| Variant ID: vg0415575776 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 15575776 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GATCGATCTCCCTCTCCTCCTCCCCCTCCGCCACCTCCACTACCTCCTCCCCCTCCGCCTCCTCCCCTTCCTCCTCCCATCCCCGGCCCTCTCCTCCCCG[T/A]
CCTCCCTTCCCATCGCTCAGATCGATCTCCCTCTCCTCCTCACCTCCTCCCTCTCAGATCGATCTCTCTCCTCCTCCCCCTCCACCTCCTCCCCTTCCCA
TGGGAAGGGGAGGAGGTGGAGGGGGAGGAGGAGAGAGATCGATCTGAGAGGGAGGAGGTGAGGAGGAGAGGGAGATCGATCTGAGCGATGGGAAGGGAGG[A/T]
CGGGGAGGAGAGGGCCGGGGATGGGAGGAGGAAGGGGAGGAGGCGGAGGGGGAGGAGGTAGTGGAGGTGGCGGAGGGGGAGGAGGAGAGGGAGATCGATC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 77.70% | 0.10% | 1.33% | 20.95% | NA |
| All Indica | 2759 | 83.80% | 0.10% | 1.74% | 14.35% | NA |
| All Japonica | 1512 | 78.30% | 0.00% | 0.26% | 21.43% | NA |
| Aus | 269 | 4.80% | 0.00% | 3.72% | 91.45% | NA |
| Indica I | 595 | 90.30% | 0.00% | 0.84% | 8.91% | NA |
| Indica II | 465 | 70.30% | 0.00% | 1.94% | 27.74% | NA |
| Indica III | 913 | 85.90% | 0.10% | 2.52% | 11.50% | NA |
| Indica Intermediate | 786 | 84.50% | 0.30% | 1.40% | 13.87% | NA |
| Temperate Japonica | 767 | 59.70% | 0.00% | 0.26% | 40.03% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.00% | 1.19% | NA |
| Japonica Intermediate | 241 | 94.60% | 0.00% | 0.83% | 4.56% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 0.00% | 7.29% | NA |
| Intermediate | 90 | 80.00% | 0.00% | 1.11% | 18.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0415575776 | T -> DEL | N | N | silent_mutation | Average:44.6; most accessible tissue: Zhenshan97 young leaf, score: 65.804 | N | N | N | N |
| vg0415575776 | T -> A | LOC_Os04g26690.1 | intron_variant ; MODIFIER | silent_mutation | Average:44.6; most accessible tissue: Zhenshan97 young leaf, score: 65.804 | N | N | N | N |