| Variant ID: vg0420967637 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 20967637 |
| 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: 286. )
TGGGTGGGTGGGTGGCGCGCCCGATTTCGTGTTGCCCCCCCAATTTGCTGTCGGTTTATTTAACAGTGTGTGTGTGTGTGTGTTGTTTTTCTCTCCCTTG[C/T]
GTTTCTGTGTGGGCAGAGGCTGGGCAGGACTGGCAGAAGGGGATTGTGGCGTCGTGCACCGAGTCGGAGGGGTTCCACAAGGTGTCCATGGCCGTGCTTG
CAAGCACGGCCATGGACACCTTGTGGAACCCCTCCGACTCGGTGCACGACGCCACAATCCCCTTCTGCCAGTCCTGCCCAGCCTCTGCCCACACAGAAAC[G/A]
CAAGGGAGAGAAAAACAACACACACACACACACACTGTTAAATAAACCGACAGCAAATTGGGGGGGCAACACGAAATCGGGCGCGCCACCCACCCACCCA
| 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 | 98.30% | 0.10% | 1.50% | 0.13% | NA |
| All Indica | 2759 | 99.40% | 0.10% | 0.47% | 0.00% | NA |
| All Japonica | 1512 | 96.00% | 0.00% | 3.70% | 0.33% | 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 | 98.90% | 0.20% | 0.86% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.10% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 98.70% | 0.30% | 1.02% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 90.10% | 0.00% | 8.93% | 0.99% | NA |
| Japonica Intermediate | 241 | 95.40% | 0.00% | 4.56% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 97.80% | 0.00% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420967637 | C -> DEL | N | N | silent_mutation | Average:53.836; most accessible tissue: Zhenshan97 panicle, score: 82.336 | N | N | N | N |
| vg0420967637 | C -> T | LOC_Os04g34650.1 | upstream_gene_variant ; 2969.0bp to feature; MODIFIER | silent_mutation | Average:53.836; most accessible tissue: Zhenshan97 panicle, score: 82.336 | N | N | N | N |
| vg0420967637 | C -> T | LOC_Os04g34670.1 | intron_variant ; MODIFIER | silent_mutation | Average:53.836; most accessible tissue: Zhenshan97 panicle, score: 82.336 | N | N | N | N |