| Variant ID: vg0128509560 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28509560 |
| 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: 54. )
CAGTGGACGATCACGCCGGCGACAGGCAATGCGGAGGGCTCGAGGGCAGATGAAGATGGTGATGAGGAAGAAGCTTAGGGCGAACGACGCGGCCAAGGCA[C/T]
CGAACAACATCATGGTGCTGCAGCATCCGGAGGCCGAGCTCGCCTGACGTCCGATCCGCCCGCCGCTCGCATCCGCATGTGCCTATCGCCGCTCCGCCCG
CGGGCGGAGCGGCGATAGGCACATGCGGATGCGAGCGGCGGGCGGATCGGACGTCAGGCGAGCTCGGCCTCCGGATGCTGCAGCACCATGATGTTGTTCG[G/A]
TGCCTTGGCCGCGTCGTTCGCCCTAAGCTTCTTCCTCATCACCATCTTCATCTGCCCTCGAGCCCTCCGCATTGCCTGTCGCCGGCGTGATCGTCCACTG
| 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 | 29.30% | 6.20% | 12.53% | 52.01% | NA |
| All Indica | 2759 | 2.10% | 7.60% | 20.99% | 69.30% | NA |
| All Japonica | 1512 | 83.90% | 5.20% | 0.40% | 10.45% | NA |
| Aus | 269 | 2.20% | 0.00% | 0.74% | 97.03% | NA |
| Indica I | 595 | 1.70% | 3.70% | 12.44% | 82.18% | NA |
| Indica II | 465 | 4.50% | 3.00% | 12.69% | 79.78% | NA |
| Indica III | 913 | 0.70% | 15.90% | 34.17% | 49.29% | NA |
| Indica Intermediate | 786 | 2.50% | 3.80% | 17.05% | 76.59% | NA |
| Temperate Japonica | 767 | 93.00% | 0.10% | 0.13% | 6.78% | NA |
| Tropical Japonica | 504 | 65.90% | 14.30% | 0.79% | 19.05% | NA |
| Japonica Intermediate | 241 | 92.90% | 2.50% | 0.41% | 4.15% | NA |
| VI/Aromatic | 96 | 13.50% | 0.00% | 1.04% | 85.42% | NA |
| Intermediate | 90 | 42.20% | 3.30% | 4.44% | 50.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128509560 | C -> T | LOC_Os01g49570.1 | missense_variant ; p.Gly5Asp; MODERATE | nonsynonymous_codon ; G5D | Average:37.821; most accessible tissue: Zhenshan97 panicle, score: 59.59 | unknown | unknown | DELETERIOUS | 0.03 |
| vg0128509560 | C -> DEL | LOC_Os01g49570.1 | N | frameshift_variant | Average:37.821; most accessible tissue: Zhenshan97 panicle, score: 59.59 | N | N | N | N |