Genes

The human-ape gene comparison has always had me confused. I know next to nothing about genetics -- which may explain the confusion -- but I'm still puzzled over this:

People say that humans and apes (or bonobos or chimps or whatever) share 98% (or 97% or whatever) of their genes.

But this statement seems ambiguous. For example, say that humans and apes have exactly 100 genes. Which of the following would be true?

1. When you line up each of the 100 genes, they all match perfectly except for 2 of them. Gene 1 of the human perfectly matches Gene 1 of the ape. And so forth. But when you get to Genes 99 and 100, they are completely different. Thus, that is a 2% difference.

2. When you line up all 100 genes, they all differ from each other by a margin of 2%, give or take. Gene 1 of the human differs by 2% from Gene 1 of the ape. And so forth. Thus, there is a 2% difference, but that difference applies to 100% of the genes.

The chart at this Panda's Thumb post seems to imply the latter. Which is it? Or is it a mixture of the two? Or does the question even make sense?