| Variant ID: vg0704650313 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 4650313 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.01, others allele: 0.00, population size: 309. )
CAATAATCTTGGCACACAACTCCTGGAATGTATCCTTTGGTTTCATCTCAACTTGAGCCATGTCGCCCTCGGCTTTGTTGGTTTTGATGGATGGTGACGG[T/C]
GTTGCAATAGCAGCTGCGGTAGTTGAGGGTGTGGATGAGTTCATAGTGGCTGGAAACACATGTTCTGGTGCAGCAAGAGAACTCTCAACTGCTGGCCTAG
CTAGGCCAGCAGTTGAGAGTTCTCTTGCTGCACCAGAACATGTGTTTCCAGCCACTATGAACTCATCCACACCCTCAACTACCGCAGCTGCTATTGCAAC[A/G]
CCGTCACCATCCATCAAAACCAACAAAGCCGAGGGCGACATGGCTCAAGTTGAGATGAAACCAAAGGATACATTCCAGGAGTTGTGTGCCAAGATTATTG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(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 | 99.80% | 0.20% | 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 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 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 | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0704650313 | T -> C | LOC_Os07g08940.1 | synonymous_variant ; p.Thr81Thr; LOW | N | Average:54.816; most accessible tissue: Zhenshan97 flag leaf, score: 66.327 | N | N | N | N |
| vg0704650313 | T -> C | LOC_Os07g08934.1 | upstream_gene_variant ; 3560.0bp to feature; MODIFIER | N | Average:54.816; most accessible tissue: Zhenshan97 flag leaf, score: 66.327 | N | N | N | N |
| vg0704650313 | T -> C | LOC_Os07g08950.1 | upstream_gene_variant ; 2480.0bp to feature; MODIFIER | N | Average:54.816; most accessible tissue: Zhenshan97 flag leaf, score: 66.327 | N | N | N | N |