| Variant ID: vg1105183275 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5183275 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 268. )
CTATTTTCTTACACTTTTTTCCCTCAAATCACTATCATCACGCCACATTGTATTTTCCTTTTTTTCAGCACACTGTACCCTATATTCAGTTGCTGCCACA[A/G]
TTGACGCCACTCGTAGGGTAGAAGGGGCCAAGAAAGGATTGATAATCTCCACTCCACTTGACGTACCAGAGATGGCTAAAACATATGAGCAAGTCACTGG
CCAGTGACTTGCTCATATGTTTTAGCCATCTCTGGTACGTCAAGTGGAGTGGAGATTATCAATCCTTTCTTGGCCCCTTCTACCCTACGAGTGGCGTCAA[T/C]
TGTGGCAGCAACTGAATATAGGGTACAGTGTGCTGAAAAAAAGGAAAATACAATGTGGCGTGATGATAGTGATTTGAGGGAAAAAAGTGTAAGAAAATAG
| 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 | 68.70% | 0.10% | 0.97% | 30.24% | NA |
| All Indica | 2759 | 51.30% | 0.00% | 1.49% | 47.23% | NA |
| All Japonica | 1512 | 98.90% | 0.00% | 0.07% | 1.06% | NA |
| Aus | 269 | 68.00% | 1.90% | 0.74% | 29.37% | NA |
| Indica I | 595 | 28.70% | 0.00% | 2.52% | 68.74% | NA |
| Indica II | 465 | 22.40% | 0.00% | 1.72% | 75.91% | NA |
| Indica III | 913 | 73.90% | 0.00% | 0.88% | 25.19% | NA |
| Indica Intermediate | 786 | 59.20% | 0.00% | 1.27% | 39.57% | NA |
| Temperate Japonica | 767 | 98.00% | 0.00% | 0.13% | 1.83% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 0.00% | 8.33% | NA |
| Intermediate | 90 | 72.20% | 0.00% | 2.22% | 25.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105183275 | A -> DEL | LOC_Os11g09710.1 | N | frameshift_variant | Average:16.421; most accessible tissue: Callus, score: 81.049 | N | N | N | N |
| vg1105183275 | A -> G | LOC_Os11g09710.1 | missense_variant ; p.Ile117Val; MODERATE | nonsynonymous_codon ; I117V | Average:16.421; most accessible tissue: Callus, score: 81.049 | unknown | unknown | TOLERATED | 0.39 |