Extended Data Table 1. Amount of data generated for Bacho Kiro Cave and Oase1 libraries for each SNP panel.

Table shows number of fragments after merging all of the sequencing libraries together for each specimen. Fragments longer than 35 bp with a mapping quality of at least 25 that overlapped different target sites were used for reporting the number of SNPs on target.

SNP panel	Specimen	Number of sequenced fragments	Number of fragments ≥35bp	Number of mapped fragments ≥35bp, MQ≥25	Number of mapped fragments on target ≥35bp, MQ≥25	Number of unique fragments on target ≥35dp, MQ≥25	Number of SNPs on target	% of SNPs on target	Number of deaminated fragments on target ≥35dp, MQ≥25	Number of SNPs on target	% of SNPs on target
390k	F6-620	42,944,497	31,607,676	10,664,089	5,417,563	3,610,135	372,571	94.61	879,932	294,287	74.73
	AA7-738	43,905,093	22,343,746	579,771	68,137	29,434	26,299	6.68	9,975	9,629	2.45
	BB7-240	48,679,210	32,531,469	5,428,952	1,666,056	893,179	311,587	79.13	307,661	191,684	48.68
	CC7-2289	16,999,931	12,126,017	51,649	19,810	9,097	8,659	2.2	1,828	1,816	0.46
	CC7-335	46,334,184	33,761,817	6,255,866	1,557,930	707,423	290,832	73.85	263,187	174,782	44.38
	BK1653	68,575,246	42,484,607	13,844,793	4,326,253	2,510,542	393,788	93.41	381,268	215,802	54.8
	Oasel	59,102,089	38,286,426	1,846,880	1,320,207	223,401	155,508	39.49	48,556	44,591	11.32
840k	F6-620	68,861,832	52,019,777	19,021,767	13,169,868	6,350,393	757,051	89.84	1,560,036	558,143	66.24
	AA7-738	62,671,011	46,507,342	790,242	478,993	64,038	58,037	6.89	21,929	21,376	2.54
	BB7-240	72,044,536	49,699,585	9,815,710	6,412,040	1,650,434	610,752	72.48	571,213	362,810	43.06
	CC7-2289	58,615,440	42,560,335	150,916	71,215	18,721	18,151	2.15	3,716	3,731	0.44
	CC7-335	68,794,275	51,231,565	10,390,207	6,599,859	1,290,666	561,737	66.66	479,284	326,926	38.8
	BK1653	66,744,975	49,155,219	14,281,786	9,230,491	3,840,020	694,592	82.43	594,397	356,855	43.35
	Oasel	56,745,317	37,030,590	3,031,789	1,920,548	368,252	270,601	32.11	80,709	75,569	8.97
1000k	F6-620	69,608,818	53,289,756	19,230,002	13,384,508	5,313,451	808,722	81.05	1,255,469	537,525	53.87
	AA7-738	61,551,239	42,095,902	677,982	398,801	41,360	39,660	3.97	13,567	13,677	1.37
	BB7-240	75,390,565	51,844,259	8,990,852	5,821,596	1,209,288	565,852	56.71	402,866	294,403	29.51
	CC7-2289	54,944,426	40,633,321	167,548	64,293	9,745	10,003	1	1,874	1,965	0.2
	CC7-335	72,464,739	54,221,955	10,907,573	6,935,567	1,062,963	536,521	53.77	383,734	286,514	28.72
	BK1653	72,387,295	49,998,398	14,529,900	9,637,535	2,911,357	726,130	72.77	434,351	305,619	30.63
	Oasel	59,348,519	38,586,583	2,347,235	1,434,618	272,943	221,020	22.15	56,420	55,309	5.54
Archaic admixture	F6-620	153,782,894	113,385,420	31,863,327	20,457,629	8,262,261	1,405,078	80.32	2,004,756	927,570	53.02
	AA7-738	74,474,294	55,404,191	741,606	316,366	72,962	67,495	3.86	22,510	24,423	1.4
	BB7-240	159,324,081	104,745,219	11,377,514	6,359,192	1,852,195	947,950	54.19	632,972	500,142	28.59
	CC7-2289	77,644,299	56,438,550	351,596	78,994	28,065	19,703	1.13	4,048	3,959	0.27
	CC7-335	156,715,471	112,448,992	14,570,648	8,134,133	1,650,897	907,904	51.9	606,177	488,615	27.93
	BK1653	159,168,237	111,693,225	22,866,297	13,162,057	4,591,355	1,257,365	71.87	702,281	533,274	30.48
	Oasel	52,319,743	33,767,952	1,719,613	890,910	306,637	278,234	15.9	64,447	71,112	4.06
“2200k”	F6-620	181,415,147	136,917,209	48,915,858	35,088,657	15,022,650	1,867,749	87.09	3,639,282	1,362,667	64.54
	AA7-738	168,127,343	110,946,990	2,047,995	1,328,039	131,193	123,265	5.75	44,375	44,610	2.08
	BB7-240	196,114,311	134,075,313	24,235,514	16,377,366	3,662,866	1,451,175	67.67	1,252,736	840,421	39.19
	CC7-2289	130,559,797	95,319,673	370,113	169,597	37,238	37,590	1.75	7,372	7,696	0.36
	CC7-335	187,593,198	139,215,337	27,553,646	18,181,311	2,967,786	1,353,413	63.11	1,093,477	776,283	36.2
	BK1653	207,707,516	141,638,224	42,656,479	29,863,646	9,098,112	1,728,159	80.59	1,387,333	874,287	40.77
	Oasel	175,195,925	113,903,599	7,225,904	4,722,435	850,586	646,646	30.15	183,143	177,336	8.27