Table 4.
Ancestral repeats - Posterior differences in first-order root distribution estimates
| First-order Markov chain | ||||
|---|---|---|---|---|
| X | πX|A | πX|C | πX|G | πX|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 | πX|A | πX|C | πX|G | πX|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%) |
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.