Ahh...I see what you mean. What it says that is certain is a formula given in the article. It said that the probability can be calculated by p = ... + .... / ... x.... However, what I confused was that there is nothing in p related to items. Basically, there is only one p. So, I guess in this case that phase might mean every item has the same p then.All you have given us is "Each item is mutated with a certain probability" and told us it's in "an article". This does not help much in terms of our understanding of the situation. Unless this is an obscure mathematical term, is it possible they are talking about DNA/genes/organisms, for example (a very common field where the term mutate is used).
I think you are right that the meaning of "certain" here is "specified or numerically known"If you told us what the items are, it might help. Without more (con)text, it is hard to distinguish between their all having the same (given/specific/certain) probability, or whether they each have their own individual (specific/given/certain) probability. The rest of the text where you found this sentence may well provide information that makes it clear to the reader - that would be useful "context" (accompanying text, literally!) to look for. On its own, the sentence remains ambiguous.