Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations

Table 1 Samples and sequencing statistics

Individual identifier¹	Mitochondrial haplogroup	chrY haplogroup	Coverage	#SNPs	#Heterozygous
JuhoansiSan_HGDP01029	L0d1b1	A1b1a1a1	46.63	3,169,565	1,968,088
JuhoansiSan_HGDP01036	L0d1c1a	A1b1b2a	41.34	3,164,150	1,947,901
KhomaniSan_A403 *	L0d2a1	A1b1b2a	23.77	3,142,132	1,877,045
TuuSan_KB1	L0d1b2	B2b1b	25.87	3,157,740	1,961,736
MbutiPygmy_HGDP00456	L0a2b	E1b1a1a1c1a1c	31.25	3,081,528	1,897,510
MbutiPygmy_HGDP00982	L0a2b	E2b1a1	40.13	3,089,676	1,930,933
BakaPygmy_A405 *	L1c1a2b	E1b1a1a1c1a1c	32.38	3,083,814	1,986,951
SouthAfricanBantu_A402 *	L2a1f	E1b1a1a1d1c	22.72	3,001,336	1,972,901
WestAfricanBantu_A404 *	L3d3a1	E1b1a1a1c1a1c	32.53	2,982,337	1,957,325
Yoruba_HGDP00927	L1b1a	E1b1a1a1c1a1	41.93	2,915,392	1,883,193
Yoruba_HGDP00936	L2a12b	E1b1a1a1c1a1	42.78	2,941,205	1,920,680
Yoruba_NA18507	L1b1a3	E1b1a1a1c1a1	43.62	2,934,201	1,912,252
Mandenka_HGDP01284	L2c3a	E1a1	33.39	2,934,343	1,914,085
Mandenka_HGDP01286	L1b1a	E1b1b1a1a1	40.07	2,927,830	1,911,253
Laal_A409 *	L3e1c	B1	25.11	2,916,350	1,899,437
Dinka_DNK02	L2c1	E2a	36.81	2,880,056	1,856,506
Dinka_DNK07	L0a1a	A1b1b2b	46.81	2,880,930	1,844,312
EastAfricanBantu_A401 *	L2a1h	E1b1a1a1c1a1c	21.01	2,893,697	1,917,226
Toubou_A408 *	M1	T1a1	24.79	2,755,888	1,756,695
Saharawi_A406 *	L3b1b1	E1b1b1b1a	24.27	2,525,396	1,545,877
Libyan_A407 *	L2a1c	E1b1b1b1a	25.02	2,540,250	1,609,582
French_HGDP00521	T1a	I1a	35.14	2,398,449	1,434,940
Sardinian_HGDP00665	H3u	I2a1a1	32.55	2,396,919	1,429,346
Han_HGDP00778	A5b1b	O3a2c1a	35.65	2,418,780	1,361,654
Dai_HGDP01307	B4a1c4	O2	35.42	2,406,526	1,362,632

ISSN: 1474-760X