| Variant ID: vg0134962633 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 34962633 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 300. )
CTCCGCGATCGCCCACTCCATCGACCACAGCGTCGTCTCGATCGCTGCAAGCAACATGGTTAACGAAAATAAATTAAAAAGAAGAAGAAGAAACTGTTAA[C/G]
TGAACCGAGGCACGCGTACCGGCAACATTGATGTTCTCGACAATGTAGAGCACGTTGTCCTCGTTGATCTCCCCCTTCTGCTGCGCCTCCAGGATGTGAT
ATCACATCCTGGAGGCGCAGCAGAAGGGGGAGATCAACGAGGACAACGTGCTCTACATTGTCGAGAACATCAATGTTGCCGGTACGCGTGCCTCGGTTCA[G/C]
TTAACAGTTTCTTCTTCTTCTTTTTAATTTATTTTCGTTAACCATGTTGCTTGCAGCGATCGAGACGACGCTGTGGTCGATGGAGTGGGCGATCGCGGAG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | 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 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0134962633 | C -> G | LOC_Os01g60440.1 | upstream_gene_variant ; 3278.0bp to feature; MODIFIER | N | Average:72.527; most accessible tissue: Zhenshan97 flag leaf, score: 85.259 | N | N | N | N |
| vg0134962633 | C -> G | LOC_Os01g60460.1 | downstream_gene_variant ; 1510.0bp to feature; MODIFIER | N | Average:72.527; most accessible tissue: Zhenshan97 flag leaf, score: 85.259 | N | N | N | N |
| vg0134962633 | C -> G | LOC_Os01g60450.1 | intron_variant ; MODIFIER | N | Average:72.527; most accessible tissue: Zhenshan97 flag leaf, score: 85.259 | N | N | N | N |