[clucas]

I just spent some time looking for the source, but I seem to have lost it, so take this all with a grain of salt, but based on some article I read:

My understanding of the "shared DNA" factoids is that they are based on a very rudimentary analysis of DNA sequences. The human-chimp 98.8% thing is "true" in that 98.8% of sequences that appear in the human genome also appear in the chimp genome. But this ignores other axes of differences: Humans may have multiple copies of certain sequences, while chimps only have one. Or certain sequences may appear in completely different parts of the genome in one or the other. And all of these differences are relevant.

TL;DR: 98.8% is true, but not really relevant for determining how "different" we are from chimps.