| Variant ID: vg0704649789 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 4649789 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 354. )
GTAGTGTACACAGCCAAATAATTGTAGTGCTCCAACTTCAGCTTTAACTTCTGCTTGAGAAGGTGGTTGCTGGGGATGTAAGAGCTTCGTCATCACCACG[C/G]
TTCCGCTGTCTTGACTCAACCATGGATCATGCCATGGTAAAGGACGATAACCTAAGGTCATCTCAGCTTTGTACCATGGAATTGCCGCTCTCCAAGGTGA
TCACCTTGGAGAGCGGCAATTCCATGGTACAAAGCTGAGATGACCTTAGGTTATCGTCCTTTACCATGGCATGATCCATGGTTGAGTCAAGACAGCGGAA[G/C]
CGTGGTGATGACGAAGCTCTTACATCCCCAGCAACCACCTTCTCAAGCAGAAGTTAAAGCTGAAGTTGGAGCACTACAATTATTTGGCTGTGTACACTAC
| 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 | 99.60% | 0.30% | 0.11% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 98.60% | 1.10% | 0.33% | 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 | 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 | 98.40% | 1.00% | 0.52% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 96.30% | 3.30% | 0.41% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0704649789 | C -> G | LOC_Os07g08940.1 | missense_variant ; p.Ser256Thr; MODERATE | N | Average:41.795; most accessible tissue: Zhenshan97 young leaf, score: 71.065 | N | N | N | N |
| vg0704649789 | C -> G | LOC_Os07g08934.1 | upstream_gene_variant ; 3036.0bp to feature; MODIFIER | N | Average:41.795; most accessible tissue: Zhenshan97 young leaf, score: 71.065 | N | N | N | N |
| vg0704649789 | C -> G | LOC_Os07g08950.1 | upstream_gene_variant ; 3004.0bp to feature; MODIFIER | N | Average:41.795; most accessible tissue: Zhenshan97 young leaf, score: 71.065 | N | N | N | N |
| vg0704649789 | C -> G | LOC_Os07g08930.1 | downstream_gene_variant ; 4860.0bp to feature; MODIFIER | N | Average:41.795; most accessible tissue: Zhenshan97 young leaf, score: 71.065 | N | N | N | N |