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Open Access Research article

The tendency to recreate ancestral CG dinucleotides in the human genome

Mingkun Li12* and Su-Shing Chen1

Author Affiliations

1 CAS-MPG Partner Institute of Computational Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 200000, Shanghai, PR China

2 Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D04103, Leipzig, Germany

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BMC Evolutionary Biology 2011, 11:3  doi:10.1186/1471-2148-11-3

Published: 5 January 2011

Additional files

Additional file 1:

Illustration of the reliability of the parsimony method to count the mutations at CpG related sites using three outgroups: chimpanzee/baboon/rhesus. The phylogeny of the four species used to infer mutations is shown in (a). Branch length indicates the rate of substitution per site at non-CpG positions. Substitution rates at CpG sites are 10 times higher than that at non-CpG sites, (b) scenario when the parsimony method is reliable, (c) scenario when the parsimony method is not reliable. Scenario (b) is 10 times more likely to be observed than scenario (c). Comparably, if chimpanzee, baboon, or rhesus is used as a single outgroup respectively, the probability ratio between (b) and (c) would be 2:1, 0.4:1, or 0.4:1.

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Additional file 2:

Derived-allele frequency estimation in CpG island regions.

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Additional file 3:

Number of SNPs and derived-allele frequency for different mutation types in different annotation categories in CEU.

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Additional file 4:

Number of SNPs and derived-allele frequency for different mutation types in different annotation categories in ASN.

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Additional file 5:

Derived-allele frequency for different mutation types in CEU.

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Additional file 6:

Derived-allele frequency for different mutation types in ASN.

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Additional file 7:

Number of SNPs and derived-allele frequency for different mutation types in the 9.4 Mb non-genic region.

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Additional file 8:

Derived-allele frequency estimated by different methods of inferring the mutation direction in the 9.4 Mb DNA alignment. Diamond symbol denotes the mean DAFs (± s.e.m).

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Additional file 9:

Phylogenetic tree for reliable back-mutations from CA to CG.

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Additional file 10:

Derived-allele frequency for different mutation types in recombination hotspots and coldspots in CEU.

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Additional file 11:

Derived-allele frequency for different mutation types in recombination hotspots and coldspots in ASN.

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