| Variant ID: vg0522747537 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr05 | Position: 22747537 |
| Reference Allele: A | Alternative Allele: AG,AGG,AGGG |
| Primary Allele: A | Secondary Allele: AG |
Inferred Ancestral Allele: Not determined.
GCCCCCCACGCGCGCACCCGATCCGCCCGCGCGTCCGCCCGCGGGAAGAGAGAAGGGGGCGATCGATCGATCGATCGCGCCGGGGCGCGCGCGCGCGTGG[A/AG,AGG,AGGG]
GGGGGGGAAGGAGAGGGCGATGGGGGGTTGGGGGAGATGGAAGGTGGGGGAGGAGGGTGGGAGATTGGGGGAGAAGGCCTTGGAGAGGGATCCAAGGGCC
GGCCCTTGGATCCCTCTCCAAGGCCTTCTCCCCCAATCTCCCACCCTCCTCCCCCACCTTCCATCTCCCCCAACCCCCCATCGCCCTCTCCTTCCCCCCC[T/CT,CCT,CCCT]
CCACGCGCGCGCGCGCCCCGGCGCGATCGATCGATCGATCGCCCCCTTCTCTCTTCCCGCGGGCGGACGCGCGGGCGGATCGGGTGCGCGCGTGGGGGGC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of AG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 28.40% | 5.40% | 8.55% | 56.18% | AGG: 1.25%; AGGG: 0.25% |
| All Indica | 2759 | 1.30% | 9.20% | 4.20% | 82.86% | AGG: 2.14%; AGGG: 0.29% |
| All Japonica | 1512 | 72.20% | 0.00% | 18.72% | 8.86% | AGGG: 0.26% |
| Aus | 269 | 34.90% | 0.00% | 0.00% | 65.06% | NA |
| Indica I | 595 | 0.70% | 32.30% | 2.18% | 64.71% | AGGG: 0.17% |
| Indica II | 465 | 1.50% | 1.30% | 4.73% | 90.11% | AGG: 2.37% |
| Indica III | 913 | 0.80% | 1.30% | 5.48% | 86.75% | AGG: 4.93%; AGGG: 0.77% |
| Indica Intermediate | 786 | 2.40% | 5.50% | 3.94% | 87.79% | AGG: 0.38% |
| Temperate Japonica | 767 | 57.60% | 0.00% | 27.51% | 14.86% | NA |
| Tropical Japonica | 504 | 88.90% | 0.00% | 8.73% | 1.59% | AGGG: 0.79% |
| Japonica Intermediate | 241 | 83.40% | 0.00% | 11.62% | 4.98% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 0.00% | 12.50% | NA |
| Intermediate | 90 | 37.80% | 3.30% | 5.56% | 53.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0522747537 | A -> AG | LOC_Os05g38770.1 | 5_prime_UTR_variant ; 340.0bp to feature; MODIFIER | silent_mutation | Average:81.102; most accessible tissue: Zhenshan97 flower, score: 89.639 | N | N | N | N |
| vg0522747537 | A -> AG | LOC_Os05g38760.1 | upstream_gene_variant ; 3086.0bp to feature; MODIFIER | silent_mutation | Average:81.102; most accessible tissue: Zhenshan97 flower, score: 89.639 | N | N | N | N |
| vg0522747537 | A -> AG | LOC_Os05g38780.1 | upstream_gene_variant ; 4005.0bp to feature; MODIFIER | silent_mutation | Average:81.102; most accessible tissue: Zhenshan97 flower, score: 89.639 | N | N | N | N |
| vg0522747537 | A -> DEL | N | N | silent_mutation | Average:81.102; most accessible tissue: Zhenshan97 flower, score: 89.639 | N | N | N | N |
| vg0522747537 | A -> AGGG | LOC_Os05g38770.1 | 5_prime_UTR_variant ; 340.0bp to feature; MODIFIER | silent_mutation | Average:81.102; most accessible tissue: Zhenshan97 flower, score: 89.639 | N | N | N | N |
| vg0522747537 | A -> AGGG | LOC_Os05g38760.1 | upstream_gene_variant ; 3086.0bp to feature; MODIFIER | silent_mutation | Average:81.102; most accessible tissue: Zhenshan97 flower, score: 89.639 | N | N | N | N |
| vg0522747537 | A -> AGGG | LOC_Os05g38780.1 | upstream_gene_variant ; 4005.0bp to feature; MODIFIER | silent_mutation | Average:81.102; most accessible tissue: Zhenshan97 flower, score: 89.639 | N | N | N | N |
| vg0522747537 | A -> AGG | LOC_Os05g38770.1 | 5_prime_UTR_variant ; 340.0bp to feature; MODIFIER | silent_mutation | Average:81.102; most accessible tissue: Zhenshan97 flower, score: 89.639 | N | N | N | N |
| vg0522747537 | A -> AGG | LOC_Os05g38760.1 | upstream_gene_variant ; 3086.0bp to feature; MODIFIER | silent_mutation | Average:81.102; most accessible tissue: Zhenshan97 flower, score: 89.639 | N | N | N | N |
| vg0522747537 | A -> AGG | LOC_Os05g38780.1 | upstream_gene_variant ; 4005.0bp to feature; MODIFIER | silent_mutation | Average:81.102; most accessible tissue: Zhenshan97 flower, score: 89.639 | N | N | N | N |