Table 1.
All Isolates (n = 195) |
Length of sequenced region (in bp) |
No. of Poly-morphisms |
No. of Mutations |
No. of Alleles |
GC content |
π/siteb |
kc |
Tajima's Dd |
Syn.e |
Nonsyn.e |
dN/dSf |
---|---|---|---|---|---|---|---|---|---|---|---|
actA | 561 | 138 | 156 | 46 | 38.40 | 0.0593 | 33.26 | 0.78 | 59 | 70 | 0.32 |
gap | 569 | 16 | 16 | 18 | 40.00 | 0.0044 | 2.50 | -0.22 | 13 | 3 | 0.02 |
inlA | 771 | 105 | 109 | 50 | 40.90 | 0.0264 | 18.90 | 0.04 | 64 | 44 | 0.10 |
prs | 633 | 57 | 58 | 21 | 40.90 | 0.0209 | 13.25 | 1.01 | 58 | 0 | n/a |
purM | 714 | 161 | 185 | 49 | 42.00 | 0.0669 | 47.74 | 1.61 | 133 | 26 | 0.05 |
ribC | 639 | 121 | 131 | 34 | 39.60 | 0.0632 | 40.41 | 2.51 | 117 | 14 | 0.02 |
sigB | 666 | 75 | 82 | 22 | 38.70 | 0.0251 | 16.63 | 0.57 | 76 | 3 | 0.02 |
Lineage I (n = 87) |
|||||||||||
actA | 561 | 15 | 15 | 15 | 38.90 | 0.0058 | 3.24 | 0.25 | 6 | 9 | 1.06 |
gap | 569 | 2 | 2 | 3 | 40.10 | 0.0009 | 0.54 | 0.55 | 2 | 0 | n/a |
inlA | 771 | 17 | 17 | 12 | 41.00 | 0.0043 | 3.07 | -0.26 | 6 | 11 | 0.32 |
prs | 633 | 8 | 8 | 5 | 40.70 | 0.0018 | 1.14 | -0.70 | 8 | 0 | n/a |
purM | 714 | 10 | 10 | 13 | 42.40 | 0.0034 | 2.41 | 0.56 | 7 | 3 | 0.02 |
ribC | 639 | 18 | 18 | 8 | 39.00 | 0.0061 | 3.91 | 0.27 | 15 | 3 | 0.06 |
sigB | 666 | 9 | 9 | 8 | 38.60 | 0.0035 | 2.30 | 0.73 | 9 | 0 | n/a |
Lineage II (n = 93) |
|||||||||||
actA | 561 | 19 | 20 | 17 | 37.90 | 0.0064 | 3.58 | -0.25 | 11 | 9 | 0.42 |
gap | 569 | 11 | 11 | 12 | 39.80 | 0.0050 | 2.85 | 0.85 | 8 | 3 | 0.04 |
inlA | 771 | 54 | 54 | 25 | 41.30 | 0.0227 | 17.72 | 2.04 | 34 | 20 | 0.12 |
prs | 633 | 18 | 18 | 4 | 41.10 | 0.0017 | 1.05 | -2.02 | 18 | 0 | n/a |
purM | 714 | 128 | 140 | 22 | 41.60 | 0.0603 | 43.05 | 1.91 | 108 | 26 | 0.08 |
ribC | 639 | 86 | 88 | 16 | 40.20 | 0.0417 | 26.66 | 1.80 | 80 | 8 | 0.02 |
sigB | 666 | 27 | 27 | 4 | 38.60 | 0.0035 | 2.35 | -1.69 | 26 | 1 | 0.01 |
a The total of 195 includes 15 lineage III isolates, which were not analyzed separately.
b Average pairwise nucleotide difference per site.
c Average pairwise nucleotide differences per sequence.
d Tajima's D values significantly different from 0 (indicating deviation from standard neutral model) are marked in bold type.
e Syn., number of synonymous mutations; Nonsyn., number of nonsynonymous mutations.
f The dN/dS ratio was determined only when some nonsynonymous mutations were observed.