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. 2009 Dec 22;38(6):e87. doi: 10.1093/nar/gkp1163

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© The Author(s) 2009. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 6. — Effects of UDG/endoVIII treatment and multiple-pass sequencing on ancient DNA sequence error rate. DNA from a Neandertal bone was subjected to 454 adaptor ligation after enzymatic repair with PNK and T4 polymerase (no repair) as well as those enzymes plus UDG and endoVIII. Approximately 12 million sequences were generated on the Illumina GAII platform for each condition, and sequences were aligned to the complete mtDNA sequence of this bone and to the human nuclear genome (hg18). Overall rates of each alignment mismatch type, and total mismatch rates, are shown for sequences from each condition, plus the result achieved when only fragments that were sequenced more than once (‘multi-pass’) are considered. For nuclear DNA, positions of CpG in the reference were excluded from the analysis since misincorporations remain frequent at these sites even after UDG/endoVIII treatment (see Figure 4).