| Variant ID: vg1115079389 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 15079389 |
| Reference Allele: TTG | Alternative Allele: T |
| Primary Allele: TTG | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ATTGAGTTATTGGAGAAGATAGAGAGAAATCAGACTGGAAGACATGATTTATTTTTTTTACTACTGCTATTGATTTCCCAGGCATAAATTCATATTATTT[TTG/T]
TATACATATATAGACGTATCCCGTATCCATGTTTTTCAGAAAATGATGTATCCTATCCATATCCGTATCCCTGTATCTCGGTAACATAGAGCAAAGGATG
CATCCTTTGCTCTATGTTACCGAGATACAGGGATACGGATATGGATAGGATACATCATTTTCTGAAAAACATGGATACGGGATACGTCTATATATGTATA[CAA/A]
AAATAATATGAATTTATGCCTGGGAAATCAATAGCAGTAGTAAAAAAAATAAATCATGTCTTCCAGTCTGATTTCTCTCTATCTTCTCCAATAACTCAAT
| Populations | Population Size | Frequency of TTG(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.80% | 0.20% | 0.87% | 0.15% | NA |
| All Indica | 2759 | 98.00% | 0.40% | 1.45% | 0.18% | NA |
| All Japonica | 1512 | 99.80% | 0.00% | 0.07% | 0.13% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 91.90% | 1.70% | 5.55% | 0.84% | NA |
| Indica II | 465 | 99.60% | 0.00% | 0.43% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.40% | 0.00% | 0.64% | 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 | 98.80% | 0.00% | 0.41% | 0.83% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1115079389 | TTG -> T | LOC_Os11g26340.1 | downstream_gene_variant ; 3424.0bp to feature; MODIFIER | silent_mutation | Average:10.248; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg1115079389 | TTG -> T | LOC_Os11g26360.1 | downstream_gene_variant ; 3440.0bp to feature; MODIFIER | silent_mutation | Average:10.248; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg1115079389 | TTG -> T | LOC_Os11g26350.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.248; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg1115079389 | TTG -> DEL | N | N | silent_mutation | Average:10.248; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |