| Variant ID: vg0811599636 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11599636 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCCGCTGATCCAGTGCGGCCCTCTCGGCGCGGACGCCTTCCAGATTGCGGCGCGCCTGCTCCTCCCGCGCTGCCTCGCGGAGGAACAGGCTGTCCGCCAG[C/T]
CGCTGCGCCGCGGCCTCGGCCTCCTCAGCCTGGTGAACCCGGACGGCCTCCTGGGCAGCCTCCTCGGCTTCCCGGAGGCGGTCCGCGGCTTCTCGCCGGT
ACCGGCGAGAAGCCGCGGACCGCCTCCGGGAAGCCGAGGAGGCTGCCCAGGAGGCCGTCCGGGTTCACCAGGCTGAGGAGGCCGAGGCCGCGGCGCAGCG[G/A]
CTGGCGGACAGCCTGTTCCTCCGCGAGGCAGCGCGGGAGGAGCAGGCGCGCCGCAATCTGGAAGGCGTCCGCGCCGAGAGGGCCGCACTGGATCAGCGGG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 0.50% | 0.10% | 8.61% | 90.80% | NA |
| All Indica | 2759 | 0.20% | 0.10% | 6.81% | 92.93% | NA |
| All Japonica | 1512 | 0.70% | 0.10% | 10.65% | 88.56% | NA |
| Aus | 269 | 2.20% | 0.00% | 16.36% | 81.41% | NA |
| Indica I | 595 | 0.20% | 0.20% | 0.17% | 99.50% | NA |
| Indica II | 465 | 0.00% | 0.00% | 2.15% | 97.85% | NA |
| Indica III | 913 | 0.30% | 0.10% | 13.58% | 85.98% | NA |
| Indica Intermediate | 786 | 0.10% | 0.00% | 6.74% | 93.13% | NA |
| Temperate Japonica | 767 | 0.50% | 0.00% | 10.69% | 88.79% | NA |
| Tropical Japonica | 504 | 0.80% | 0.20% | 12.30% | 86.71% | NA |
| Japonica Intermediate | 241 | 1.20% | 0.00% | 7.05% | 91.70% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 7.29% | 90.62% | NA |
| Intermediate | 90 | 1.10% | 0.00% | 7.78% | 91.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811599636 | C -> T | LOC_Os08g19400.1 | synonymous_variant ; p.Arg89Arg; LOW | synonymous_codon | Average:17.158; most accessible tissue: Zhenshan97 root, score: 30.989 | N | N | N | N |
| vg0811599636 | C -> DEL | LOC_Os08g19400.1 | N | frameshift_variant | Average:17.158; most accessible tissue: Zhenshan97 root, score: 30.989 | N | N | N | N |