Extended data – Table 2.

Statistics of the genome sequence data used in the study and high confidence genotype calls. AvgDepth: average depth. Cov >1: fraction of the genome covered with at least 1 read. HomRef: Homozygote reference call, Het: Heterozygote call, HomAlt: Homozygote alternative call.

Sample	Region	Population	Reference	Gender	Avg. Depth	Cov >1X	HomRef	Het	HomAlt	Accessible
DNK02	Africa	Dinka	Meyer et al, 2012	Male	24.3	0.90	1,356,439,142	1,194,183	653,791	1,358,287,116
HGDP00456	Africa	Mbuti	Meyer et al, 2012	Male	20.3	0.90	1,333,191,748	1,198,421	741,996	1,335,132,165
HGDP00521	Europe	French	Meyer et al, 2012	Male	22.6	0.90	1,352,074,026	928,373	611,106	1,353,613,505
HGDP00542	SE Asia	Papuan	Meyer et al, 2012	Male	21.6	0.90	1,343,127,185	745,786	753,954	1,344,626,925
HGDP00665	Europe	Sardinian	Meyer et al, 2012	Male	19.9	0.90	1,334,884,400	908,557	606,234	1,336,399,191
HGDP00778	Han	Han	Meyer et al, 2012	Male	22.3	0.90	1,349,104,846	879,299	668,621	1,350,652,766
HGDP00927	Africa	Yoruba	Meyer et al, 2012	Male	26.7	0.90	1,361,142,931	1,221,258	664,333	1,363,028,522
HGDP00998	S. America	Karitiana	Meyer et al, 2012	Male	21.3	0.90	1,343,817,819	667,456	753,001	1,345,238,276
HGDP01029	Africa	San	Meyer et al, 2012	Male	26.9	0.90	1,362,464,890	1,273,369	774,869	1,364,513,128
HGDP01284	Africa	Mandenka	Meyer et al, 2012	Male	20.6	0.90	1,338,712,364	1,210,852	646,656	1,340,569,872
HGDP01307	SE Asia	Dai	Meyer et al, 2012	Male	23.8	0.90	1,350,414,031	879,716	660,662	1,351,954,409
HGDP00877	S. America	Mayan	This study	Male	13.2	0.90	1,130,447,805	673,358	547,730	1,131,668,893
BI16	S. America	Karitiana	This study	Female	23.4	0.89	1,278,750,988	664,223	684,479	1,280,099,690
Avar	SC Asia	Avar	Raghavan et al, 2013	Male	12.8	0.83	622,360,039	468,944	299,356	623,128,339
Indian	SC Asia	Indian	Raghavan et al, 2013	Female	15.9	0.89	861,422,992	643,238	389,937	862,456,167
Mari	SC Asia	Mari	Raghavan et al, 2013	Male	12.0	0.87	235,202,480	199,301	120,287	235,522,068
Tadjik	SC Asia	Tajik	Raghavan et al, 2013	Male	16.4	0.88	939,846,482	687,749	431,934	940,966,165
AusAboriginal	SE Asia	Australian Aboriginal	Rasmussen et al, 2011	Male	6.3	0.50	356,126,648	240,732	220,901	356,588,281
Saqqaq	Greenlander	Saqqaq	Rasmussen et al, 2010	Male	12.8	0.79	515,972,797	307,585	306,065	516,586,447
Anzick-1	N. America	Clovis	This study	Male	14.4	0.87	780,953,901	864,870	409,731	782,228,502