Perhaps it's only counting 2% of the DNA that we didn't already share with Neanderthals prior to cross-breeding. As in, 2% of what had diverged from a common an

Perhaps it's only counting 2% of the DNA that we didn't already share with Neanderthals prior to cross-breeding. As in, 2% of what had diverged from a common ancestor. So, you could look at DNA of neanderthals and humans prior to cross-breeding events, and then eliminate everything in common, which would probably be the 99+% you would expect. Then take what's left and look at how much we picked up after cross breeding.