| Variant ID: vg0432301656 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 32301656 |
| Reference Allele: T | Alternative Allele: TA,TAA |
| Primary Allele: TA | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 232. )
ATTGTTTAGATCTTTAATGTTTTTTATGCTCTCCATTCAGTGAATTATGTAGAGCGGCTGTAGCTCTTTTAAGCAAAGGTTGAGAATCTTTCCATTCTCT[T/TA,TAA]
AAAAAAATTCCATACCAAATTGAATTGAATTACAGATCTGACTATCATTCAGTAACAAGTGGTAAGTATTAAGTACAAACTAGATTGCTACCATTTCTTC
GAAGAAATGGTAGCAATCTAGTTTGTACTTAATACTTACCACTTGTTACTGAATGATAGTCAGATCTGTAATTCAATTCAATTTGGTATGGAATTTTTTT[A/TA,TTA]
AGAGAATGGAAAGATTCTCAACCTTTGCTTAAAAGAGCTACAGCCGCTCTACATAATTCACTGAATGGAGAGCATAAAAAACATTAAAGATCTAAACAAT
| Populations | Population Size | Frequency of TA(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 67.70% | 32.00% | 0.17% | 0.00% | TAA: 0.06% |
| All Indica | 2759 | 92.50% | 7.30% | 0.11% | 0.00% | TAA: 0.11% |
| All Japonica | 1512 | 30.20% | 69.60% | 0.20% | 0.00% | NA |
| Aus | 269 | 26.40% | 72.90% | 0.74% | 0.00% | NA |
| Indica I | 595 | 90.40% | 9.10% | 0.50% | 0.00% | NA |
| Indica II | 465 | 93.50% | 6.50% | 0.00% | 0.00% | NA |
| Indica III | 913 | 95.60% | 4.20% | 0.00% | 0.00% | TAA: 0.22% |
| Indica Intermediate | 786 | 89.70% | 10.20% | 0.00% | 0.00% | TAA: 0.13% |
| Temperate Japonica | 767 | 22.80% | 77.20% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 45.00% | 55.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 22.40% | 76.30% | 1.24% | 0.00% | NA |
| VI/Aromatic | 96 | 69.80% | 30.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 62.20% | 37.80% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0432301656 | T -> TAA | LOC_Os04g54240.1 | 3_prime_UTR_variant ; 437.0bp to feature; MODIFIER | silent_mutation | Average:48.539; most accessible tissue: Minghui63 panicle, score: 85.556 | N | N | N | N |
| vg0432301656 | T -> TAA | LOC_Os04g54230.1 | upstream_gene_variant ; 3525.0bp to feature; MODIFIER | silent_mutation | Average:48.539; most accessible tissue: Minghui63 panicle, score: 85.556 | N | N | N | N |
| vg0432301656 | T -> TAA | LOC_Os04g54250.1 | downstream_gene_variant ; 3160.0bp to feature; MODIFIER | silent_mutation | Average:48.539; most accessible tissue: Minghui63 panicle, score: 85.556 | N | N | N | N |
| vg0432301656 | T -> TA | LOC_Os04g54240.1 | 3_prime_UTR_variant ; 437.0bp to feature; MODIFIER | silent_mutation | Average:48.539; most accessible tissue: Minghui63 panicle, score: 85.556 | N | N | N | N |
| vg0432301656 | T -> TA | LOC_Os04g54230.1 | upstream_gene_variant ; 3525.0bp to feature; MODIFIER | silent_mutation | Average:48.539; most accessible tissue: Minghui63 panicle, score: 85.556 | N | N | N | N |
| vg0432301656 | T -> TA | LOC_Os04g54250.1 | downstream_gene_variant ; 3160.0bp to feature; MODIFIER | silent_mutation | Average:48.539; most accessible tissue: Minghui63 panicle, score: 85.556 | N | N | N | N |