| Variant ID: vg0131446075 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 31446075 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CAACGTGACCCCCGCACCGGCGCCCTGAAGAGACAGGGAGCCGTCGAACTGCATCACCCAGTGGGCGGTGAGGCAGCTGCGAGGGGTCCGTGCTGGCCTC[G/T]
GGGATCGAGACGGGCTCGGGAGCCGGGGTCCACTCTGCCACAAAATCGGCGAGGGCCTGGCTCTTGATAGCGTGGCGTGGTTCAAAGTGCAAATCGAACT
AGTTCGATTTGCACTTTGAACCACGCCACGCTATCAAGAGCCAGGCCCTCGCCGATTTTGTGGCAGAGTGGACCCCGGCTCCCGAGCCCGTCTCGATCCC[C/A]
GAGGCCAGCACGGACCCCTCGCAGCTGCCTCACCGCCCACTGGGTGATGCAGTTCGACGGCTCCCTGTCTCTTCAGGGCGCCGGTGCGGGGGTCACGTTG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 28.90% | 2.70% | 0.76% | 67.63% | NA |
| All Indica | 2759 | 2.60% | 0.20% | 1.01% | 96.19% | NA |
| All Japonica | 1512 | 76.10% | 7.20% | 0.46% | 16.27% | NA |
| Aus | 269 | 1.10% | 0.00% | 0.37% | 98.51% | NA |
| Indica I | 595 | 4.40% | 0.00% | 0.67% | 94.96% | NA |
| Indica II | 465 | 0.60% | 0.20% | 0.22% | 98.92% | NA |
| Indica III | 913 | 0.50% | 0.10% | 1.75% | 97.59% | NA |
| Indica Intermediate | 786 | 4.70% | 0.50% | 0.89% | 93.89% | NA |
| Temperate Japonica | 767 | 87.60% | 0.10% | 0.13% | 12.13% | NA |
| Tropical Japonica | 504 | 70.20% | 20.20% | 0.79% | 8.73% | NA |
| Japonica Intermediate | 241 | 51.50% | 2.50% | 0.83% | 45.23% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 55.60% | 14.40% | 0.00% | 30.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0131446075 | G -> T | LOC_Os01g54660.1 | synonymous_variant ; p.Pro1420Pro; LOW | synonymous_codon | Average:14.857; most accessible tissue: Zhenshan97 flag leaf, score: 42.807 | N | N | N | N |
| vg0131446075 | G -> DEL | LOC_Os01g54660.1 | N | frameshift_variant | Average:14.857; most accessible tissue: Zhenshan97 flag leaf, score: 42.807 | N | N | N | N |