| Variant ID: vg0228078985 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 28078985 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, T: 0.00, others allele: 0.00, population size: 286. )
AAAAATCCAATACCTCAGTGTTTACATAAAAAAATATATTTTTTGTTTTGCTCAGATTACCAAAAATTGGGAATTTTCACATCAGTATCCATCTGTTGTG[A/T]
TGTAGTACGTAGAAGAAAAACAGCATGTTGTGATTATTCCGAGCATATTGCAAGCATGAAACCAACTTTTTAGTACCTGAAATAGGTAAATGTACAAAAC
GTTTTGTACATTTACCTATTTCAGGTACTAAAAAGTTGGTTTCATGCTTGCAATATGCTCGGAATAATCACAACATGCTGTTTTTCTTCTACGTACTACA[T/A]
CACAACAGATGGATACTGATGTGAAAATTCCCAATTTTTGGTAATCTGAGCAAAACAAAAAATATATTTTTTTATGTAAACACTGAGGTATTGGATTTTT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 97.00% | 3.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 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 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0228078985 | A -> T | LOC_Os02g46080.2 | 3_prime_UTR_variant ; 193.0bp to feature; MODIFIER | N | Average:60.759; most accessible tissue: Callus, score: 81.712 | N | N | N | N |
| vg0228078985 | A -> T | LOC_Os02g46070.1 | downstream_gene_variant ; 3683.0bp to feature; MODIFIER | N | Average:60.759; most accessible tissue: Callus, score: 81.712 | N | N | N | N |
| vg0228078985 | A -> T | LOC_Os02g46080.1 | downstream_gene_variant ; 10.0bp to feature; MODIFIER | N | Average:60.759; most accessible tissue: Callus, score: 81.712 | N | N | N | N |