There is a significant body of evidence that supports the idea that the chimpanzee is the closest genetic relative of humans. This was first determined through a large number of studies, some of which used genomic DNA hybridization to detect the level of sequence mismatches, as well as analyses of individual protein molecules. These early findings suggested that chimps and humans might typically have sequences that diverge from one another by only about 1 percent.
We now have large regions of the chimpanzee genome fully sequenced and can compare them to human sequences. Most studies indicate that when genomic regions are compared between chimpanzees and humans, they share about 98.5 percent sequence identity. The actual relationship depends on what types of sequences are being compared and the size of the comparison unit. A report published in the Proceedings of the National Academy of Sciences in 2002 suggested that under the most rigorous alignments, the match would be only 95 percent similarity overall. This resulted from the researchers treating changes involving small insertions and deletions of bases differently than previous investigators did over a very large region. A few questions still remain as to whether the chimpanzee genome sequence data are of high enough quality at this point for reliable comparison. In general, however, the overall conclusion is that most genes would share about 98.5 percent similarity. The actual protein sequences encoded by these genes would then typically be slightly more similar to one another, because many of the mutations in the DNA are "silent" and are not reflected in the protein sequence.
Given the very strong similarity between the chimpanzee and human genomes, many people wonder how we can be so different. At this point, there have been only a few isolated examples of genes that are functionally present in chimpanzees but not in humans, and vice versa. Thus, chimps and humans may share as many as 99.9 percent of the same genes with most of those genes being 99 percent similar in their sequences. Chromosomes do not exhibit big structural differences either. Although there are a number of small chromosomal changes that rearrange the order of genes on regions of those chromosomes, most of these are thought to leave gene function unchanged. It seems likely that the differences between human and chimpanzee phenotypes depend more on subtle regulatory changes more than on the presence of different genes. For instance, it may be that there are changes in some genes that alter the amount of protein produced by that gene at different stages in the development of a chimp versus a human. Alternatively, there may be small changes to the structures of the proteins (from the 1 percent divergence) that produce changes in how they interact with other cellular components and therefore subtly alter the pathways in which they are involved. At this point, we do not know which types of changes are responsible for the relatively big differences between chimps and humans.
It is worth noting that individual humans generally differ by about 0.1 percent genetically. Thus, chimps differ from humans by about 15-fold more, on the average, than humans do from one another. The 0.1 percent human divergence certainly results in significant variation in physical appearance and traits between different humans. Therefor, perhaps we shouldnt be so surprised that chimps could be 98.5 percent related to humans. Relatively small genetic changes can produce major phenotypic changes.