A base by base comparison of chimp and human DNA

     It's been a sideline interest of mine to determine, genetically, how similar we really are to our closest cousins on the tree of life.  Since 2008 I've been using DNA to trace family history, revealing ethnic ancestry and the close relationships between seemingly unrelated surnames.  DNA analysis has traced our lineages back further, and yielded all kinds of diverse information unknown through paper records alone. 

     Of course the same methodology can be used to trace back further, beyond (and before) the time of anatomically modern humans.  We now have a several complete Neanderthal genomes, and DNA from the recently discovered Denisovan fossils in southern Siberia.  Genetic anthropologists also have the reconstructed genome of "Mitochondrial Eve," the maternal ancestor to all living humans.  We know this DNA sequence not because we have identified a fossil of such an ancestor, but rather we have traced back the nested mutations of all humans tested to date, and have reconstructed what this "original" genome looked like--at least in reference to mitochondrial DNA.
    Genetic anthropologists define "Mitochondrial Eve" as the most recent human ancestor of all living human populations today, and therefore automatically exclude Neanderthal, Denisovan, and all other archaic human populations that are now extinct.  Now we have genomes from these ancient ancestors.  Doesn't it make sense to determine genetically how they (and us) fit into a primate tree?  There are plenty of samples of chimp and bonobo DNA available as well. All the DNA required to construct a base by base comparison is available to the public.  Someone just needs to begin the painstaking work of documenting the comparison piece by piece, aligning the sequences, discovering the insertions and deletions, recording every deviation and accounting for every variation within the populations tested.
     This work is far to important to be overlooked. If the differences between chimps and humans are based in genetics, then these sequence differences between our species are especially significant. Once compiled, we'll better determine what exactly defines us as human genetically.  As we learn what every difference means, there will certainly be surprises, I suspect surprises both in regards to our similarities and our differences.
    Human mitochondrial DNA is composed of 16,569 base pairs, a manageable number, easily contained within a standard excel spreadsheet.  So far, I've compared the first 1,008 base pairs, and found 30 absolute base-pair distinctions between "us" and "them."  That's 97.02% similarity.  The 3% tagged as distinct, must cause all the difference.
    Actually 25 of those absolute base-pair distinctions were found within the first 576 bases, what geneticists called the Hyper-Variable Region (HVR).  The other five distinct bases were found in the region 577-1008, a coding region where DNA expresses proteins, and is therefore less susceptible to mutations.  Most of the DNA moving forward in the sequence (beyond marker 1008), is also coding. I suspect the current 97% similarity will increase, perhaps to 98% or 98.5%, as I complete the comparison of the full mitochondrial genome of 16,569 bases. 
    A chimp/human comparison of the Y-chromosome should also reveal some interesting results, however our Y-DNA is something on the order of 59 million base pairs long, so for now I'll focus on the mitochondria.   You can download a pdf of my work in progress, a base of base comparison (57 pages) of the first 1,008 nucleotides here.