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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