| Variant ID: vg0522747581 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 22747581 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GAAGAGAGAAGGGGGCGATCGATCGATCGATCGCGCCGGGGCGCGCGCGCGCGTGGAGGGGGGGAAGGAGAGGGCGATGGGGGGTTGGGGGAGATGGAAG[G/T]
TGGGGGAGGAGGGTGGGAGATTGGGGGAGAAGGCCTTGGAGAGGGATCCAAGGGCCTTCTCTGGAAGGAGGGGAGGGAGGAAGGAGAGGGGGAGGGGAGG
CCTCCCCTCCCCCTCTCCTTCCTCCCTCCCCTCCTTCCAGAGAAGGCCCTTGGATCCCTCTCCAAGGCCTTCTCCCCCAATCTCCCACCCTCCTCCCCCA[C/A]
CTTCCATCTCCCCCAACCCCCCATCGCCCTCTCCTTCCCCCCCTCCACGCGCGCGCGCGCCCCGGCGCGATCGATCGATCGATCGCCCCCTTCTCTCTTC
| 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 | 17.60% | 1.50% | 23.38% | 57.58% | NA |
| All Indica | 2759 | 15.40% | 0.10% | 6.85% | 77.60% | NA |
| All Japonica | 1512 | 24.50% | 0.00% | 52.65% | 22.88% | NA |
| Aus | 269 | 2.20% | 19.30% | 19.70% | 58.74% | NA |
| Indica I | 595 | 25.40% | 0.00% | 12.94% | 61.68% | NA |
| Indica II | 465 | 12.90% | 0.20% | 6.24% | 80.65% | NA |
| Indica III | 913 | 14.80% | 0.00% | 3.83% | 81.38% | NA |
| Indica Intermediate | 786 | 10.20% | 0.30% | 6.11% | 83.46% | NA |
| Temperate Japonica | 767 | 20.70% | 0.00% | 52.54% | 26.73% | NA |
| Tropical Japonica | 504 | 28.20% | 0.00% | 54.56% | 17.26% | NA |
| Japonica Intermediate | 241 | 28.60% | 0.00% | 48.96% | 22.41% | NA |
| VI/Aromatic | 96 | 13.50% | 14.60% | 42.71% | 29.17% | NA |
| Intermediate | 90 | 16.70% | 1.10% | 28.89% | 53.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0522747581 | G -> T | LOC_Os05g38770.1 | 5_prime_UTR_variant ; 383.0bp to feature; MODIFIER | silent_mutation | Average:79.563; most accessible tissue: Zhenshan97 flower, score: 89.409 | N | N | N | N |
| vg0522747581 | G -> T | LOC_Os05g38760.1 | upstream_gene_variant ; 3129.0bp to feature; MODIFIER | silent_mutation | Average:79.563; most accessible tissue: Zhenshan97 flower, score: 89.409 | N | N | N | N |
| vg0522747581 | G -> T | LOC_Os05g38780.1 | upstream_gene_variant ; 3962.0bp to feature; MODIFIER | silent_mutation | Average:79.563; most accessible tissue: Zhenshan97 flower, score: 89.409 | N | N | N | N |
| vg0522747581 | G -> DEL | N | N | silent_mutation | Average:79.563; most accessible tissue: Zhenshan97 flower, score: 89.409 | N | N | N | N |