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Table 2 Results of lineage-specific positive selection analysis of the slpA gene

From: Surface layer proteins from virulent Clostridium difficile ribotypes exhibit signatures of positive selection with consequences for innate immune response

Branch Model P lnL Estimation of parameters PS Sites
1 A 3 −16283.290 p0 = 0.612 p1 = 0.379
p2 = 0.004 p3 = 0.002
Background:
ω0 = 0.081 ω1 = 1.000 ω2 = 1.000
Foreground:
ω0 = 0.081 ω1 = 1.000 ω2 = 999.0
BEB
3 > 0.99
2 A 3 −16287.406 p0 = 0.613 p1 = 0.379
p2 = 0.004 p3 = 0.002
Background:
ω0 = 0.081 ω1 = 1.000 ω2 = 1.000
Foreground:
ω0 = 0.081 ω1 = 1.000 ω2 = 999.0
BEB
3 > 0.99
3 A 3 −16273.156 p0 = 0.546 p1 = 0.325
p2 = 0.080 p3 = 0.047
Background:
ω0 = 0.077 ω1 = 1.000 ω2 = 1.000
Foreground:
ω0 = 0.078 ω1 = 1.000 ω2 = 305.086
BEB
52 > 0.50
11 > 0.95
1 > 0.99
4 A 3 −16254.536 p0 = 0.534 p1 = 0.326
p2 = 0.086 p3 = 0.052
Background:
ω0 = 0.076 ω1 = 1.000 ω2 = 1.000
Foreground:
ω0 = 0.078 ω1 = 1.000 ω2 = 49.513
BEB
51 > 0.50
21 > 0.95
8 > 0.99
7 A 3 −16267.493 p0 = 0.577 p1 = 0.364
p2 = 0.035 p3 = 0.022
Background:
ω0 = 0.082 ω1 = 1.000 ω2 = 1.000
Foreground:
ω0 = 0.082 ω1 = 1.000 ω2 = 999.000
BEB
15 > 0.50
8 A 3 −16286.517 p0 = 0.599 p1 = 0.369
p2 = 0.019 p3 = 0.012
Background:
ω0 = 0.080 ω1 = 1.000 ω2 = 1.000
Foreground:
ω0 = 0.080 ω1 = 1.000 ω2 = 65.618
BEB
9 > 0.50
1 > 0.95
9 A 3 −16280.189 p0 = 0.585 p1 = 0.366
p2 = 0.029 p3 = 0.018
Background:
ω0 = 0.080 ω1 = 1.000 ω2 = 1.000
Foreground:
ω0 = 0.081 ω1 = 1.000 ω2 = 998.998
BEB
11 > 0.50
1 > 0.95
11 A 3 −16289.170 p0 = 0.593 p1 = 0.372
p2 = 0.020 p3 = 0.013
Background:
ω0 = 0.082 ω1 = 1.000 ω2 = 1.000
Foreground:
ω0 = 0.081 ω1 = 1.000 ω2 = 998.975
BEB
3 > 0.50
12 A 3 −16288.187 p0 = 0.604 p1 = 0.367
p2 = 0.017 p3 = 0.010
Background:
ω0 = 0.080 ω1 = 1.000 ω2 = 1.000
Foreground:
ω0 = 0.080 ω1 = 1.000 ω2 = 998.952
BEB
6 > 0.50
1 > 0.95
13 A 3 −16280.744 p0 = 0.601 p1 = 0.341
p2 = 0.036 p3 = 0.020
Background:
ω0 = 0.079 ω1 = 1.000 ω2 = 1.000
Foreground:
ω0 = 0.079 ω1 = 1.000 ω2 = 32.021
BEB
18 > 0.50
1 > 0.99
14 A 3 −16287.185 p0 = 0.606 p1 = 0.376
p2 = 0.010 p3 = 0.006
Background:
ω0 = 0.079 ω1 = 1.000 ω2 = 1.000
Foreground:
ω0 = 0.081 ω1 = 1.000 ω2 = 67.858
BEB
3 > 0.50
2 > 0.95
15 A 3 −16278.296 p0 = 0.598 p1 = 0.354
p2 = 0.029 p3 = 0.017
Background:
ω0 = 0.077 ω1 = 1.000 ω2 = 1.000
Foreground:
ω0 = 0.078 ω1 = 1.000 ω2 = 8.993
BEB
12 > 0.50
4 > 0.95
1 > 0.99
18 A 3 −16277.205 p0 = 0.560 p1 = 0.337
p2 = 0.063 p3 = 0.038
Background:
ω0 = 0.078 ω1 = 1.000 ω2 = 1.000
Foreground:
ω0 = 0.077 ω1 = 1.000 ω2 = 94.127
BEB
45 > 0.50
7 > 0.95
2 > 0.99
  1. The table shown the number of residues predicted to be under positive selection for each site-specific model in the analyses. All models tested are displayed, along with number of parameters (P), log likelihood scores (L), estimates of parameters (where p = proportion of sites under a particular omega value, and ω = the ratio of non-synonymous substitution per non-synonymous site to synonymous substitution per synonymous site (DN/DS). The number of positively selected sites with a given posterior probability is also given