| Variant ID: vg0811599505 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11599505 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 63. )
TGCGCCCTGCGGCTCGGCGATGGTGTGTTCGGCGGCTGCGAGGCGGGCGGCTAGGTCGCCCTGGCCCGCGGCCGCCCCGCCGCTGTGCGCTCTCGCGTCC[A/G]
GCTCCTTCGCCCGCGCCTCGAGCTCAGCGGCCCGCTGATCCAGTGCGGCCCTCTCGGCGCGGACGCCTTCCAGATTGCGGCGCGCCTGCTCCTCCCGCGC
GCGCGGGAGGAGCAGGCGCGCCGCAATCTGGAAGGCGTCCGCGCCGAGAGGGCCGCACTGGATCAGCGGGCCGCTGAGCTCGAGGCGCGGGCGAAGGAGC[T/C]
GGACGCGAGAGCGCACAGCGGCGGGGCGGCCGCGGGCCAGGGCGACCTAGCCGCCCGCCTCGCAGCCGCCGAACACACCATCGCCGAGCCGCAGGGCGCA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 0.60% | 0.40% | 3.66% | 95.32% | NA |
| All Indica | 2759 | 1.00% | 0.40% | 2.46% | 96.16% | NA |
| All Japonica | 1512 | 0.00% | 0.30% | 5.82% | 93.92% | NA |
| Aus | 269 | 0.00% | 1.10% | 4.83% | 94.05% | NA |
| Indica I | 595 | 0.20% | 0.50% | 0.84% | 98.49% | NA |
| Indica II | 465 | 0.00% | 0.00% | 0.22% | 99.78% | NA |
| Indica III | 913 | 2.20% | 0.40% | 5.81% | 91.57% | NA |
| Indica Intermediate | 786 | 0.80% | 0.50% | 1.15% | 97.58% | NA |
| Temperate Japonica | 767 | 0.00% | 0.30% | 7.43% | 92.31% | NA |
| Tropical Japonica | 504 | 0.00% | 0.20% | 4.17% | 95.63% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.40% | 4.15% | 95.44% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0811599505 | A -> G | LOC_Os08g19400.1 | missense_variant ; p.Leu133Pro; MODERATE | nonsynonymous_codon ; L133P | Average:17.325; most accessible tissue: Zhenshan97 root, score: 30.989 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0811599505 | A -> DEL | LOC_Os08g19400.1 | N | frameshift_variant | Average:17.325; most accessible tissue: Zhenshan97 root, score: 30.989 | N | N | N | N |