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Table 1 Ancestral repeats - First-order root sequence distribution

From: Modelling the ancestral sequence distribution and model frequencies in context-dependent models for primate non-coding sequences

 

Root

X

Ï€ X|A

Ï€ X|C

Ï€ X|G

Ï€ X|T

A

0.3114

[0.3063; 0.3162]

0.1682

[0.1641; 0.1723]

0.2355

[0.2307; 0.2400]

0.2849

[0.2799; 0.2899]

C

0.3760

[0.3697; 0.3826]

0.2439

[0.2380; 0.2496]

0.0069

[0.0057; 0.0083]

0.3733

[0.3668; 0.3799]

G

0.3014

[0.2954; 0.3077]

0.1926

[0.1873; 0.1981]

0.2448

[0.2389; 0.2504]

0.2612

[0.2554; 0.2672]

T

0.2287

[0.2241; 0.2331]

0.1966

[0.1924; 0.2012]

0.2451

[0.2405; 0.2497]

0.3296

[0.3247; 0.3347]

 

Rest of the tree

 

Ï€ A

Ï€ C

Ï€ G

Ï€ T

 

0.3114

[0.3015; 0.3217]

0.1676

[0.1610; 0.1739]

0.1730

[0.1665; 0.1798]

0.3480

[0.3374; 0.3582]

  1. Estimates (mean and accompanying 95% credibility interval) for the four sets of base frequencies at the ancestral root sequence and the set of base frequencies used in the remainder of the tree, for the context-dependent model with independent model frequencies and a first-order Markov chain at the ancestral root. The extremely low estimate for the probability of observing a G when the preceding base is a C, is a direct consequence of the CpG-methylation-deamination process in mammalian sequences. Note that the base frequencies used throughout the remainder of the tree differ from those when assuming a zero order Markov chain at the ancestral root sequence.
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BMC Ecology and Evolution

ISSN: 2730-7182

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