| Variant ID: vg0227216800 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 27216800 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.74, C: 0.25, others allele: 0.00, population size: 286. )
AAAGAAGAAGAGAAAAACAACAGTCGCATCAGCACCCGACGTGCCGACCACTAAACATGCACACTGCCTACTGACGAACCATTGCATGAACATTTTAATA[C/T]
CAACAAGATCAACACCATTTCTTCATCAATCACAAGGTGGCATCCCATTTTGTCAGCGAAGAAAGATTTGACTCATGCATCTCAGATTATGACGGGAACG
CGTTCCCGTCATAATCTGAGATGCATGAGTCAAATCTTTCTTCGCTGACAAAATGGGATGCCACCTTGTGATTGATGAAGAAATGGTGTTGATCTTGTTG[G/A]
TATTAAAATGTTCATGCAATGGTTCGTCAGTAGGCAGTGTGCATGTTTAGTGGTCGGCACGTCGGGTGCTGATGCGACTGTTGTTTTTCTCTTCTTCTTT
| 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 | 63.50% | 36.50% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 97.70% | 2.30% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 0.90% | 99.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 95.90% | 4.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 95.40% | 4.50% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 0.50% | 99.50% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 1.60% | 98.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 0.40% | 99.60% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 1.00% | 99.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 38.90% | 61.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0227216800 | C -> T | LOC_Os02g44910.1 | upstream_gene_variant ; 4153.0bp to feature; MODIFIER | silent_mutation | Average:69.046; most accessible tissue: Callus, score: 89.914 | N | N | N | N |
| vg0227216800 | C -> T | LOC_Os02g44920.1 | intron_variant ; MODIFIER | silent_mutation | Average:69.046; most accessible tissue: Callus, score: 89.914 | N | N | N | N |