| Variant ID: vg1227342895 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 27342895 |
| Reference Allele: C | Alternative Allele: T,A |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 322. )
ATTTACTCGTCTGGTTTTAGCAATGCCGACAAGATGGCATAAGGAAATTTATACAGCAAGAAACTTACAGGAAACGAAGGTGAGTAAGGCTTCCAATGGA[C/T,A]
GCCGGTATTGTGCCCCTCAACAGGTTGCTGGACAAGTCCCTGCAGATGGCACGCATTAGACCAAGAATAAGCAGTGAATCAGATCAGGGTATTTTGCTAA
TTAGCAAAATACCCTGATCTGATTCACTGCTTATTCTTGGTCTAATGCGTGCCATCTGCAGGGACTTGTCCAGCAACCTGTTGAGGGGCACAATACCGGC[G/A,T]
TCCATTGGAAGCCTTACTCACCTTCGTTTCCTGTAAGTTTCTTGCTGTATAAATTTCCTTATGCCATCTTGTCGGCATTGCTAAAACCAGACGAGTAAAT
| 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 | 97.70% | 2.30% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 68.80% | 31.20% | 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 | 99.70% | 0.30% | 0.00% | 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 | 87.50% | 12.50% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 8.90% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1227342895 | C -> A | LOC_Os12g44090.1 | synonymous_variant ; p.Ala182Ala; LOW | N | Average:53.372; most accessible tissue: Zhenshan97 panicle, score: 82.888 | N | N | N | N |
| vg1227342895 | C -> A | LOC_Os12g44100.1 | downstream_gene_variant ; 3227.0bp to feature; MODIFIER | N | Average:53.372; most accessible tissue: Zhenshan97 panicle, score: 82.888 | N | N | N | N |
| vg1227342895 | C -> T | LOC_Os12g44090.1 | synonymous_variant ; p.Ala182Ala; LOW | synonymous_codon | Average:53.372; most accessible tissue: Zhenshan97 panicle, score: 82.888 | N | N | N | N |