| Variant ID: vg1126903438 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26903438 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CTGGACGACGAGTGATGTCCATGTGGCTGATAACGGGGAAGAGGAGGAGGTAGGAGTCGATCCTGCTCTGAACATCCCTGAACTTTTCAGCCTGCCTCCC[G/T]
GCCATCACCAACCTGTACATGGCGCTATTGTCCTGGCATGCCATCACAAGCTCGTGCGCCTCCCGGAGCGTGTCGTCGAGCCCGGTGAAGACGCGGCGGG
CCCGCCGCGTCTTCACCGGGCTCGACGACACGCTCCGGGAGGCGCACGAGCTTGTGATGGCATGCCAGGACAATAGCGCCATGTACAGGTTGGTGATGGC[C/A]
GGGAGGCAGGCTGAAAAGTTCAGGGATGTTCAGAGCAGGATCGACTCCTACCTCCTCCTCTTCCCCGTTATCAGCCACATGGACATCACTCGTCGTCCAG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 21.40% | 0.10% | 2.77% | 75.75% | NA |
| All Indica | 2759 | 13.10% | 0.10% | 3.59% | 83.18% | NA |
| All Japonica | 1512 | 38.50% | 0.10% | 1.32% | 60.12% | NA |
| Aus | 269 | 15.60% | 0.00% | 0.74% | 83.64% | NA |
| Indica I | 595 | 19.70% | 0.50% | 5.38% | 74.45% | NA |
| Indica II | 465 | 8.20% | 0.00% | 1.51% | 90.32% | NA |
| Indica III | 913 | 6.20% | 0.00% | 4.05% | 89.70% | NA |
| Indica Intermediate | 786 | 19.10% | 0.00% | 2.93% | 77.99% | NA |
| Temperate Japonica | 767 | 63.80% | 0.00% | 1.56% | 34.68% | NA |
| Tropical Japonica | 504 | 7.30% | 0.00% | 0.99% | 91.67% | NA |
| Japonica Intermediate | 241 | 23.20% | 0.40% | 1.24% | 75.10% | NA |
| VI/Aromatic | 96 | 8.30% | 0.00% | 8.33% | 83.33% | NA |
| Intermediate | 90 | 18.90% | 0.00% | 2.22% | 78.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126903438 | G -> T | LOC_Os11g44460.1 | synonymous_variant ; p.Ala79Ala; LOW | synonymous_codon | Average:16.004; most accessible tissue: Callus, score: 62.316 | N | N | N | N |
| vg1126903438 | G -> DEL | LOC_Os11g44460.1 | N | frameshift_variant | Average:16.004; most accessible tissue: Callus, score: 62.316 | N | N | N | N |