| Variant ID: vg0811599502 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11599502 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 63. )
CAGTGCGCCCTGCGGCTCGGCGATGGTGTGTTCGGCGGCTGCGAGGCGGGCGGCTAGGTCGCCCTGGCCCGCGGCCGCCCCGCCGCTGTGCGCTCTCGCG[T/A]
CCAGCTCCTTCGCCCGCGCCTCGAGCTCAGCGGCCCGCTGATCCAGTGCGGCCCTCTCGGCGCGGACGCCTTCCAGATTGCGGCGCGCCTGCTCCTCCCG
CGGGAGGAGCAGGCGCGCCGCAATCTGGAAGGCGTCCGCGCCGAGAGGGCCGCACTGGATCAGCGGGCCGCTGAGCTCGAGGCGCGGGCGAAGGAGCTGG[A/T]
CGCGAGAGCGCACAGCGGCGGGGCGGCCGCGGGCCAGGGCGACCTAGCCGCCCGCCTCGCAGCCGCCGAACACACCATCGCCGAGCCGCAGGGCGCACTG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 0.60% | 0.30% | 3.43% | 95.66% | NA |
| All Indica | 2759 | 1.00% | 0.30% | 1.96% | 96.74% | NA |
| All Japonica | 1512 | 0.00% | 0.10% | 6.08% | 93.78% | NA |
| Aus | 269 | 0.00% | 1.10% | 4.46% | 94.42% | NA |
| Indica I | 595 | 0.20% | 0.30% | 0.84% | 98.66% | NA |
| Indica II | 465 | 0.00% | 0.00% | 0.22% | 99.78% | NA |
| Indica III | 913 | 2.20% | 0.30% | 4.27% | 93.21% | NA |
| Indica Intermediate | 786 | 0.80% | 0.50% | 1.15% | 97.58% | NA |
| Temperate Japonica | 767 | 0.00% | 0.10% | 7.69% | 92.18% | NA |
| Tropical Japonica | 504 | 0.00% | 0.20% | 4.17% | 95.63% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.00% | 4.98% | 95.02% | NA |
| VI/Aromatic | 96 | 0.00% | 1.00% | 1.04% | 97.92% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0811599502 | T -> A | LOC_Os08g19400.1 | missense_variant ; p.Asp134Val; MODERATE | nonsynonymous_codon ; D134V | Average:17.766; most accessible tissue: Zhenshan97 root, score: 32.766 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0811599502 | T -> DEL | LOC_Os08g19400.1 | N | frameshift_variant | Average:17.766; most accessible tissue: Zhenshan97 root, score: 32.766 | N | N | N | N |