SNP’s are differences in genetic regions, not over the entire genome. As such, one can say based upon the supposed “miscalculation” that our GENETIC DNA is some 99.9% the same. That is not in any way a miscalculation that our GENOME DNA is only 99.5% the same.
Similarly, our GENETIC DNA is 98.5% similar to a chimpanzee, but over our entire GENOME we are some 96% similar to a chimpanzee.
It is common that people outside of science mistake the two numbers, and confuse and/or conflate the two. You are not the first to make this common mistake.
The end result of a genomic comparison puts our similarity with neanderthals at 99.5%, while any two human beings are 99.9% similar.
Exactly what one would expect if we diverged from them some 500,000 years ago, while any two human populations diverged, at most, 100,000 years ago. A 0.1% genomic DNA difference between any two modern humans is about a 0.5% genomic difference between a human and a neanderthal.
I see only one set of numbers reported here.
This report's language clearly equates the units of measure for SNPs, nucleotides and "base pairs":
"Nucleotide diversity is based on single mutations called single nucleotide polymorphisms (SNPs)."The nucleotide diversity between humans is about 0.1%, which is 1 difference per 1,000 base pairs.[4][5][6]
"A difference of 1 in 1,000 nucleotides between two humans chosen at random amounts to approximately 3 million nucleotide differences since the human genome has about 3 billion nucleotides."
This report clearly says that human genetic diversity amounts to 3 million out of 3 billion base pairs, or .1%.
The report on Neanderthals says they are "more than 99.5 percent identical, differing by only about 3 million bases".
There is no suggestion here that they are talking "apples and oranges".
No explanation of how 3 million bases amongst humans is somehow different from 3 million bases between Neanderthals and humans.
In both cases the denominator must be our 3 billion base pairs, making the identical nucleotides 99.9%.
So, as far as I can see, this is only a discussion of "apples".
Now if you wish to introduce "oranges" into the discussion, then you will have to explain just what an "orange" is, how it differs from an "apple" and, most important, how that somehow changes the denominator of 3 billion base pairs to some other number -- a number which mathematically reduces the identical DNA of Neanderthals & humans to 99.5%.
This will be interesting... ;-)
"It is estimated that approximately 0.4% of the genomes of unrelated people typically differ with respect to copy number. When copy number variation is included, human to human genetic variation is estimated to be at least 0.5% (99.5% similarity)."
Ooooops, there's an "orange", showing human DNA only 99.5% identical. Wouldn't want to get that mixed up with those other "apples," would we?