| Variant ID: vg0202540302 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 2540302 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 286. )
TTTATCATACCTATTCAGATCATACAGAATTGTCAGATCTATAATTTATTATGTTTACCTAGAGCATGTCTTTTATACAATATCTATTGCACGAGTATTT[C/T]
CGACGTTAAACCGACTACGGTCTAACGCTGGGGGCTTGCTCTGTTCTCTTCTGTATGAATCATGCTTGTTTACGGTTTACGTAATGCCTGATATTTACAT
ATGTAAATATCAGGCATTACGTAAACCGTAAACAAGCATGATTCATACAGAAGAGAACAGAGCAAGCCCCCAGCGTTAGACCGTAGTCGGTTTAACGTCG[G/A]
AAATACTCGTGCAATAGATATTGTATAAAAGACATGCTCTAGGTAAACATAATAAATTATAGATCTGACAATTCTGTATGATCTGAATAGGTATGATAAA
| 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 | 93.70% | 6.30% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 97.60% | 2.40% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Aus | 269 | 19.70% | 80.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 95.50% | 4.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 88.90% | 11.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0202540302 | C -> T | LOC_Os02g05270.1 | upstream_gene_variant ; 4127.0bp to feature; MODIFIER | silent_mutation | Average:38.586; most accessible tissue: Zhenshan97 flower, score: 47.586 | N | N | N | N |
| vg0202540302 | C -> T | LOC_Os02g05280.1 | downstream_gene_variant ; 1632.0bp to feature; MODIFIER | silent_mutation | Average:38.586; most accessible tissue: Zhenshan97 flower, score: 47.586 | N | N | N | N |
| vg0202540302 | C -> T | LOC_Os02g05300.1 | downstream_gene_variant ; 1788.0bp to feature; MODIFIER | silent_mutation | Average:38.586; most accessible tissue: Zhenshan97 flower, score: 47.586 | N | N | N | N |
| vg0202540302 | C -> T | LOC_Os02g05290.1 | intron_variant ; MODIFIER | silent_mutation | Average:38.586; most accessible tissue: Zhenshan97 flower, score: 47.586 | N | N | N | N |