| Variant ID: vg0138753723 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 38753723 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.02, others allele: 0.00, population size: 227. )
TCAAAATGTATTCAATGTTATATCTAATGGAACTAATTTGGTATTGTAGATGTTGTTAATTTTTTCTTTAAACTTTGCCAAACCTAAAGAAGTTTAACTA[C/T]
GAAAAAAAATCAAAACAAATTATAATATGAAACGGAGGAATTACTGTTTATGGTACTGCTACTTTTGAACTACTTCTTTGATCCGACGGAGGAAAAAAAT
ATTTTTTTCCTCCGTCGGATCAAAGAAGTAGTTCAAAAGTAGCAGTACCATAAACAGTAATTCCTCCGTTTCATATTATAATTTGTTTTGATTTTTTTTC[G/A]
TAGTTAAACTTCTTTAGGTTTGGCAAAGTTTAAAGAAAAAATTAACAACATCTACAATACCAAATTAGTTCCATTAGATATAACATTGAATACATTTTGA
| 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 | 95.20% | 4.80% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 97.60% | 2.40% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 40.10% | 59.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 95.00% | 5.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.00% | 2.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.00% | 2.00% | 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 | 97.80% | 2.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0138753723 | C -> T | LOC_Os01g66710.1 | downstream_gene_variant ; 2955.0bp to feature; MODIFIER | silent_mutation | Average:33.956; most accessible tissue: Callus, score: 74.601 | N | N | N | N |
| vg0138753723 | C -> T | LOC_Os01g66730.1 | downstream_gene_variant ; 1335.0bp to feature; MODIFIER | silent_mutation | Average:33.956; most accessible tissue: Callus, score: 74.601 | N | N | N | N |
| vg0138753723 | C -> T | LOC_Os01g66730.2 | downstream_gene_variant ; 1363.0bp to feature; MODIFIER | silent_mutation | Average:33.956; most accessible tissue: Callus, score: 74.601 | N | N | N | N |
| vg0138753723 | C -> T | LOC_Os01g66720.1 | intron_variant ; MODIFIER | silent_mutation | Average:33.956; most accessible tissue: Callus, score: 74.601 | N | N | N | N |