| Variant ID: vg1123253212 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 23253212 |
| Reference Allele: G | Alternative Allele: A,C |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GCCATTGCACCCTCTCGAACGCCAGGATGGAGTCGACGTACCCCTGCGCCAATAATGGCGCAACGGCGGCTGGCTTCTGCGGCTCGCCGGCGGCGGTGGC[G/A,C]
GCCGCCGCCGCCGTCGTCTTCTTTGCCTCGTCGGCTGATGCCACCGCAGAGGCGTCCATGGATGATGGATCAGTATTCACTTGGAGTGCGTATGTCGACG
CGTCGACATACGCACTCCAAGTGAATACTGATCCATCATCCATGGACGCCTCTGCGGTGGCATCAGCCGACGAGGCAAAGAAGACGACGGCGGCGGCGGC[C/T,G]
GCCACCGCCGCCGGCGAGCCGCAGAAGCCAGCCGCCGTTGCGCCATTATTGGCGCAGGGGTACGTCGACTCCATCCTGGCGTTCGAGAGGGTGCAATGGC
| 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 | 95.30% | 2.60% | 1.93% | 0.19% | C: 0.04% |
| All Indica | 2759 | 98.20% | 1.40% | 0.33% | 0.07% | C: 0.04% |
| All Japonica | 1512 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 69.10% | 1.10% | 27.14% | 2.60% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.00% | 0.22% | 0.22% | C: 0.22% |
| Indica III | 913 | 96.60% | 3.30% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 97.80% | 1.10% | 0.89% | 0.13% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 25.00% | 70.80% | 4.17% | 0.00% | NA |
| Intermediate | 90 | 86.70% | 6.70% | 5.56% | 0.00% | C: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1123253212 | G -> A | LOC_Os11g39060.1 | synonymous_variant ; p.Ala20Ala; LOW | synonymous_codon | Average:69.47; most accessible tissue: Callus, score: 82.581 | N | N | N | N |
| vg1123253212 | G -> DEL | LOC_Os11g39060.1 | N | frameshift_variant | Average:69.47; most accessible tissue: Callus, score: 82.581 | N | N | N | N |
| vg1123253212 | G -> C | LOC_Os11g39060.1 | synonymous_variant ; p.Ala20Ala; LOW | synonymous_codon | Average:69.47; most accessible tissue: Callus, score: 82.581 | N | N | N | N |