In popular science books and articles, I often see it stated that humans are >99 % similar to each other (wikipedia has it a 99.5 %, referencing Craig Venter and this PLOS Biology article) and ~96-99 % similar to chimpanzees or bonobos (Smithsonian Institute, National geographic). I have previously thought that this referred to the entire genome, but the wording on the Smithsonian Institute page I linked, makes it appear that it might refer to genes only, which also seems to be the case according to the answers to this post Do apes and humans share 99% of DNA or 99% of genes? What is the difference?.
How big are these percentages when comparing only the coding regions (exons) instead of entire genes, both within our species and compared to other species, such as primates? And, not as importantly, what are these numbers when including the entire genome with all non-coding DNA?