| Variant ID: vg0420967638 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 20967638 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: Unkown |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 277. )
GGGTGGGTGGGTGGCGCGCCCGATTTCGTGTTGCCCCCCCAATTTGCTGTCGGTTTATTTAACAGTGTGTGTGTGTGTGTGTTGTTTTTCTCTCCCTTGC[G/T]
TTTCTGTGTGGGCAGAGGCTGGGCAGGACTGGCAGAAGGGGATTGTGGCGTCGTGCACCGAGTCGGAGGGGTTCCACAAGGTGTCCATGGCCGTGCTTGA
TCAAGCACGGCCATGGACACCTTGTGGAACCCCTCCGACTCGGTGCACGACGCCACAATCCCCTTCTGCCAGTCCTGCCCAGCCTCTGCCCACACAGAAA[C/A]
GCAAGGGAGAGAAAAACAACACACACACACACACACTGTTAAATAAACCGACAGCAAATTGGGGGGGCAACACGAAATCGGGCGCGCCACCCACCCACCC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of Unkown(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.90% | 0.00% | 0.44% | 1.61% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 94.40% | 0.00% | 1.39% | 4.23% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 86.30% | 0.00% | 3.57% | 10.12% | NA |
| Japonica Intermediate | 241 | 93.40% | 0.00% | 1.24% | 5.39% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 0.00% | 10.42% | NA |
| Intermediate | 90 | 97.80% | 0.00% | 0.00% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420967638 | G -> T | LOC_Os04g34650.1 | upstream_gene_variant ; 2970.0bp to feature; MODIFIER | N | Average:53.836; most accessible tissue: Zhenshan97 panicle, score: 82.336 | N | N | N | N |
| vg0420967638 | G -> T | LOC_Os04g34670.1 | intron_variant ; MODIFIER | N | Average:53.836; most accessible tissue: Zhenshan97 panicle, score: 82.336 | N | N | N | N |