When we say we have 2% Neanderthal DNA (in Europe, less elsewhere), this is usually done with SNPs [0] which are used as a way to quickly differentiate between populations without sequencing the whole genome. In practice when companies like 23 and me tell you that you are 20% Pacific Islander it means that they have detected a number of single base-pair variations that is statistically compatible with that result, but it doesn't mean that Pacific Islanders and Scandinavians are not largely the same genetically, just that we know some easy places to look to tell them apart.
I should probably also mention that one interesting and politically relevant result of these population studies is that the concept of race doesn't really have a solid statistical base, because we have found the variation inside the group to be so large compared to the variation across groups, that there is no unambiguous way to cluster the human population.
[0] https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism