Reading the Ultimate X-men #15 I see that Xavier claims that "98% of all known mutants test positive for the X-FACTOR gene". Isn't the X-FACTOR gene what makes a mutant or does this simply include mutates (genetically altered individuals who wasn't born a mutant) too? Either way I think that it just sounds wrong.
If it does not include mutates then I guess there would be some other factor who defines a mutant. The only reasonably explaination, I can come up with, then would be that there are so few mutants out there that Wolverine, and the other "original" Weapon X mutates, counts as mutants but do not exhibit the X-FACTOR gene and is roughly 2% of all mutants.
If this includes mutates (such as Spider-man) 98% sounds pretty high.