| Variant ID: vg1115079390 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 15079390 |
| Reference Allele: TG | Alternative Allele: T |
| Primary Allele: TG | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTGAGTTATTGGAGAAGATAGAGAGAAATCAGACTGGAAGACATGATTTATTTTTTTTACTACTGCTATTGATTTCCCAGGCATAAATTCATATTATTTT[TG/T]
TATACATATATAGACGTATCCCGTATCCATGTTTTTCAGAAAATGATGTATCCTATCCATATCCGTATCCCTGTATCTCGGTAACATAGAGCAAAGGATG
CATCCTTTGCTCTATGTTACCGAGATACAGGGATACGGATATGGATAGGATACATCATTTTCTGAAAAACATGGATACGGGATACGTCTATATATGTATA[CA/A]
AAAATAATATGAATTTATGCCTGGGAAATCAATAGCAGTAGTAAAAAAAATAAATCATGTCTTCCAGTCTGATTTCTCTCTATCTTCTCCAATAACTCAA
| 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 | 88.20% | 2.50% | 7.81% | 1.54% | NA |
| All Indica | 2759 | 81.00% | 4.00% | 12.79% | 2.25% | NA |
| All Japonica | 1512 | 99.20% | 0.10% | 0.33% | 0.40% | NA |
| Aus | 269 | 94.40% | 1.90% | 2.60% | 1.12% | NA |
| Indica I | 595 | 79.70% | 1.30% | 17.65% | 1.34% | NA |
| Indica II | 465 | 84.50% | 4.90% | 10.54% | 0.00% | NA |
| Indica III | 913 | 81.20% | 4.90% | 10.30% | 3.61% | NA |
| Indica Intermediate | 786 | 79.60% | 4.30% | 13.36% | 2.67% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.26% | 0.39% | NA |
| Tropical Japonica | 504 | 99.40% | 0.20% | 0.20% | 0.20% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.83% | 0.83% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 1.10% | 4.44% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1115079390 | TG -> T | LOC_Os11g26340.1 | downstream_gene_variant ; 3425.0bp to feature; MODIFIER | silent_mutation | Average:10.248; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg1115079390 | TG -> T | LOC_Os11g26360.1 | downstream_gene_variant ; 3439.0bp to feature; MODIFIER | silent_mutation | Average:10.248; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg1115079390 | TG -> T | LOC_Os11g26350.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.248; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg1115079390 | TG -> DEL | N | N | silent_mutation | Average:10.248; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |