Different services use different reference populations than we do and choose to emphasize alternative streams of ancestry. All results are reductions of true human population genetic complexity to give value to the users, but the decisions made differ from service to service. Ideally, different services will give you different insights on the same question.
Why is my Neanderthal percentage different from National Geographic or 23andMe?
The method we use to estimate of your Neanderthal and Denisovan percentages depends on particular population genetic assumptions. The qualitative presence (>0%) or absence (0.0%) of Neanderthal ancestry is assured by all calculation methods, but your quantitative result varies based on these assumptions. The models we use to calculate your percentage are informed by the latest science, and this means the percentage may change slightly as new scientific discoveries are made. Insitome uses the latest science, so you can rest assured that our estimates are the most up-to-date available.