| Variant ID: vg1126903366 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26903366 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CGAGTTTTTTATGTTTGGTTAAAGGGTAGGGTGGATGGGGCGGCCCGGAATAGAAAATATTCTCTTAATAGGCTGGACGACGAGTGATGTCCATGTGGCT[G/A]
ATAACGGGGAAGAGGAGGAGGTAGGAGTCGATCCTGCTCTGAACATCCCTGAACTTTTCAGCCTGCCTCCCGGCCATCACCAACCTGTACATGGCGCTAT
ATAGCGCCATGTACAGGTTGGTGATGGCCGGGAGGCAGGCTGAAAAGTTCAGGGATGTTCAGAGCAGGATCGACTCCTACCTCCTCCTCTTCCCCGTTAT[C/T]
AGCCACATGGACATCACTCGTCGTCCAGCCTATTAAGAGAATATTTTCTATTCCGGGCCGCCCCATCCACCCTACCCTTTAACCAAACATAAAAAACTCG
| 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 | 68.80% | 1.10% | 1.02% | 29.12% | NA |
| All Indica | 2759 | 60.50% | 0.90% | 0.83% | 37.69% | NA |
| All Japonica | 1512 | 82.20% | 0.10% | 1.19% | 16.53% | NA |
| Aus | 269 | 72.10% | 7.80% | 1.86% | 18.22% | NA |
| Indica I | 595 | 53.60% | 0.20% | 0.84% | 45.38% | NA |
| Indica II | 465 | 66.90% | 0.60% | 0.65% | 31.83% | NA |
| Indica III | 913 | 59.70% | 0.80% | 0.77% | 38.77% | NA |
| Indica Intermediate | 786 | 63.00% | 1.90% | 1.02% | 34.10% | NA |
| Temperate Japonica | 767 | 85.70% | 0.10% | 1.43% | 12.78% | NA |
| Tropical Japonica | 504 | 79.40% | 0.00% | 1.39% | 19.25% | NA |
| Japonica Intermediate | 241 | 77.20% | 0.00% | 0.00% | 22.82% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 1.04% | 9.38% | NA |
| Intermediate | 90 | 65.60% | 2.20% | 1.11% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126903366 | G -> A | LOC_Os11g44460.1 | synonymous_variant ; p.Ile103Ile; LOW | synonymous_codon | Average:13.198; most accessible tissue: Callus, score: 46.436 | N | N | N | N |
| vg1126903366 | G -> DEL | LOC_Os11g44460.1 | N | frameshift_variant | Average:13.198; most accessible tissue: Callus, score: 46.436 | N | N | N | N |