| Variant ID: vg0415575759 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 15575759 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCCTCTTCTCCCTCTCAGATCGATCTCCCTCTCCTCCTCCCCCTCCGCCACCTCCACTACCTCCTCCCCCTCCGCCTCCTCCCCTTCCTCCTCCCATCCC[C/T]
GGCCCTCTCCTCCCCGTCCTCCCTTCCCATCGCTCAGATCGATCTCCCTCTCCTCCTCACCTCCTCCCTCTCAGATCGATCTCTCTCCTCCTCCCCCTCC
GGAGGGGGAGGAGGAGAGAGATCGATCTGAGAGGGAGGAGGTGAGGAGGAGAGGGAGATCGATCTGAGCGATGGGAAGGGAGGACGGGGAGGAGAGGGCC[G/A]
GGGATGGGAGGAGGAAGGGGAGGAGGCGGAGGGGGAGGAGGTAGTGGAGGTGGCGGAGGGGGAGGAGGAGAGGGAGATCGATCTGAGAGGGAGAAGAGGG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 77.40% | 0.30% | 2.07% | 20.17% | NA |
| All Indica | 2759 | 83.40% | 0.50% | 2.68% | 13.48% | NA |
| All Japonica | 1512 | 78.40% | 0.10% | 0.53% | 20.97% | NA |
| Aus | 269 | 5.20% | 0.00% | 5.20% | 89.59% | NA |
| Indica I | 595 | 90.10% | 0.30% | 0.84% | 8.74% | NA |
| Indica II | 465 | 70.10% | 0.20% | 3.66% | 26.02% | NA |
| Indica III | 913 | 85.30% | 0.50% | 3.50% | 10.62% | NA |
| Indica Intermediate | 786 | 83.80% | 0.60% | 2.54% | 12.98% | NA |
| Temperate Japonica | 767 | 59.60% | 0.30% | 1.04% | 39.11% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.00% | 1.19% | NA |
| Japonica Intermediate | 241 | 95.40% | 0.00% | 0.00% | 4.56% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 0.00% | 7.29% | NA |
| Intermediate | 90 | 80.00% | 0.00% | 2.22% | 17.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0415575759 | C -> DEL | N | N | silent_mutation | Average:44.068; most accessible tissue: Zhenshan97 young leaf, score: 63.653 | N | N | N | N |
| vg0415575759 | C -> T | LOC_Os04g26690.1 | intron_variant ; MODIFIER | silent_mutation | Average:44.068; most accessible tissue: Zhenshan97 young leaf, score: 63.653 | N | N | N | N |