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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 4. — Effect of UDG/endoVIII treatment on all nucleotide misincorporation rates and on C→T rates at CpN dinucleotides along Neandertal DNA sequences. 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 identified that aligned best to the complete mtDNA sequence of this bone AM948969 (947 and 1084 sequences for the no repair and UDG/endoVIII conditions, respectively, left panels) and to the human nuclear genome sequence hg18 (242 070 and 286 737 sequences, right panels). (a) All 12-nt mismatch frequencies are plotted as a function of position along the aligned fragments for the no repair and UDG/endoVIII conditions. (b) The rate of C→T misincorporations along DNA fragments is shown separately for the four dinucleotides that contain cytosine in the 5′-position.