| Variant ID: vg0332982231 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 32982231 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GATGCGTGCATCAATCAACAACAAGCTTAACAAATGGATGATTTCTATCACCTAAACAAAGATCTGTTCTTTTGGCTCATAAATAAAGATTATTGTCAAT[G/T]
GGAACATGTTTCTTCAGTGAAAACAAATACTAAATTACATGCAAGTATTCAATCTTACATGTTTCAGAACAGATCACTGAGCTTGCTACTCAATGTTTGC
GCAAACATTGAGTAGCAAGCTCAGTGATCTGTTCTGAAACATGTAAGATTGAATACTTGCATGTAATTTAGTATTTGTTTTCACTGAAGAAACATGTTCC[C/A]
ATTGACAATAATCTTTATTTATGAGCCAAAAGAACAGATCTTTGTTTAGGTGATAGAAATCATCCATTTGTTAAGCTTGTTGTTGATTGATGCACGCATC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.70% | 0.20% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 99.60% | 0.40% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.30% | 1.50% | 0.22% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.40% | 0.00% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0332982231 | G -> T | LOC_Os03g57900.1 | 3_prime_UTR_variant ; 162.0bp to feature; MODIFIER | N | Average:73.106; most accessible tissue: Minghui63 flower, score: 86.285 | N | N | N | N |
| vg0332982231 | G -> T | LOC_Os03g57910.1 | downstream_gene_variant ; 2283.0bp to feature; MODIFIER | N | Average:73.106; most accessible tissue: Minghui63 flower, score: 86.285 | N | N | N | N |
| vg0332982231 | G -> T | LOC_Os03g57920.1 | downstream_gene_variant ; 4812.0bp to feature; MODIFIER | N | Average:73.106; most accessible tissue: Minghui63 flower, score: 86.285 | N | N | N | N |