Extended Data Table 8. Effect of filtering on amount of nuclear data available for analysis.

		All fragments			Deaminated fragments only
Panel	Target SNPs	No. SNPs hit ≥1×	% SNPs hit ≥1×	Average coverage	No. SNPs hit ≥1×	% SNPs hit ≥1×	Average coverage
Panels 1–3	2,051,902	1,038,619	50.6%	1.03	271,326	13.2%	0.16
Panel 4 subset*	954,849	361,681	37.9%	0.69	87,803	9.2%	0.11
Panels 1–4	3,801,245	1,685,891	44.4%	0.85	426,027	11.2%	0.13

^*The Panel 4 subset excludes the sites where only Denisova differs from the African panel. Note: Numbers differ from Extended Data Table 7 because only sites with base quality ≥20 were used.