| Variant ID: vg0318607864 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 18607864 |
| 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: 286. )
AAAGTGCAGATATATATCAATGTGATGAATTTTCAATCATAACTTCTTTCTTGAAGAGATATCGCATAGAATCGATGGAGCATTTTGCTAGCCTGGCATA[T/C]
TATCTAAAACCATGGAAAGCACTTTTTCTGGTGAAATTATGTCTCAAGTTCCCCATAGCCCTTCCAAATGTAGGAGCGCAGATAAGTAACTAACATTGTC
GACAATGTTAGTTACTTATCTGCGCTCCTACATTTGGAAGGGCTATGGGGAACTTGAGACATAATTTCACCAGAAAAAGTGCTTTCCATGGTTTTAGATA[A/G]
TATGCCAGGCTAGCAAAATGCTCCATCGATTCTATGCGATATCTCTTCAAGAAAGAAGTTATGATTGAAAATTCATCACATTGATATATATCTGCACTTT
| 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 | 85.10% | 0.30% | 11.89% | 2.75% | NA |
| All Indica | 2759 | 84.90% | 0.10% | 14.14% | 0.83% | NA |
| All Japonica | 1512 | 91.00% | 0.10% | 1.92% | 6.94% | NA |
| Aus | 269 | 50.90% | 0.00% | 49.07% | 0.00% | NA |
| Indica I | 595 | 80.50% | 0.00% | 18.49% | 1.01% | NA |
| Indica II | 465 | 80.60% | 0.00% | 16.99% | 2.37% | NA |
| Indica III | 913 | 91.50% | 0.40% | 8.11% | 0.00% | NA |
| Indica Intermediate | 786 | 83.10% | 0.00% | 16.16% | 0.76% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 76.40% | 0.40% | 4.76% | 18.45% | NA |
| Japonica Intermediate | 241 | 92.90% | 0.00% | 2.07% | 4.98% | NA |
| VI/Aromatic | 96 | 86.50% | 7.30% | 6.25% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 0.00% | 5.56% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0318607864 | T -> C | LOC_Os03g32540.1 | upstream_gene_variant ; 3329.0bp to feature; MODIFIER | silent_mutation | Average:7.571; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg0318607864 | T -> C | LOC_Os03g32526.1 | intron_variant ; MODIFIER | silent_mutation | Average:7.571; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg0318607864 | T -> DEL | N | N | silent_mutation | Average:7.571; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |