| Variant ID: vg1100141429 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 141429 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCGTCTGGGAACATCGCTTTAACAGCTAAGGGCATCCACAATGCTATTATTTGGTAATAAGTAATGCTACTACTTAACTGCAGCAACTGTATGTCCCATG[C/T]
GTTATACGGAGGGACCTATCCCAAGATATGCTCGCCCCGACGATGCCTTGCAGATCCTCTCTCTCCAAGTGATAGAAGCAAAAGATGGTCTTAACTGGCC
GGCCAGTTAAGACCATCTTTTGCTTCTATCACTTGGAGAGAGAGGATCTGCAAGGCATCGTCGGGGCGAGCATATCTTGGGATAGGTCCCTCCGTATAAC[G/A]
CATGGGACATACAGTTGCTGCAGTTAAGTAGTAGCATTACTTATTACCAAATAATAGCATTGTGGATGCCCTTAGCTGTTAAAGCGATGTTCCCAGACGC
| Populations | Population Size | Frequency of C(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 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.30% | 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 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 3.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1100141429 | C -> T | LOC_Os11g01250.1 | upstream_gene_variant ; 1111.0bp to feature; MODIFIER | N | Average:68.926; most accessible tissue: Callus, score: 90.654 | N | N | N | N |
| vg1100141429 | C -> T | LOC_Os11g01240.1 | downstream_gene_variant ; 2470.0bp to feature; MODIFIER | N | Average:68.926; most accessible tissue: Callus, score: 90.654 | N | N | N | N |
| vg1100141429 | C -> T | LOC_Os11g01270.1 | downstream_gene_variant ; 2736.0bp to feature; MODIFIER | N | Average:68.926; most accessible tissue: Callus, score: 90.654 | N | N | N | N |
| vg1100141429 | C -> T | LOC_Os11g01260.1 | intron_variant ; MODIFIER | N | Average:68.926; most accessible tissue: Callus, score: 90.654 | N | N | N | N |