| Variant ID: vg0727002006 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 27002006 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCAAATATCAAACTTTGATGTCTGATATTTGTGGTAAGGGACAAATGTTTGGTTTCATTTATTTTTGGGTTGATACAGATTTACCCCCAACCTTATTGAT[C/T]
ACTTTGCTGTAAAATTTGCAAACTTTAATATAGCCCCTAAATTCAACACTGATTTGATACATGGAAATCTCATTGTTTGGTGTAGGATTTTGGAACAAAC
GTTTGTTCCAAAATCCTACACCAAACAATGAGATTTCCATGTATCAAATCAGTGTTGAATTTAGGGGCTATATTAAAGTTTGCAAATTTTACAGCAAAGT[G/A]
ATCAATAAGGTTGGGGGTAAATCTGTATCAACCCAAAAATAAATGAAACCAAACATTTGTCCCTTACCACAAATATCAGACATCAAAGTTTGATATTTGG
| 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 | 99.50% | 0.40% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 99.20% | 0.80% | 0.04% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 97.60% | 2.30% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0727002006 | C -> T | LOC_Os07g45194.1 | upstream_gene_variant ; 980.0bp to feature; MODIFIER | N | Average:54.425; most accessible tissue: Callus, score: 89.929 | N | N | N | N |
| vg0727002006 | C -> T | LOC_Os07g45260.1 | upstream_gene_variant ; 4617.0bp to feature; MODIFIER | N | Average:54.425; most accessible tissue: Callus, score: 89.929 | N | N | N | N |
| vg0727002006 | C -> T | LOC_Os07g45250.1 | intron_variant ; MODIFIER | N | Average:54.425; most accessible tissue: Callus, score: 89.929 | N | N | N | N |