| Variant ID: vg0811599507 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11599507 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CGCCCTGCGGCTCGGCGATGGTGTGTTCGGCGGCTGCGAGGCGGGCGGCTAGGTCGCCCTGGCCCGCGGCCGCCCCGCCGCTGTGCGCTCTCGCGTCCAG[C/T]
TCCTTCGCCCGCGCCTCGAGCTCAGCGGCCCGCTGATCCAGTGCGGCCCTCTCGGCGCGGACGCCTTCCAGATTGCGGCGCGCCTGCTCCTCCCGCGCTG
CAGCGCGGGAGGAGCAGGCGCGCCGCAATCTGGAAGGCGTCCGCGCCGAGAGGGCCGCACTGGATCAGCGGGCCGCTGAGCTCGAGGCGCGGGCGAAGGA[G/A]
CTGGACGCGAGAGCGCACAGCGGCGGGGCGGCCGCGGGCCAGGGCGACCTAGCCGCCCGCCTCGCAGCCGCCGAACACACCATCGCCGAGCCGCAGGGCG
| 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 | 0.60% | 0.50% | 3.41% | 95.58% | NA |
| All Indica | 2759 | 0.90% | 0.50% | 1.99% | 96.63% | NA |
| All Japonica | 1512 | 0.00% | 0.30% | 5.69% | 94.05% | NA |
| Aus | 269 | 0.00% | 1.10% | 5.95% | 92.94% | NA |
| Indica I | 595 | 0.20% | 0.70% | 0.50% | 98.66% | NA |
| Indica II | 465 | 0.00% | 0.00% | 0.22% | 99.78% | NA |
| Indica III | 913 | 2.10% | 0.40% | 4.60% | 92.88% | NA |
| Indica Intermediate | 786 | 0.60% | 0.60% | 1.15% | 97.58% | NA |
| Temperate Japonica | 767 | 0.00% | 0.30% | 7.30% | 92.44% | NA |
| Tropical Japonica | 504 | 0.00% | 0.20% | 4.17% | 95.63% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.40% | 3.73% | 95.85% | NA |
| VI/Aromatic | 96 | 0.00% | 2.10% | 1.04% | 96.88% | NA |
| Intermediate | 90 | 1.10% | 0.00% | 3.33% | 95.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811599507 | C -> T | LOC_Os08g19400.1 | synonymous_variant ; p.Glu132Glu; LOW | synonymous_codon | Average:17.245; most accessible tissue: Zhenshan97 root, score: 30.989 | N | N | N | N |
| vg0811599507 | C -> DEL | LOC_Os08g19400.1 | N | frameshift_variant | Average:17.245; most accessible tissue: Zhenshan97 root, score: 30.989 | N | N | N | N |