| Variant ID: vg0420967564 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 20967564 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 116. )
CTGTGTTCGAGCCGCTGCTGTTCGAGGAGGTGAAGGCGCAGATCGTCCAGGGGCGCAGCGACGAGGAGGAAGGTGGGTGGGTGGGTGGCGCGCCCGATTT[C/T]
GTGTTGCCCCCCCAATTTGCTGTCGGTTTATTTAACAGTGTGTGTGTGTGTGTGTTGTTTTTCTCTCCCTTGCGTTTCTGTGTGGGCAGAGGCTGGGCAG
CTGCCCAGCCTCTGCCCACACAGAAACGCAAGGGAGAGAAAAACAACACACACACACACACACTGTTAAATAAACCGACAGCAAATTGGGGGGGCAACAC[G/A]
AAATCGGGCGCGCCACCCACCCACCCACCTTCCTCCTCGTCGCTGCGCCCCTGGACGATCTGCGCCTTCACCTCCTCGAACAGCAGCGGCTCGAACACAG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 75.90% | 0.70% | 13.67% | 9.75% | NA |
| All Indica | 2759 | 62.60% | 1.20% | 21.53% | 14.68% | NA |
| All Japonica | 1512 | 94.50% | 0.00% | 2.18% | 3.31% | NA |
| Aus | 269 | 98.50% | 0.40% | 0.37% | 0.74% | NA |
| Indica I | 595 | 84.90% | 0.30% | 9.75% | 5.04% | NA |
| Indica II | 465 | 70.30% | 0.20% | 21.29% | 8.17% | NA |
| Indica III | 913 | 47.80% | 2.20% | 26.40% | 23.66% | NA |
| Indica Intermediate | 786 | 58.50% | 1.10% | 24.94% | 15.39% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 86.70% | 0.00% | 5.75% | 7.54% | NA |
| Japonica Intermediate | 241 | 93.80% | 0.00% | 1.24% | 4.98% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 11.46% | 1.04% | NA |
| Intermediate | 90 | 88.90% | 0.00% | 7.78% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420967564 | C -> DEL | N | N | silent_mutation | Average:55.574; most accessible tissue: Zhenshan97 panicle, score: 85.254 | N | N | N | N |
| vg0420967564 | C -> T | LOC_Os04g34650.1 | upstream_gene_variant ; 2896.0bp to feature; MODIFIER | silent_mutation | Average:55.574; most accessible tissue: Zhenshan97 panicle, score: 85.254 | N | N | N | N |
| vg0420967564 | C -> T | LOC_Os04g34670.1 | intron_variant ; MODIFIER | silent_mutation | Average:55.574; most accessible tissue: Zhenshan97 panicle, score: 85.254 | N | N | N | N |