Back in 2018 I wrote a blog post entitled “How similar are human and chimpanzee genomes?” This reported my analysis of the data available at the time, concluding:
“The percentage of nucleotides in the human genome that had one-to-one exact matches in the chimpanzee genome was 82.34%.”
This was based on human and chimpanzee genome assemblies hg38 and pantro6.
Critics of my analysis said that this figure could not be trusted because both the human and chimpanzee genome assemblies were incomplete at the time.
Since then, much more complete genome assemblies have been published for both species.
Last month, the Nature paper “Complete sequencing of ape genomes” reported various comparisons of telomere-to-telomere genome assemblies.
When the latest human genome assembly was used as a target, and the latest chimpanzee assembly was aligned to it, the authors report gap divergence of 13.3% and single nucleotide variant divergence of 1.6% (these results can be found in Supplementary Figure III.11 and 12 respectively, for hg0002 vs PanTro3).
As I understand their methods, gap divergence was based on counting base (A, T, G or C) positions in the human genome that have no aligning base from the chimp genome in the whole genome alignment. Single nucleotide variant divergence was based on counting bases that align to a different base (e.g. an A aligning to a T). The authors calculated these divergences for each 1 million base segment of the human genome then averaged them all to get a genome-wide figure.
Adding the average gap divergence and average single nucleotide variant divergence together gives a total difference of 14.9%.
Thus, as I understand it, for the latest assemblies, 85.1 % of the nucleotides in the human genome have one-to-one exact matches in the chimpanzee genome.
This is clearly a slightly higher figure than the 82.3% that I calculated in 2018. But it is not far off.
The new result of 85.1% is just for autosomes (non-sex chromosomes). The same Nature paper reports 4.18% and 75.6% gap divergence and 1.15% and 3.98% single nucleotide variant divergence for X and Y chromosomes respectively.
At some point I would like to repeat exactly the same analysis as I did in 2018 on the 2025 data. But until then, the figures reported by the authors of the Nature paper provide a helpful comparison.