From what I understand they test for some fraction, like 1/4 to 3/8 ish of total number of known Neanderthal SNPs. Dunno quite how representative that is of the total but I imagine probably a decent correlation.

However, around 2013-14 they either changed the number of SNPs they considered Neanderthal origin or their algorithm changed, and I was PISSED because I went from 95th percentile to 47th-ish myself.