| Variant ID: vg0605309966 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 5309966 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 286. )
TTCTACGGACATAATTTTCTGTTCAATTTGTATGAGACTATGAGTTCCTTGTTTAATGAGCGAGTAAATAAATTGCCCTGGAACTCATAGTGAAATGATG[G/T]
TAACTTGTTATGGTTCATCCGTTCATGCAATTGGAAGCTGGAATTACACATAGGCTTTTGCTTTTGCATTTTCAGATTGGTGGAAACGAGAAATTTCTGA
TCAGAAATTTCTCGTTTCCACCAATCTGAAAATGCAAAAGCAAAAGCCTATGTGTAATTCCAGCTTCCAATTGCATGAACGGATGAACCATAACAAGTTA[C/A]
CATCATTTCACTATGAGTTCCAGGGCAATTTATTTACTCGCTCATTAAACAAGGAACTCATAGTCTCATACAAATTGAACAGAAAATTATGTCCGTAGAA
| 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 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.70% | 0.30% | 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 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0605309966 | G -> T | LOC_Os06g10320.1 | downstream_gene_variant ; 3235.0bp to feature; MODIFIER | N | Average:52.767; most accessible tissue: Callus, score: 85.554 | N | N | N | N |
| vg0605309966 | G -> T | LOC_Os06g10330.1 | downstream_gene_variant ; 2219.0bp to feature; MODIFIER | N | Average:52.767; most accessible tissue: Callus, score: 85.554 | N | N | N | N |
| vg0605309966 | G -> T | LOC_Os06g10340.1 | intron_variant ; MODIFIER | N | Average:52.767; most accessible tissue: Callus, score: 85.554 | N | N | N | N |