According to "MUMmer4: A fast and versatile genome alignment system" (Plos Computational Biology 2018):
"First we aligned the current assemblies of human and chimpanzee, using the default nucmer4 options with 32 parallel threads ... We used human as the reference and chimpanzee as the query sequence. The human GRCh38 assembly contains 3.088 Gb of sequence while chimpanzee assembly, with 3.31 Gb, contains 7% more DNA. (Note that the chimpanzee genome is far less polished than human, and much of the extra DNA might be explained by haplotype variants or incompletely merged regions; thus the two genomes might be much closer in size than these numbers indicate.)
MUMmer had 2.782 Gb of the sequence in mutual best alignments, where each location in the chimp was aligned to its best hit in human and vice versa, with an average identity of 98.07%. The 1.93% nucleotide-level divergence found here is higher than the 1.23% reported in the original chimpanzee genome paper [25]. Our higher divergence is likely due to two factors: first, the 2005 report was based on 2.4 Gb of aligned sequence from older versions of both genomes, while ours is based on 2.782 Gb (16% more sequence) aligned between the current, more-complete versions of both genomes. Second, the original report used different methods, and may have counted fewer small indels than were counted in our alignments. Approximately 306 Mb (9.91%) of the human sequence did not align to the chimpanzee sequence, while 138 Mb (4.15%) of the chimpanzee sequence did not align to human. We detected 390 Mb in alignments where multiple sequences from chimpanzee aligned to the same location in human sequence and thus only one was chosen as the best alignment based on alignment identity. The genomes are very similar across all chromosomes, with the percent identity varying only slightly, from 97.5% to 98.2% for chromosomes 1-22 and X. Chromosome Y was an outlier at 96.6% identity over 84.6% of its length; however this is likely due to the fact that the chimpanzee Y chromosome is much less complete than the human Y."
A more recent 2020 paper (https://doi.org/10.3389/fgene.2020.00292) found:
"Since centromeres and unsequenced regions correspond to biological features, calculations including N’s and centromeres are listed in parentheses. Initial alignment coverage is 95.57% (90.9%) of the Hg38 reference, and identity within the alignment of 98.65%."
So, it seems that if you include the noncoding genome, the sequence identity between human and chimp genomes is around ~90–91%.
