| Variant ID: vg0302709667 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 2709667 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.89, A: 0.10, others allele: 0.00, population size: 241. )
ACATTTAGGTAACATGGTGTCCTTAGCTGCTTCTAATATTCTTGATCTGCGTATCCATTTTCGTTTATTCCATCAATTAATTCTCTATGTGAGTAGTAGT[A/T]
GTTAGTAGCCTGCCTAGATGCCATGCGGAGCTGATCTGCGGATTCCAGAGTAAATGTATGGCATAGCTATACTTCCATTGGAAAAATGCGTCTTTTTATG
CATAAAAAGACGCATTTTTCCAATGGAAGTATAGCTATGCCATACATTTACTCTGGAATCCGCAGATCAGCTCCGCATGGCATCTAGGCAGGCTACTAAC[T/A]
ACTACTACTCACATAGAGAATTAATTGATGGAATAAACGAAAATGGATACGCAGATCAAGAATATTAGAAGCAGCTAAGGACACCATGTTACCTAAATGT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 64.40% | 35.30% | 0.13% | 0.11% | NA |
| All Indica | 2759 | 96.70% | 2.90% | 0.18% | 0.14% | NA |
| All Japonica | 1512 | 0.50% | 99.50% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| Indica II | 465 | 94.40% | 5.60% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.70% | 0.00% | 0.11% | 0.22% | NA |
| Indica Intermediate | 786 | 93.30% | 6.00% | 0.51% | 0.25% | NA |
| Temperate Japonica | 767 | 0.40% | 99.60% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 0.60% | 99.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 0.80% | 99.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 54.20% | 45.80% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 54.40% | 43.30% | 1.11% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0302709667 | A -> T | LOC_Os03g05480.1 | downstream_gene_variant ; 3646.0bp to feature; MODIFIER | silent_mutation | Average:54.89; most accessible tissue: Callus, score: 80.443 | N | N | N | N |
| vg0302709667 | A -> T | LOC_Os03g05470.1 | intron_variant ; MODIFIER | silent_mutation | Average:54.89; most accessible tissue: Callus, score: 80.443 | N | N | N | N |
| vg0302709667 | A -> DEL | N | N | silent_mutation | Average:54.89; most accessible tissue: Callus, score: 80.443 | N | N | N | N |