| Variant ID: vg1100141415 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 141415 |
| Reference Allele: CTG | Alternative Allele: C |
| Primary Allele: CTG | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GCAAGACTTCCGTCGCGTCTGGGAACATCGCTTTAACAGCTAAGGGCATCCACAATGCTATTATTTGGTAATAAGTAATGCTACTACTTAACTGCAGCAA[CTG/C]
TATGTCCCATGCGTTATACGGAGGGACCTATCCCAAGATATGCTCGCCCCGACGATGCCTTGCAGATCCTCTCTCTCCAAGTGATAGAAGCAAAAGATGG
CCATCTTTTGCTTCTATCACTTGGAGAGAGAGGATCTGCAAGGCATCGTCGGGGCGAGCATATCTTGGGATAGGTCCCTCCGTATAACGCATGGGACATA[CAG/G]
TTGCTGCAGTTAAGTAGTAGCATTACTTATTACCAAATAATAGCATTGTGGATGCCCTTAGCTGTTAAAGCGATGTTCCCAGACGCGACGGAAGTCTTGC
| Populations | Population Size | Frequency of CTG(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.10% | 1.70% | 0.19% | 0.00% | NA |
| All Indica | 2759 | 99.20% | 0.70% | 0.11% | 0.00% | NA |
| All Japonica | 1512 | 95.70% | 3.90% | 0.40% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.10% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 98.30% | 1.40% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 87.30% | 11.70% | 0.99% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 3.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1100141415 | CTG -> C | LOC_Os11g01250.1 | upstream_gene_variant ; 1098.0bp to feature; MODIFIER | silent_mutation | Average:68.973; most accessible tissue: Zhenshan97 flower, score: 87.172 | N | N | N | N |
| vg1100141415 | CTG -> C | LOC_Os11g01240.1 | downstream_gene_variant ; 2457.0bp to feature; MODIFIER | silent_mutation | Average:68.973; most accessible tissue: Zhenshan97 flower, score: 87.172 | N | N | N | N |
| vg1100141415 | CTG -> C | LOC_Os11g01270.1 | downstream_gene_variant ; 2749.0bp to feature; MODIFIER | silent_mutation | Average:68.973; most accessible tissue: Zhenshan97 flower, score: 87.172 | N | N | N | N |
| vg1100141415 | CTG -> C | LOC_Os11g01260.1 | intron_variant ; MODIFIER | silent_mutation | Average:68.973; most accessible tissue: Zhenshan97 flower, score: 87.172 | N | N | N | N |