| Variant ID: vg0128797534 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28797534 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 359. )
GAGCATGGCAATGGTGAGATTGGTCATGGAGACGTCATGGAATCCAAACAGTAATCTTTCGGGAGATTGATCAGGGAATAAGTTGACCATGAGAAAACAT[G/T]
TAAGAACAGCTTGTCTGCTGAGTCATGACCGGTGATGTGTATGTGATGGAAGAAAACGTATGTACGACTTAATGCTTGCACCTATACTACTGCTGTGTGC
GCACACAGCAGTAGTATAGGTGCAAGCATTAAGTCGTACATACGTTTTCTTCCATCACATACACATCACCGGTCATGACTCAGCAGACAAGCTGTTCTTA[C/A]
ATGTTTTCTCATGGTCAACTTATTCCCTGATCAATCTCCCGAAAGATTACTGTTTGGATTCCATGACGTCTCCATGACCAATCTCACCATTGCCATGCTC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.80% | 0.60% | 0.55% | 0.00% | NA |
| All Indica | 2759 | 98.00% | 1.10% | 0.94% | 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 | 97.30% | 0.00% | 2.69% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.00% | 0.43% | 0.00% | NA |
| Indica III | 913 | 96.40% | 3.20% | 0.44% | 0.00% | NA |
| Indica Intermediate | 786 | 99.50% | 0.00% | 0.51% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0128797534 | G -> T | LOC_Os01g50110.1 | 3_prime_UTR_variant ; 47.0bp to feature; MODIFIER | N | Average:70.647; most accessible tissue: Callus, score: 86.238 | N | N | N | N |
| vg0128797534 | G -> T | LOC_Os01g50100.1 | upstream_gene_variant ; 4234.0bp to feature; MODIFIER | N | Average:70.647; most accessible tissue: Callus, score: 86.238 | N | N | N | N |
| vg0128797534 | G -> T | LOC_Os01g50120.1 | upstream_gene_variant ; 1340.0bp to feature; MODIFIER | N | Average:70.647; most accessible tissue: Callus, score: 86.238 | N | N | N | N |
| vg0128797534 | G -> T | LOC_Os01g50120.2 | upstream_gene_variant ; 1340.0bp to feature; MODIFIER | N | Average:70.647; most accessible tissue: Callus, score: 86.238 | N | N | N | N |