Table 1.

MtDNA contamination and mtDNA to nuclear DNA ratios in some DNA extracts and sequencing libraries used to study the Neandertal genome

Extract	N	H	Extract cont.	Library	N	H	Library cont.	Nuclear-mtDNA ratio
A	111	1	0.8% (0.0–4.9%)	A.1	67	8	10.7% (4.7–19.9%)	375
				A.2	4	0	0% (0.0–60.2%)	222
B	103	0	0.0% (0.0–3.5%)	BC.1	22	0	0.0% (0.0–15.4%)	186
C	112	0	0.0% (0.0–3.2%)	BC.2	1822	7	0.4% (0.2–0.8%)	157
D	152	8	5.0% (2.2–9.6%)	DEF.1	30	1	3.2% (0.1–16.7%)	419
E	100	1	1.0% (0.0–5.4%)
F	174	8	4.4% (1.9–8.5%)
Six extracts of Neandertal bone Vindija Vi33.16 (A–F) were prepared and analysed with respect to mtDNA contamination using PCR. N and H refer to Neandertal- and current human-like clones of mtDNA amplification products, respectively. These extracts were used to construct libraries used for sequencing. Library A.1 was constructed outside the clean room facility using standard 454 sequencing adapters and is published in Green et al (2006). The other libraries were constructed in the clean room using tagged adapters. Library designations refer to the extracts used to construct them. N and H refer to Neandertal- and current human-like mtDNA fragments, respectively. For each library the mtDNA to nuclear DNA ratios are given. For contamination estimates, 95% confidence intervals are given in parentheses.