| Variant ID: vg0132053235 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 32053235 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGGGAGATGTTGTTGCATTGCCTGCTGGTGTAGCTCATTGGTGCTACAATGATGGTGATGTACCAATTGTTGCCATATACGTCACTGATATATATATAAC[A/T]
GTGCTAACCAGCTTGATCCTAGAAAAAAGGTAATTAATCATAGCTTATTTATTGCCAACAACCCAAGCATTCTTTGAATTCGTTTGATTTATTGCAGTTC
GAACTGCAATAAATCAAACGAATTCAAAGAATGCTTGGGTTGTTGGCAATAAATAAGCTATGATTAATTACCTTTTTTCTAGGATCAAGCTGGTTAGCAC[T/A]
GTTATATATATATCAGTGACGTATATGGCAACAATTGGTACATCACCATCATTGTAGCACCAATGAGCTACACCAGCAGGCAATGCAACAACATCTCCCT
| 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% | 0.20% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 99.60% | 0.40% | 0.07% | 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 | 98.20% | 1.50% | 0.34% | 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 | 99.90% | 0.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0132053235 | A -> T | LOC_Os01g55630.1 | synonymous_variant ; p.Thr30Thr; LOW | N | Average:45.306; most accessible tissue: Callus, score: 69.065 | N | N | N | N |
| vg0132053235 | A -> T | LOC_Os01g55620.1 | upstream_gene_variant ; 2469.0bp to feature; MODIFIER | N | Average:45.306; most accessible tissue: Callus, score: 69.065 | N | N | N | N |
| vg0132053235 | A -> T | LOC_Os01g55640.1 | upstream_gene_variant ; 3920.0bp to feature; MODIFIER | N | Average:45.306; most accessible tissue: Callus, score: 69.065 | N | N | N | N |
| vg0132053235 | A -> T | LOC_Os01g55650.1 | downstream_gene_variant ; 4148.0bp to feature; MODIFIER | N | Average:45.306; most accessible tissue: Callus, score: 69.065 | N | N | N | N |