| Variant ID: vg0826584839 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 26584839 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 124. )
AAGCCACTAGTGGATATGTTTTCACACTGGGTGGTGGTGCTGTTTCATGGAGGTCTTGCAAACAGACAATTTTGACGAGGTCAACCATGGAAGCAGAGCT[A/G]
ACGGCACTGGATACTGCTACTGTTGAGGCAGAATGGCTGCGTGATCTATTAATGGATCTGCCTGTTGTTGAAAAACCGGTGCCGGCTATCCTTATGAACT
AGTTCATAAGGATAGCCGGCACCGGTTTTTCAACAACAGGCAGATCCATTAATAGATCACGCAGCCATTCTGCCTCAACAGTAGCAGTATCCAGTGCCGT[T/C]
AGCTCTGCTTCCATGGTTGACCTCGTCAAAATTGTCTGTTTGCAAGACCTCCATGAAACAGCACCACCACCCAGTGTGAAAACATATCCACTAGTGGCTT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 3.20% | 0.00% | 23.68% | 73.13% | NA |
| All Indica | 2759 | 0.30% | 0.10% | 21.13% | 78.54% | NA |
| All Japonica | 1512 | 4.40% | 0.00% | 30.75% | 64.88% | NA |
| Aus | 269 | 0.70% | 0.00% | 11.52% | 87.73% | NA |
| Indica I | 595 | 0.00% | 0.00% | 15.13% | 84.87% | NA |
| Indica II | 465 | 0.40% | 0.40% | 5.38% | 93.76% | NA |
| Indica III | 913 | 0.20% | 0.00% | 36.36% | 63.42% | NA |
| Indica Intermediate | 786 | 0.40% | 0.00% | 17.30% | 82.32% | NA |
| Temperate Japonica | 767 | 2.30% | 0.00% | 24.12% | 73.53% | NA |
| Tropical Japonica | 504 | 7.50% | 0.00% | 42.06% | 50.40% | NA |
| Japonica Intermediate | 241 | 4.10% | 0.00% | 28.22% | 67.63% | NA |
| VI/Aromatic | 96 | 71.90% | 0.00% | 14.58% | 13.54% | NA |
| Intermediate | 90 | 5.60% | 0.00% | 28.89% | 65.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0826584839 | A -> G | LOC_Os08g42090.1 | synonymous_variant ; p.Leu1194Leu; LOW | synonymous_codon | Average:9.425; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg0826584839 | A -> G | LOC_Os08g42090.1 | synonymous_variant ; p.Leu1194Leu; LOW | nonsynonymous_codon ; L1194P | Average:9.425; most accessible tissue: Minghui63 panicle, score: 16.27 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0826584839 | A -> DEL | LOC_Os08g42090.1 | N | frameshift_variant | Average:9.425; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |