Some places, not everywhere...
Just to avoid confusion, if you read this, it doesn't imply this.
We are suggesting that humans and orangutans are closer related than either to the chimpanzees in ~0.5% of the genome (and chimpanzees and orangutans are closer related than either to humans in another ~0.5%). That has to do with incomplete lineage sorting, and does not, in any way, imply that we as a species are closer related to orangutans than to chimpanzees.
Oh, and it doesn't really mean that orangutan is our closest living relative in ~0.5% of the genome either. It is just closer than chimpanzee, but the gorilla could be closer related to us in those positions, so...