| Variant ID: vg0132053054 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 32053054 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 291. )
ATCCTTTTATTAATGTGGAATCCTGGATTTGTAGGTAGAGGTGTAACAGGACCAACTTTCCCAGGATGTCCTCAGGCTTACCAACAATAGTTTCAACAAT[C/T]
CGGGCAAAACCAATCATTCAAGGGACAAAGCCAAAATTATAAATTCATAGATGAACATCAACAGATCCATCGTTTCAGATAGGGAGATGTTGTTGCATTG
CAATGCAACAACATCTCCCTATCTGAAACGATGGATCTGTTGATGTTCATCTATGAATTTATAATTTTGGCTTTGTCCCTTGAATGATTGGTTTTGCCCG[G/A]
ATTGTTGAAACTATTGTTGGTAAGCCTGAGGACATCCTGGGAAAGTTGGTCCTGTTACACCTCTACCTACAAATCCAGGATTCCACATTAATAAAAGGAT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 86.10% | 13.80% | 0.11% | 0.00% | NA |
| All Indica | 2759 | 76.40% | 23.50% | 0.14% | 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 | 96.00% | 4.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 95.50% | 4.30% | 0.22% | 0.00% | NA |
| Indica III | 913 | 53.00% | 46.90% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 77.40% | 22.40% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 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 | 97.80% | 1.10% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0132053054 | C -> T | LOC_Os01g55620.1 | upstream_gene_variant ; 2288.0bp to feature; MODIFIER | silent_mutation | Average:50.908; most accessible tissue: Callus, score: 71.356 | N | N | N | N |
| vg0132053054 | C -> T | LOC_Os01g55640.1 | upstream_gene_variant ; 4101.0bp to feature; MODIFIER | silent_mutation | Average:50.908; most accessible tissue: Callus, score: 71.356 | N | N | N | N |
| vg0132053054 | C -> T | LOC_Os01g55650.1 | downstream_gene_variant ; 4329.0bp to feature; MODIFIER | silent_mutation | Average:50.908; most accessible tissue: Callus, score: 71.356 | N | N | N | N |
| vg0132053054 | C -> T | LOC_Os01g55630.1 | intron_variant ; MODIFIER | silent_mutation | Average:50.908; most accessible tissue: Callus, score: 71.356 | N | N | N | N |