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1.
Figure 4

Figure 4. Nucleotide base frequencies at the 5′ end of the human contaminants present in the prehistoric Iberian lynx.. From: Fragmentation of Contaminant and Endogenous DNA in Ancient Samples Determined by Shotgun Sequencing; Prospects for Human Palaeogenomics.

The base composition is plotted as a function of distance from the 5′-end (N = 5.078 reads).

Marc García-Garcerà, et al. PLoS One. 2011;6(8):e24161.

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2.
Figure 6

Figure 6. Purine and pyrimidine frequencies at the 5′ and 3′ end of the Neandertal sequences.. From: Fragmentation of Contaminant and Endogenous DNA in Ancient Samples Determined by Shotgun Sequencing; Prospects for Human Palaeogenomics.

A–G and C–T have been grouped because of the low number of sequences available (N = 503). Nevertheless, the purine-associated fragmentation pattern can be seen.

Marc García-Garcerà, et al. PLoS One. 2011;6(8):e24161.

CitationFull text

3.
Figure 5

Figure 5. Nucleotide base frequencies at the 5′ end of the human Neolithic sequences.. From: Fragmentation of Contaminant and Endogenous DNA in Ancient Samples Determined by Shotgun Sequencing; Prospects for Human Palaeogenomics.

The base composition is plotted as a function of distance from the 5′-end. The depurination-based pattern can be seen, despite the small sample size (N = 1,117 reads).

Marc García-Garcerà, et al. PLoS One. 2011;6(8):e24161.

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4.
Figure 1

Figure 1. Sequence length distribution of the human contaminant sequences obtained from DNA extracted from bone samples of a Myotragus balearicus and an ancient lynx, and the putatively endogenous sequences from a Neolithic human and a Neandertal specimen obtained by 454-FLX pyrosequencing.. From: Fragmentation of Contaminant and Endogenous DNA in Ancient Samples Determined by Shotgun Sequencing; Prospects for Human Palaeogenomics.

The contaminant reads in Myotragus are possibly fragmented by the bleach treatment; nevertheless, a large overlapping in the distribution length can be observed among samples.

Marc García-Garcerà, et al. PLoS One. 2011;6(8):e24161.

CitationFull text

5.
Figure 2

Figure 2. Nucleotide base frequencies at the 5′ end of the Myotragus human contaminants, treated with a depurinating agent, bleach.. From: Fragmentation of Contaminant and Endogenous DNA in Ancient Samples Determined by Shotgun Sequencing; Prospects for Human Palaeogenomics.

The base composition is plotted as a function of distance from the 5′-end. Despite the small sample size (N = 337 reads), the pattern matches that previously described in ancient endogenous sequences, including Neandertals.

Marc García-Garcerà, et al. PLoS One. 2011;6(8):e24161.

CitationFull text

6.
Figure 3

Figure 3. Entropy at the 5′ end of the Myotragus, the human contaminants in the lynx, the Neolithic and the Neandertal reads, estimated using Shannon equation and 100 bootstraps.. From: Fragmentation of Contaminant and Endogenous DNA in Ancient Samples Determined by Shotgun Sequencing; Prospects for Human Palaeogenomics.

It can be seen that in Myotragus and Neolithic the entropy drops at the breaking point, indicating that sequences are not randomly fragmented, while in lynx and Neandertal, the entropy is stable (in the latter this is due to the small sample size of the Neandertal reads available).

Marc García-Garcerà, et al. PLoS One. 2011;6(8):e24161.

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