| Variant ID: vg0811599568 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11599568 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GCCCGCGGCCGCCCCGCCGCTGTGCGCTCTCGCGTCCAGCTCCTTCGCCCGCGCCTCGAGCTCAGCGGCCCGCTGATCCAGTGCGGCCCTCTCGGCGCGG[A/G]
CGCCTTCCAGATTGCGGCGCGCCTGCTCCTCCCGCGCTGCCTCGCGGAGGAACAGGCTGTCCGCCAGCCGCTGCGCCGCGGCCTCGGCCTCCTCAGCCTG
CAGGCTGAGGAGGCCGAGGCCGCGGCGCAGCGGCTGGCGGACAGCCTGTTCCTCCGCGAGGCAGCGCGGGAGGAGCAGGCGCGCCGCAATCTGGAAGGCG[T/C]
CCGCGCCGAGAGGGCCGCACTGGATCAGCGGGCCGCTGAGCTCGAGGCGCGGGCGAAGGAGCTGGACGCGAGAGCGCACAGCGGCGGGGCGGCCGCGGGC
| 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 | 2.80% | 0.30% | 2.71% | 94.20% | NA |
| All Indica | 2759 | 1.10% | 0.40% | 3.59% | 94.89% | NA |
| All Japonica | 1512 | 5.70% | 0.00% | 1.06% | 93.25% | NA |
| Aus | 269 | 4.10% | 0.00% | 4.09% | 91.82% | NA |
| Indica I | 595 | 0.70% | 0.20% | 1.01% | 98.15% | NA |
| Indica II | 465 | 0.00% | 0.00% | 0.43% | 99.57% | NA |
| Indica III | 913 | 1.60% | 1.00% | 8.21% | 89.16% | NA |
| Indica Intermediate | 786 | 1.40% | 0.30% | 2.04% | 96.31% | NA |
| Temperate Japonica | 767 | 6.90% | 0.00% | 1.17% | 91.92% | NA |
| Tropical Japonica | 504 | 4.20% | 0.00% | 0.79% | 95.04% | NA |
| Japonica Intermediate | 241 | 5.00% | 0.00% | 1.24% | 93.78% | NA |
| VI/Aromatic | 96 | 4.20% | 0.00% | 1.04% | 94.79% | NA |
| Intermediate | 90 | 3.30% | 0.00% | 1.11% | 95.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811599568 | A -> G | LOC_Os08g19400.1 | missense_variant ; p.Val112Ala; MODERATE | nonsynonymous_codon ; V112A | Average:16.824; most accessible tissue: Zhenshan97 root, score: 29.203 | unknown | unknown | TOLERATED | 1.00 |
| vg0811599568 | A -> DEL | LOC_Os08g19400.1 | N | frameshift_variant | Average:16.824; most accessible tissue: Zhenshan97 root, score: 29.203 | N | N | N | N |