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Genetic Blueprints. To map the chimp genome, researchers used DNA from the blood of a male common chimpanzee (Pan troglodytes) named Clint, who lived at the Yerkes National Primate Research Center in Atlanta. Clint died last year from heart failure at the relatively young age of 24. A comparison of Clint's genetic blueprints with that of the human genome shows that our closest living relatives share 96 percent of our DNA.
Joshua links to a paper with a different way of describing the similarity between chimp and human genomes that accounts for insertions and deletions (INDELs) and the number is closer to 95%. The extra ~3.5% difference comes from INDELs found mostly in non-coding regions of the DNA. This extra 3.5% is the subject of the paper linked in the blogs, more on that later. No matter how you slice it the sequence differences between humans and chimps are not large. The above numbers from Chen et al.