mutations to occur at all.

For example, if you set the mutation rate to 25%, then for each creature created through recombination of its two parents there is a 25% chance that its chromosome will additionally also be randomly mutated.

Note that this is just a probability and not a guarantee. The might be a generation with 0 or 100% mutated creatures. The larger your population size is, the closer the actual number of mutated creatures tends to be to what is predicted by the mutation rate.