| Variant ID: vg0332987119 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 32987119 |
| Reference Allele: TGA | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: TGA |
Inferred Ancestral Allele : TGA (evidence from allele frequency in Oryza rufipogon: TGA: 0.80, T: 0.20, others allele: 0.00, population size: 250. )
GAGTACTGGCGCTGATCCACTAAGTAGCTGTAAATAAAGACTTGTACTTTGCTTCTGCACATATCAATCGATCCAAATAGATACATCAACTGAATTAAAC[TGA/T]
CTCTGTTACAGCGAACTACAACTAACTTTTCTTTGACGAAAATTACATCAAATTAATTGTGCGCTGAGCACAGAAAATCGATCATTGCAAACAAGGATTC
GAATCCTTGTTTGCAATGATCGATTTTCTGTGCTCAGCGCACAATTAATTTGATGTAATTTTCGTCAAAGAAAAGTTAGTTGTAGTTCGCTGTAACAGAG[TCA/A]
GTTTAATTCAGTTGATGTATCTATTTGGATCGATTGATATGTGCAGAAGCAAAGTACAAGTCTTTATTTACAGCTACTTAGTGGATCAGCGCCAGTACTC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of TGA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 61.10% | 38.80% | 0.15% | 0.00% | NA |
| All Indica | 2759 | 93.70% | 6.20% | 0.18% | 0.00% | NA |
| All Japonica | 1512 | 0.90% | 99.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 91.40% | 8.60% | 0.00% | 0.00% | NA |
| Indica I | 595 | 96.00% | 3.90% | 0.17% | 0.00% | NA |
| Indica II | 465 | 95.30% | 4.50% | 0.22% | 0.00% | NA |
| Indica III | 913 | 93.60% | 6.10% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 91.00% | 8.90% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 0.70% | 99.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 1.40% | 98.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 0.40% | 99.60% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 45.60% | 52.20% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0332987119 | TGA -> T | LOC_Os03g57920.1 | 3_prime_UTR_variant ; 188.0bp to feature; MODIFIER | silent_mutation | Average:74.291; most accessible tissue: Minghui63 flower, score: 85.758 | N | N | N | N |
| vg0332987119 | TGA -> T | LOC_Os03g57900.1 | upstream_gene_variant ; 4151.0bp to feature; MODIFIER | silent_mutation | Average:74.291; most accessible tissue: Minghui63 flower, score: 85.758 | N | N | N | N |
| vg0332987119 | TGA -> T | LOC_Os03g57910.1 | upstream_gene_variant ; 954.0bp to feature; MODIFIER | silent_mutation | Average:74.291; most accessible tissue: Minghui63 flower, score: 85.758 | N | N | N | N |
| vg0332987119 | TGA -> T | LOC_Os03g57930.1 | downstream_gene_variant ; 1914.0bp to feature; MODIFIER | silent_mutation | Average:74.291; most accessible tissue: Minghui63 flower, score: 85.758 | N | N | N | N |