| Variant ID: vg0725680887 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 25680887 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCTAGAAAATATCTTCTATGCAATGATGATTACAGAACAGAGTATTTCAAAGGTCCATTCGTTTCATTGACTCGTCCAAGTTCTGTAAAAAAAAAATATA[A/T]
ATAGTTCAAATGATCAATATTTCTAAGCAAAAAAAAGATACATTTTTTCTAAAATAAAGCATTAATAAAGCTTTCTAAAATATTGAATTATTGGTGATGA
TCATCACCAATAATTCAATATTTTAGAAAGCTTTATTAATGCTTTATTTTAGAAAAAATGTATCTTTTTTTTGCTTAGAAATATTGATCATTTGAACTAT[T/A]
TATATTTTTTTTTTACAGAACTTGGACGAGTCAATGAAACGAATGGACCTTTGAAATACTCTGTTCTGTAATCATCATTGCATAGAAGATATTTTCTAGC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.70% | 0.30% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 99.50% | 0.40% | 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 | 98.60% | 1.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0725680887 | A -> T | LOC_Os07g42885.1 | upstream_gene_variant ; 4142.0bp to feature; MODIFIER | N | Average:37.281; most accessible tissue: Zhenshan97 flower, score: 61.872 | N | N | N | N |
| vg0725680887 | A -> T | LOC_Os07g42890.1 | downstream_gene_variant ; 1039.0bp to feature; MODIFIER | N | Average:37.281; most accessible tissue: Zhenshan97 flower, score: 61.872 | N | N | N | N |
| vg0725680887 | A -> T | LOC_Os07g42900.1 | downstream_gene_variant ; 2386.0bp to feature; MODIFIER | N | Average:37.281; most accessible tissue: Zhenshan97 flower, score: 61.872 | N | N | N | N |
| vg0725680887 | A -> T | LOC_Os07g42890.2 | downstream_gene_variant ; 1084.0bp to feature; MODIFIER | N | Average:37.281; most accessible tissue: Zhenshan97 flower, score: 61.872 | N | N | N | N |
| vg0725680887 | A -> T | LOC_Os07g42895.1 | intron_variant ; MODIFIER | N | Average:37.281; most accessible tissue: Zhenshan97 flower, score: 61.872 | N | N | N | N |