Table 2 Mean diversity measures for 48 STS loci
From: Genomic patterns of nucleotide diversity in divergent populations of U.S. weedy rice
| Â | Â | U.S. weedy rice populations | O. sativapopulations | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Statistic | Site type | O. rufipogon | All Weedy | SH | BHA1 | BHA2 | BRH | O. sativa | indica | Aus | temp. japonica | trop. japonica | aromatic |
θ W per Kb | All | 5.606 | 1.363 | 0.490 | 0.827 | 0.619 | 0.278 | 2.292 | 1.650 | 1.092 | 0.814 | 1.370 | 1.590 |
| Â | Silent | 7.787 | 1.694 | 0.638 | 0.933 | 0.695 | 0.349 | 2.985 | 2.216 | 1.401 | 1.050 | 1.694 | 2.353 |
| Â | Non-synonymous | 2.830 | 0.540 | 0.300 | 0.420 | 0.460 | 0.100 | 1.030 | 0.670 | 0.950 | 0.300 | 0.570 | 0.340 |
| Â | Synonymous | 9.015 | 1.896 | 0.585 | 0.736 | 0.424 | - | 3.204 | 2.225 | 1.308 | 0.263 | 1.716 | 3.510 |
θπ per Kb | All | 4.382 | 1.480 | 0.564 | 0.750 | 0.564 | 0.230 | 2.461 | 1.614 | 1.189 | 0.552 | 1.073 | 1.447 |
| Â | Silent | 6.354 | 1.848 | 0.692 | 0.829 | 0.657 | 0.311 | 3.278 | 2.179 | 1.568 | 0.650 | 1.337 | 2.176 |
| Â | Non-synonymous | 1.790 | 0.754 | 0.337 | 0.463 | 0.373 | 0.080 | 0.750 | 0.584 | 0.883 | 0.360 | 0.405 | 0.300 |
| Â | Synonymous | 7.019 | 1.312 | 0.505 | 0.650 | 0.476 | - | 4.228 | 1.982 | 1.026 | 0.345 | 1.257 | 3.029 |
Tajima's D | All | -0.729 | 0.220 | -0.441 | -0.177 | 0.042 | -0.266 | 0.232 | -0.026 | 0.092 | -0.754 | -0.773 | -0.408 |
| Â | Silent | -0.607 | 0.240 | -0.404 | -0.173 | 0.017 | 0.013 | 0.354 | 0.039 | 0.145 | -1.043 | -0.731 | -0.451 |
| Â | Non-synonymous | -0.724 | 0.358 | -0.155 | -0.132 | -0.185 | -0.197 | 0.339 | -0.132 | 0.277 | -0.816 | -0.685 | -0.214 |
| Â | Synonymous | -0.442 | -0.343 | -0.355 | -0.165 | 0.484 | - | 0.383 | 0.030 | 1.081 | -0.498 | -0.826 | -0.629 |
# of polymorphic STS (all sites) | 48 | 35 | 12 | 14 | 12 | 3 | 43 | 33 | 26 | 21 | 33 | 19 | |
# of polymorphic STS (silent sites) | 48 | 33 | 11 | 13 | 11 | 2 | 39 | 30 | 23 | 18 | 26 | 18 | |