| Variant ID: vg0800071768 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 71768 |
| 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: 363. )
AAAAGAGAAGGAATTATCCATCCATCCATCCATTGGACCGGTGGCCTAGATGTCGTCGTCTAGCTCGTTCTTCTCTTCCTCTGCACCATCTTCATCTTCT[T/C]
GGTCGTCTTCATCAGTGCCTTTCTTGGGTGGCTGATCTACCTCCTGCTCGCCTGCGTTGCCACCAACATTGTTCTCCTGCCATCACAATATTGATCAATT
AATTGATCAATATTGTGATGGCAGGAGAACAATGTTGGTGGCAACGCAGGCGAGCAGGAGGTAGATCAGCCACCCAAGAAAGGCACTGATGAAGACGACC[A/G]
AGAAGATGAAGATGGTGCAGAGGAAGAGAAGAACGAGCTAGACGACGACATCTAGGCCACCGGTCCAATGGATGGATGGATGGATAATTCCTTCTCTTTT
| 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 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 95.20% | 4.80% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 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 | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0800071768 | T -> C | LOC_Os08g01100.1 | missense_variant ; p.Gln186Arg; MODERATE | N | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0800071768 | T -> C | LOC_Os08g01090.1 | upstream_gene_variant ; 4129.0bp to feature; MODIFIER | N | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0800071768 | T -> C | LOC_Os08g01090.2 | upstream_gene_variant ; 3929.0bp to feature; MODIFIER | N | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |