| Variant ID: vg0221166710 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21166710 |
| 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: 363. )
CTCTACTTCCTCTTTACTCAAACCTAACCTTGTTTCACTTCCATGTATGCCTCTTGCCTGAGCATGCCATGGCTAGTGCTACTTTTGGTGCAATGGACTC[T/C]
GTCCTCAGCAAGCTCACCGACTTGCTGACCTTCGAATACAAGTTGCTTGAGGAAGTGAAACGAGACATTGTTTTCGTGAAATCTGAGCTAGAGAGCATGC
GCATGCTCTCTAGCTCAGATTTCACGAAAACAATGTCTCGTTTCACTTCCTCAAGCAACTTGTATTCGAAGGTCAGCAAGTCGGTGAGCTTGCTGAGGAC[A/G]
GAGTCCATTGCACCAAAAGTAGCACTAGCCATGGCATGCTCAGGCAAGAGGCATACATGGAAGTGAAACAAGGTTAGGTTTGAGTAAAGAGGAAGTAGAG
| 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 | 99.60% | 0.20% | 0.19% | 0.00% | NA |
| All Indica | 2759 | 99.30% | 0.40% | 0.33% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.70% | 0.00% | 1.34% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.00% | 0.13% | 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 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0221166710 | T -> C | LOC_Os02g35210.1 | synonymous_variant ; p.Ser11Ser; LOW | N | Average:74.442; most accessible tissue: Zhenshan97 young leaf, score: 88.259 | N | N | N | N |
| vg0221166710 | T -> C | LOC_Os02g35200.1 | downstream_gene_variant ; 1024.0bp to feature; MODIFIER | N | Average:74.442; most accessible tissue: Zhenshan97 young leaf, score: 88.259 | N | N | N | N |
| vg0221166710 | T -> C | LOC_Os02g35220.1 | downstream_gene_variant ; 3819.0bp to feature; MODIFIER | N | Average:74.442; most accessible tissue: Zhenshan97 young leaf, score: 88.259 | N | N | N | N |