Table 1.

Results of Sequencing 12 Ancient Samples Before and After WISC

ID	Pre- or Postcapture	Read Pairs (#)	Read Pairs Discarded (Contain Adaptor) (#)	Individual Reads after Merging and Trimming (#)	Mapped Human Reads (%)	Fold Enrichment in # Mappeda	Unique Reads (%)	Fold Enrichment in # Uniquesb	Duplicate Reads (of Mapped) (%)	Precapture Reads Present in Postcapture (%)	Positions Covered (#)	Reads in Repeats (%)	Fold mtDNA Coverage	SNPs Overlapping with 1000G (#)
Bulgaria 1500–500 BC Tooth
V2	pre	1,390,960	98,697	1,331,130	0.3%		0.3%		9%		38,908	34%	0.01	5,281
	post	1,390,960	30,681	1,446,302	20.2%	70	2.7%	10	87%	46%	4,077,324	45%	0.4	40,583
P192-1	pre	819,844	118,493	705,234	4.3%		3.9%		9%		2,248,978	35%	0.3	30,081
	post	819,844	14,993	829,256	23.2%	6	7.8%	2	66%	52%	5,000,399	45%	2	67,221
T2G2	pre	1,596,526	20,644	1,633,734	0.05%		0.05%		14%		45,111	33%	0.3	597
	post	1,596,526	16,168	1,870,076	7.4%	159	0.3%	8	96%	15%	303,848	30%	16.1	4,068
K8	pre	1,817,223	76,872	1,980,966	1.0%		0.8%		14%		1,506,968	35%	0.06	19,960
	post	1,817,223	15,322	2,537,422	36.0%	48	3.4%	5	90%	90%	7,093,382	37%	0.3	94,394
Denmark ∼1350 BC Hair
M4	pre	1,000,000	210,491	828,494	0.5%		0.5%		7%		364,855	35%	0.06	5,115
	post	1,000,000	26,695	1,269,181	36.6%	114	2.2%	8	94%	70%	3,152,432	37%	0.6	40,340
Peru ∼900–1500 AD Bone
NA39	pre	1,000,000	50,534	1,192,685	1.1%		1.0%		14%		1,066,246	34%	5.3	14,751
	post	1,000,000	6,472	1,419,774	59.5%	62	2.1%	3	96%	56%	4,301,252	37%	19.9	40,048
NA40	pre	1,000,000	89,763	1,010,267	0.72%		0.7%		2%		642,917	36%	0.05	9,119
	post	1,000,000	24,214	1,191,241	26.5%	44	7.7%	13	70%	42%	17,253,987	38%	2.7	129,872
NA41	pre	1,000,000	76,485	1,358,860	0.30%		0.3%		10%		334,441	33%	0.01	4,621
	post	1,000,000	12,319	1,628,753	23.2%	92	1.3%	6	94%	75%	1,966,403	36%	0.6	26,118
NA42	pre	1,000,000	74,460	1,117,389	6.2%		4.9%		20%		5,197,492	36%	3.5	73,266
	post	1,000,000	14,847	1,341,546	41.0%	8	7.9%	2	80%	57%	16,609,757	37%	10.9	147,243
NA43	pre	1,000,000	116,780	966,013	0.18%		0.2%		11%		113,616	38%	0.01	1,553
	post	1,000,000	81,544	1,036,263	7.4%	45	0.6%	4	91%	68%	579,192	40%	0.4	6,337
NA47	pre	1,000,000	92,800	973,662	0.13%		0.1%		4%		93,784	38%	0.01	1,279
	post	1,000,000	32,741	1,107,880	9.1%	77	0.8%	7	90%	58%	833,067	42%	0.5	9,393
NA50	pre	1,000,000	126,605	1,001,135	0.035%		0.03%		3%		15,135	40%	0	217
	post	1,000,000	37,653	1,292,570	1.7%	61	0.3%	10	78%	24%	377,875	43%	0.5	3,062

The first four samples were adjusted to have identical numbers of pre- and postcapture reads, based on the number of reads obtained from MiSeq sequencing of the postcapture libraries. The last eight samples were adjusted to 1 million reads each for ease of comparison with the first four samples. Prior to mapping, overlapping paired-end reads were computationally merged, and adapters were trimmed from both merged and unmerged reads (note that the number of reads listed after merging and trimming includes both forward and reverse reads for pairs that were not merged). Mapped reads were filtered for mapping qualities ≥30. Overlap with repeats was determined by intersection with the RepeatMasker annotation of human genome repeats. 1000G: 1000 Genomes reference panel.

^aDoes not vary with amount of sequencing

^bVaries with library complexity and amount of sequencing