| Variant ID: vg0114587310 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 14587310 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 254. )
TATTGCGCTGCTGTCCTGTGAACTTCTCTTATGGGCAGCAATTCCATAGCCACATGCTTATCTTGCACAAACAAATTTTCAAAAATTCATTAATCAATTC[T/C]
ACTGCTTTATGCATAAAAATTGTTTAAGCATCTCAATGTATCAAATGTTAACCAAAACTAAACTGAAGCGGTTAAATAAGCTTTTTTTTTTATTGCTGAA
TTCAGCAATAAAAAAAAAAGCTTATTTAACCGCTTCAGTTTAGTTTTGGTTAACATTTGATACATTGAGATGCTTAAACAATTTTTATGCATAAAGCAGT[A/G]
GAATTGATTAATGAATTTTTGAAAATTTGTTTGTGCAAGATAAGCATGTGGCTATGGAATTGCTGCCCATAAGAGAAGTTCACAGGACAGCAGCGCAATA
| 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 | 78.70% | 0.70% | 1.18% | 19.40% | NA |
| All Indica | 2759 | 64.10% | 1.20% | 1.99% | 32.69% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 50.30% | 0.00% | 1.01% | 48.74% | NA |
| Indica II | 465 | 70.80% | 0.00% | 0.22% | 29.03% | NA |
| Indica III | 913 | 68.10% | 2.50% | 3.61% | 25.74% | NA |
| Indica Intermediate | 786 | 65.90% | 1.40% | 1.91% | 30.79% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 84.40% | 0.00% | 1.11% | 14.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0114587310 | T -> DEL | N | N | silent_mutation | Average:64.347; most accessible tissue: Zhenshan97 young leaf, score: 78.644 | N | N | N | N |
| vg0114587310 | T -> C | LOC_Os01g25730.1 | downstream_gene_variant ; 3932.0bp to feature; MODIFIER | silent_mutation | Average:64.347; most accessible tissue: Zhenshan97 young leaf, score: 78.644 | N | N | N | N |
| vg0114587310 | T -> C | LOC_Os01g25740.1 | intron_variant ; MODIFIER | silent_mutation | Average:64.347; most accessible tissue: Zhenshan97 young leaf, score: 78.644 | N | N | N | N |