| Variant ID: vg1227342909 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 27342909 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 350. )
TTTTAGCAATGCCGACAAGATGGCATAAGGAAATTTATACAGCAAGAAACTTACAGGAAACGAAGGTGAGTAAGGCTTCCAATGGACGCCGGTATTGTGC[C/T]
CCTCAACAGGTTGCTGGACAAGTCCCTGCAGATGGCACGCATTAGACCAAGAATAAGCAGTGAATCAGATCAGGGTATTTTGCTAAGAACCTACAAGATT
AATCTTGTAGGTTCTTAGCAAAATACCCTGATCTGATTCACTGCTTATTCTTGGTCTAATGCGTGCCATCTGCAGGGACTTGTCCAGCAACCTGTTGAGG[G/A]
GCACAATACCGGCGTCCATTGGAAGCCTTACTCACCTTCGTTTCCTGTAAGTTTCTTGCTGTATAAATTTCCTTATGCCATCTTGTCGGCATTGCTAAAA
| 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 | 99.80% | 0.20% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 99.60% | 0.30% | 0.07% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.90% | 1.00% | 0.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1227342909 | C -> T | LOC_Os12g44090.1 | missense_variant ; p.Gly178Ser; MODERATE | N | Average:51.211; most accessible tissue: Zhenshan97 panicle, score: 81.135 | N | N | N | N |
| vg1227342909 | C -> T | LOC_Os12g44100.1 | downstream_gene_variant ; 3213.0bp to feature; MODIFIER | N | Average:51.211; most accessible tissue: Zhenshan97 panicle, score: 81.135 | N | N | N | N |