| Variant ID: vg1115079454 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 15079454 |
| Reference Allele: CCGTATCCCTG | Alternative Allele: C,CTATCCCTG |
| Primary Allele: CCGTATCCCTG | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GCTATTGATTTCCCAGGCATAAATTCATATTATTTTTGTATACATATATAGACGTATCCCGTATCCATGTTTTTCAGAAAATGATGTATCCTATCCATAT[CCGTATCCCTG/C,CTATCCCTG]
TATCTCGGTAACATAGAGCAAAGGATGTTGCTTGCTGCAGATGGGGTGACGGCCGCAGCGGCAGCGACAGTGAGTAGTTTAGAACTTCAGATTAGCTATC
GATAGCTAATCTGAAGTTCTAAACTACTCACTGTCGCTGCCGCTGCGGCCGTCACCCCATCTGCAGCAAGCAACATCCTTTGCTCTATGTTACCGAGATA[CAGGGATACGG/G,CAGGGATAG]
ATATGGATAGGATACATCATTTTCTGAAAAACATGGATACGGGATACGTCTATATATGTATACAAAAATAATATGAATTTATGCCTGGGAAATCAATAGC
| Populations | Population Size | Frequency of CCGTATCCCTG(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 58.10% | 1.20% | 37.03% | 3.62% | CTATCCCTG: 0.04% |
| All Indica | 2759 | 31.00% | 2.10% | 61.29% | 5.58% | CTATCCCTG: 0.07% |
| All Japonica | 1512 | 98.30% | 0.00% | 1.26% | 0.46% | NA |
| Aus | 269 | 91.40% | 0.00% | 5.58% | 2.97% | NA |
| Indica I | 595 | 25.40% | 0.70% | 66.89% | 7.06% | NA |
| Indica II | 465 | 29.70% | 4.10% | 65.38% | 0.65% | CTATCCCTG: 0.22% |
| Indica III | 913 | 33.10% | 1.90% | 58.05% | 7.01% | NA |
| Indica Intermediate | 786 | 33.50% | 2.30% | 58.40% | 5.73% | CTATCCCTG: 0.13% |
| Temperate Japonica | 767 | 97.90% | 0.00% | 1.69% | 0.39% | NA |
| Tropical Japonica | 504 | 99.00% | 0.00% | 0.79% | 0.20% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 0.83% | 1.24% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 70.00% | 1.10% | 26.67% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1115079454 | CCGTATCCCTG -> CTATCCCTG | LOC_Os11g26340.1 | downstream_gene_variant ; 3489.0bp to feature; MODIFIER | silent_mutation | Average:8.066; most accessible tissue: Callus, score: 10.872 | N | N | N | N |
| vg1115079454 | CCGTATCCCTG -> CTATCCCTG | LOC_Os11g26360.1 | downstream_gene_variant ; 3375.0bp to feature; MODIFIER | silent_mutation | Average:8.066; most accessible tissue: Callus, score: 10.872 | N | N | N | N |
| vg1115079454 | CCGTATCCCTG -> CTATCCCTG | LOC_Os11g26350.1 | intron_variant ; MODIFIER | silent_mutation | Average:8.066; most accessible tissue: Callus, score: 10.872 | N | N | N | N |
| vg1115079454 | CCGTATCCCTG -> DEL | N | N | silent_mutation | Average:8.066; most accessible tissue: Callus, score: 10.872 | N | N | N | N |
| vg1115079454 | CCGTATCCCTG -> C | LOC_Os11g26340.1 | downstream_gene_variant ; 3489.0bp to feature; MODIFIER | silent_mutation | Average:8.066; most accessible tissue: Callus, score: 10.872 | N | N | N | N |
| vg1115079454 | CCGTATCCCTG -> C | LOC_Os11g26360.1 | downstream_gene_variant ; 3375.0bp to feature; MODIFIER | silent_mutation | Average:8.066; most accessible tissue: Callus, score: 10.872 | N | N | N | N |
| vg1115079454 | CCGTATCCCTG -> C | LOC_Os11g26350.1 | intron_variant ; MODIFIER | silent_mutation | Average:8.066; most accessible tissue: Callus, score: 10.872 | N | N | N | N |