The catalogue shows chimpanzees have a much more complex genetic history than humans, researchers said.
Researchers sequenced a total of 79 great apes, including chimpanzees, bonobos, eastern and western gorillas, orangutans and humans, as well as seven ape, 'LiveScience' reported.
The animals were wild- and captive-born individuals from populations in Africa and Southeast Asia.
"If we want to understand the genetic diversity of humans, we need to measure the genetic diversity of our nearest relatives," said study researcher Tomas Marques-Bonet, a geneticist at the Institut de Biologia Evolutiva in Spain.
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Marques-Bonet said human populations encountered a bottleneck when they left Africa, and have since expanded to colonise the whole planet. By contrast, chimpanzee populations have undergone at least two to three bottlenecks and expansions.
Researchers said the findings also settle a hot debate over the relationships among the four chimpanzee subspecies - Central chimpanzee, Western chimpanzee, Nigeria-Cameroon chimpanzee and Eastern chimpanzee.
"Now, we have the full genome for all four," Marques-Bonet said.
The new findings don't change humans' position in the great-ape evolutionary tree. Chimpanzees and bonobos remain humans' closest living relatives, splitting off from humanity about 5 million years ago, researchers said.
Humans' next-closest living relatives are gorillas, and orangutans are the most distantly related of the great apes.