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Table 4 Ancestral repeats - Posterior differences in first-order root distribution estimates

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

 

First-order Markov chain

X

Ï€ X|A

Ï€ X|C

Ï€ X|G

Ï€ X|T

A

0.3112

[0.3059; 0.3165]

0.1699

[0.1657; 0.1744]

0.2335

[0.2286; 0.2383]

0.2854

[0.2801; 0.2908]

C

0.3583

[0.3515; 0.3653]

0.2464

[0.2403; 0.2527]

0.0345

[0.0308; 0.0382]

0.3607

[0.3539; 0.3678]

G

0.2988

[0.2926; 0.3054]

0.1938

[0.1883; 0.1991]

0.2481

[0.2423; 0.2541]

0.2593

[0.2533; 0.2656]

T

0.2341

[0.2296; 0.2385]

0.1997

[0.1954; 0.2041]

0.2361

[0.2314; 0.2409]

0.3300

[0.3250; 0.3350]

 

First-order successive approximation

X

Ï€ X|A

Ï€ X|C

Ï€ X|G

Ï€ X|T

A

0.3176

[0.3117; 0.3237]

(11.40%)

0.1689

[0.1641; 0.1738]

(76.38%)

0.2241

[0.2186; 0.2295]

(1.28%)

0.2894

[0.2835; 0.2953]

(32.79%)

C

0.3632

[0.3540; 0.3724]

(41.70%)

0.2351

[0.2265; 0.2437]

(3.96%)

0.0262

[0.0241; 0.0283]

(0.00%)

0.3755

[0.3656; 0.3855]

(2.12%)

G

0.3130

[0.3055; 0.3205]

(0.62%)

0.1887

[0.1822; 0.1953]

(22.97%)

0.2307

[0.2238; 0.2375]

(0.07%)

0.2677

[0.2606; 0.2750]

(7.94%)

T

0.2399

[0.2343; 0.2455]

(11.93%)

0.1901

[0.1846; 0.1957]

(0.98%)

0.2333

[0.2276; 0.2390]

(44.57%)

0.3367

[0.3302; 0.3433]

(11.10%)

  1. Estimates (mean and accompanying 95% credibility interval) for the four sets of base frequencies at the ancestral root, for both first-order Markov chain approach and the successive approximation first-order approach using our context-dependent model with context-dependent model frequencies. Bayesian p-values are reported within brackets with the successive approximation estimates, shedding light on whether the root distribution probabilities are significantly different from one another under both approaches.