| Variant ID: vg1101752260 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 1752260 |
| Reference Allele: TG | Alternative Allele: T |
| Primary Allele: TG | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GAAATACGATTCTACTTTTACATCGATAGCAAATACAACGGATCTGTTGGTGAACCGAAACATAAATAGCATCATCAGCAGCTTTGAACCTGCTGCTGCT[TG/T]
GGCAGCGCGTAGCGGCAGAGAGGGCAGAGGCAGCTATCCCTGAGCCAACGGAAGAGGCAGTTCTCGTGGAAGGAGTGGTTACACGGCATCGTCCTCAGCC
GGCTGAGGACGATGCCGTGTAACCACTCCTTCCACGAGAACTGCCTCTTCCGTTGGCTCAGGGATAGCTGCCTCTGCCCTCTCTGCCGCTACGCGCTGCC[CA/A]
AGCAGCAGCAGGTTCAAAGCTGCTGATGATGCTATTTATGTTTCGGTTCACCAACAGATCCGTTGTATTTGCTATCGATGTAAAAGTAGAATCGTATTTC
| Populations | Population Size | Frequency of TG(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101752260 | TG -> T | LOC_Os11g04280.1 | frameshift_variant ; p.Lys211fs; HIGH | N | Average:41.824; most accessible tissue: Callus, score: 67.863 | N | N | N | N |
| vg1101752260 | TG -> T | LOC_Os11g04270.1 | upstream_gene_variant ; 1365.0bp to feature; MODIFIER | N | Average:41.824; most accessible tissue: Callus, score: 67.863 | N | N | N | N |
| vg1101752260 | TG -> T | LOC_Os11g04240.1 | downstream_gene_variant ; 3437.0bp to feature; MODIFIER | N | Average:41.824; most accessible tissue: Callus, score: 67.863 | N | N | N | N |
| vg1101752260 | TG -> T | LOC_Os11g04267.1 | downstream_gene_variant ; 4685.0bp to feature; MODIFIER | N | Average:41.824; most accessible tissue: Callus, score: 67.863 | N | N | N | N |