| Variant ID: vg0128509559 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28509559 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.69, G: 0.31, others allele: 0.00, population size: 42. )
CCAGTGGACGATCACGCCGGCGACAGGCAATGCGGAGGGCTCGAGGGCAGATGAAGATGGTGATGAGGAAGAAGCTTAGGGCGAACGACGCGGCCAAGGC[A/G]
CCGAACAACATCATGGTGCTGCAGCATCCGGAGGCCGAGCTCGCCTGACGTCCGATCCGCCCGCCGCTCGCATCCGCATGTGCCTATCGCCGCTCCGCCC
GGGCGGAGCGGCGATAGGCACATGCGGATGCGAGCGGCGGGCGGATCGGACGTCAGGCGAGCTCGGCCTCCGGATGCTGCAGCACCATGATGTTGTTCGG[T/C]
GCCTTGGCCGCGTCGTTCGCCCTAAGCTTCTTCCTCATCACCATCTTCATCTGCCCTCGAGCCCTCCGCATTGCCTGTCGCCGGCGTGATCGTCCACTGG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 25.00% | 10.50% | 8.42% | 56.12% | NA |
| All Indica | 2759 | 1.40% | 9.00% | 13.95% | 75.57% | NA |
| All Japonica | 1512 | 72.10% | 15.30% | 0.40% | 12.24% | NA |
| Aus | 269 | 4.10% | 0.00% | 0.37% | 95.54% | NA |
| Indica I | 595 | 1.70% | 4.90% | 4.20% | 89.24% | NA |
| Indica II | 465 | 2.60% | 5.60% | 6.88% | 84.95% | NA |
| Indica III | 913 | 0.50% | 16.00% | 29.03% | 54.44% | NA |
| Indica Intermediate | 786 | 1.70% | 6.10% | 8.02% | 84.22% | NA |
| Temperate Japonica | 767 | 93.00% | 0.00% | 0.13% | 6.91% | NA |
| Tropical Japonica | 504 | 32.50% | 42.70% | 0.79% | 24.01% | NA |
| Japonica Intermediate | 241 | 88.40% | 6.60% | 0.41% | 4.56% | NA |
| VI/Aromatic | 96 | 13.50% | 0.00% | 3.12% | 83.33% | NA |
| Intermediate | 90 | 31.10% | 15.60% | 3.33% | 50.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128509559 | A -> G | LOC_Os01g49570.1 | synonymous_variant ; p.Gly5Gly; LOW | synonymous_codon | Average:37.821; most accessible tissue: Zhenshan97 panicle, score: 59.59 | N | N | N | N |
| vg0128509559 | A -> G | LOC_Os01g49570.1 | synonymous_variant ; p.Gly5Gly; LOW | nonsynonymous_codon ; G5D | Average:37.821; most accessible tissue: Zhenshan97 panicle, score: 59.59 | unknown | unknown | DELETERIOUS | 0.03 |
| vg0128509559 | A -> DEL | LOC_Os01g49570.1 | N | frameshift_variant | Average:37.821; most accessible tissue: Zhenshan97 panicle, score: 59.59 | N | N | N | N |