| Variant ID: vg0228078907 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 28078907 |
| 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: 300. )
AAGGCCGGACGCTCTAGATCGGTGGCGTCCAATTGTTTTAATGGGACGCTGCGGAATTACGTTGTCCTGCTTACGAATAAAAATCCAATACCTCAGTGTT[T/C]
ACATAAAAAAATATATTTTTTGTTTTGCTCAGATTACCAAAAATTGGGAATTTTCACATCAGTATCCATCTGTTGTGATGTAGTACGTAGAAGAAAAACA
TGTTTTTCTTCTACGTACTACATCACAACAGATGGATACTGATGTGAAAATTCCCAATTTTTGGTAATCTGAGCAAAACAAAAAATATATTTTTTTATGT[A/G]
AACACTGAGGTATTGGATTTTTATTCGTAAGCAGGACAACGTAATTCCGCAGCGTCCCATTAAAACAATTGGACGCCACCGATCTAGAGCGTCCGGCCTT
| 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 | 99.50% | 0.10% | 0.38% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.07% | 0.00% | NA |
| Aus | 269 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 12.50% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 0.00% | 5.56% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0228078907 | T -> C | LOC_Os02g46080.2 | 3_prime_UTR_variant ; 271.0bp to feature; MODIFIER | silent_mutation | Average:56.495; most accessible tissue: Zhenshan97 flower, score: 71.071 | N | N | N | N |
| vg0228078907 | T -> C | LOC_Os02g46070.1 | downstream_gene_variant ; 3605.0bp to feature; MODIFIER | silent_mutation | Average:56.495; most accessible tissue: Zhenshan97 flower, score: 71.071 | N | N | N | N |
| vg0228078907 | T -> C | LOC_Os02g46080.1 | downstream_gene_variant ; 88.0bp to feature; MODIFIER | silent_mutation | Average:56.495; most accessible tissue: Zhenshan97 flower, score: 71.071 | N | N | N | N |