Table 1.

Allele Frequencies of Regionally Stratified Variants Shared with High-Coverage Archaic Genomes but Not Found in African Populations

Position	Size (bp)	Variant	EUR	CSA	EA	ME	AMR	OCE	Gene	PBS Rank (%)	Neanderthal	Denisova
chr1: 64992619–64992994	375	DEL	0	0	0	0	0	0.44	JAK1a	98.4	REF	DEL
chr2:3684113–3690212	6,099	DEL	0.02	0.003	0.05	0.03	0	0.26	ALLCa	90.3	DEL Vindija	REF
chr3:177287011–177292441	5,430	DEL	0	0	0	0	0	0.39	LINC00501	97.7	REF	DEL
chr8:23124835–23130567	5,732	DEL	0	0.02	0	0	0	0.36	TNFRSF10D	96.8	DEL	REF
chr8:23134649–23164796	30,147	DUP	0	0	0	0	0	0.48	TNFRSF10Da	99	DUP	DUP
chr11:60460681–60461880	1,199	DEL	0	0	0.02	0	0.17	0	MS4A1a	–	DEL	REF
chr12:101882163–101883377	1,214	DEL	0.02	0.08	0.32	0.01	0.01	0.33	DRAM1a	–	DEL	REF
chr12:104799951–104803150	3,199	DUP	0.003	0.009	0	0.01	0	0.33	SLC41A2a	96.8	DUP	REF
chr15:34920811–34925992	5,181	DEL	0	0	0	0	0	0.63	AQRa	99.8	REF	DEL
chr16p12.2	complex	DUP	0	0	0	0	0	0.82	multiple	99.99	REF	DUP
chr16:75059992–75060055	63	DEL	0	0	0	0	0	0.34	ZNRF1a	96.4	DEL	DEL
chr17:3038851–3041981	3,130	DEL	0	0	0	0	0	0.16	RAP1GAP2	86.1	DEL	DEL
chr19:42529806–42531042	1,236	DEL	0	0	0	0	0	0.54	CEACAM1a	99.4	DEL	DEL

Neanderthal refers to both published high-coverage genomes. The deletion within ALLC is only shared with the Vindija Neanderthal. The TNFRSF10D duplication common in Oceania is also present at low frequency (5%) in Africa. Africans do not have both deletion and duplication variants, which are in linkage disequilibrium in Oceanians (r² = 0.48). The duplications at chr16p12.2 at high frequency in Oceania (82%) are part of a complex structural variant (Figures S6 and S7). Population branch statistic (PBS) rank is presented for stratified variants common only in Oceania. REF, Reference; DEL, Deletion; DUP, Duplication; EUR, Europe; EA, East Asia; ME, Middle East; AMR, America; CSA, Central South Asia; OCE, Oceania.

^aA variant that lies within or intersects a gene; otherwise, the nearest gene is presented.