| Variant ID: vg1202831374 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 2831374 |
| 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: 350. )
ACTGATGAGGCTTGGAAATTACTTGATAAAATGCCATTTGAACCAACTGCATCTATGTGGGGATCTTTGCTTGGATCAAGCAGGATCCACAAGAATATTA[G/T]
ATTAGCCAGAATAGCAGCTGAACAGCTTTTCCGTCTTGAGCCTGAAAATGGAGGGAACCATGTTTTGCTATCAAATGTATATGCTGCCAGTGGAAACTGG
CCAGTTTCCACTGGCAGCATATACATTTGATAGCAAAACATGGTTCCCTCCATTTTCAGGCTCAAGACGGAAAAGCTGTTCAGCTGCTATTCTGGCTAAT[C/A]
TAATATTCTTGTGGATCCTGCTTGATCCAAGCAAAGATCCCCACATAGATGCAGTTGGTTCAAATGGCATTTTATCAAGTAATTTCCAAGCCTCATCAGT
| 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 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.20% | 0.80% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1202831374 | G -> T | LOC_Os12g06070.1 | missense_variant ; p.Arg444Ile; MODERATE | N | Average:48.888; most accessible tissue: Zhenshan97 flower, score: 69.775 | N | N | N | N |
| vg1202831374 | G -> T | LOC_Os12g06080.1 | downstream_gene_variant ; 4647.0bp to feature; MODIFIER | N | Average:48.888; most accessible tissue: Zhenshan97 flower, score: 69.775 | N | N | N | N |