| Variant ID: vg0228079799 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 28079799 |
| Reference Allele: T | Alternative Allele: TA |
| Primary Allele: TA | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 345. )
CGAAGAGGCTCAGAAAGGCGGAAGCGAGTTATGGATGGATCAAGAGCAAATTCACGCCTCTTTAAATATGCATCACCTATAGTCCTTGAAACCTGGTAAG[T/TA]
AATCACAAAATGTGACAATAGTTTTACATCAAGTACCTAGTTTGCATATGCGGAAAATCTTGATAATGTACTGCTCAACATGTTTGGGCCATCATTGGGG
CCCCAATGATGGCCCAAACATGTTGAGCAGTACATTATCAAGATTTTCCGCATATGCAAACTAGGTACTTGATGTAAAACTATTGTCACATTTTGTGATT[A/TA]
CTTACCAGGTTTCAAGGACTATAGGTGATGCATATTTAAAGAGGCGTGAATTTGCTCTTGATCCATCCATAACTCGCTTCCGCCTTTCTGAGCCTCTTCG
| 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 | 60.00% | 39.90% | 0.11% | 0.00% | NA |
| All Indica | 2759 | 95.10% | 4.70% | 0.18% | 0.00% | NA |
| All Japonica | 1512 | 0.60% | 99.40% | 0.00% | 0.00% | NA |
| Aus | 269 | 61.70% | 38.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.50% | 1.30% | 0.17% | 0.00% | NA |
| Indica II | 465 | 97.40% | 2.20% | 0.43% | 0.00% | NA |
| Indica III | 913 | 91.60% | 8.30% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 95.20% | 4.70% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 0.30% | 99.70% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 1.20% | 98.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 0.40% | 99.60% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 1.00% | 99.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 40.00% | 60.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0228079799 | T -> TA | LOC_Os02g46070.1 | downstream_gene_variant ; 4498.0bp to feature; MODIFIER | silent_mutation | Average:52.087; most accessible tissue: Callus, score: 79.824 | N | N | N | N |
| vg0228079799 | T -> TA | LOC_Os02g46080.1 | intron_variant ; MODIFIER | silent_mutation | Average:52.087; most accessible tissue: Callus, score: 79.824 | N | N | N | N |
| vg0228079799 | T -> TA | LOC_Os02g46080.2 | intron_variant ; MODIFIER | silent_mutation | Average:52.087; most accessible tissue: Callus, score: 79.824 | N | N | N | N |