| Variant ID: vg1202836288 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 2836288 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.93, C: 0.06, others allele: 0.00, population size: 245. )
CCGACGCCGCGCTGCTGCTCTTGGCGTCTGCTTCTCTCTGCGACTCTCCTGCAAATTGTTCCACCGCGAAAGGTATATGATCTTTAATCACTTGCTGTAG[T/C]
TGCATGTTAATTATAGTATCAAAGTGCTTAATTAATTTGTTCTTGAGTTTCTACTACTAGATATGCAATTGCGTGTTTAGTTAGTTACCTGCGTGTAGTA
TACTACACGCAGGTAACTAACTAAACACGCAATTGCATATCTAGTAGTAGAAACTCAAGAACAAATTAATTAAGCACTTTGATACTATAATTAACATGCA[A/G]
CTACAGCAAGTGATTAAAGATCATATACCTTTCGCGGTGGAACAATTTGCAGGAGAGTCGCAGAGAGAAGCAGACGCCAAGAGCAGCAGCGCGGCGTCGG
| 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 | 94.80% | 5.10% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 95.30% | 4.60% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 59.10% | 40.50% | 0.37% | 0.00% | NA |
| Indica I | 595 | 92.60% | 7.20% | 0.17% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 94.20% | 5.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.20% | 3.80% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.00% | 1.00% | 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 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1202836288 | T -> C | LOC_Os12g06070.1 | downstream_gene_variant ; 4352.0bp to feature; MODIFIER | silent_mutation | Average:77.118; most accessible tissue: Zhenshan97 flower, score: 86.268 | N | N | N | N |
| vg1202836288 | T -> C | LOC_Os12g06080.1 | intron_variant ; MODIFIER | silent_mutation | Average:77.118; most accessible tissue: Zhenshan97 flower, score: 86.268 | N | N | N | N |