How many base pairs of DNA represent the haploid human genome? How many base pairs of DNA represent the haploid chimpanzee genome? Assume the similarity between human and chimpanzee genomes is 97.5%. Based on 97.5% similarity how many base pairs do the chimpanzee and human genomes differ by? Solution 3 billion DNA base pairs represent haploid genome there are 24 base pairs of DNA in the haploid chimpanzee genome. humans and chimpanzee differ by 1 base pair .The humans have 23 base pairs and chimpanzee have 24.