| Variant ID: vg0415575717 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 15575717 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTCCTCCACAACCGCCTCACACTTATCCTCTCAGATCGATCTCCCTCTTCTCCCTCTCAGATCGATCTCCCTCTCCTCCTCCCCCTCCGCCACCTCCACT[A/T]
CCTCCTCCCCCTCCGCCTCCTCCCCTTCCTCCTCCCATCCCCGGCCCTCTCCTCCCCGTCCTCCCTTCCCATCGCTCAGATCGATCTCCCTCTCCTCCTC
GAGGAGGAGAGGGAGATCGATCTGAGCGATGGGAAGGGAGGACGGGGAGGAGAGGGCCGGGGATGGGAGGAGGAAGGGGAGGAGGCGGAGGGGGAGGAGG[T/A]
AGTGGAGGTGGCGGAGGGGGAGGAGGAGAGGGAGATCGATCTGAGAGGGAGAAGAGGGAGATCGATCTGAGAGGATAAGTGTGAGGCGGTTGTGGAGGAG
| 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 | 60.40% | 10.60% | 5.65% | 23.40% | NA |
| All Indica | 2759 | 64.00% | 10.80% | 7.25% | 17.91% | NA |
| All Japonica | 1512 | 62.60% | 12.20% | 3.57% | 21.69% | NA |
| Aus | 269 | 3.00% | 0.40% | 0.74% | 95.91% | NA |
| Indica I | 595 | 72.80% | 9.20% | 6.72% | 11.26% | NA |
| Indica II | 465 | 54.40% | 8.80% | 7.31% | 29.46% | NA |
| Indica III | 913 | 63.50% | 11.90% | 7.34% | 17.20% | NA |
| Indica Intermediate | 786 | 63.70% | 11.80% | 7.51% | 16.92% | NA |
| Temperate Japonica | 767 | 50.60% | 6.00% | 3.26% | 40.16% | NA |
| Tropical Japonica | 504 | 74.60% | 20.80% | 3.37% | 1.19% | NA |
| Japonica Intermediate | 241 | 75.50% | 13.70% | 4.98% | 5.81% | NA |
| VI/Aromatic | 96 | 77.10% | 9.40% | 4.17% | 9.38% | NA |
| Intermediate | 90 | 65.60% | 7.80% | 7.78% | 18.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0415575717 | A -> DEL | N | N | silent_mutation | Average:41.43; most accessible tissue: Zhenshan97 flag leaf, score: 61.322 | N | N | N | N |
| vg0415575717 | A -> T | LOC_Os04g26690.1 | intron_variant ; MODIFIER | silent_mutation | Average:41.43; most accessible tissue: Zhenshan97 flag leaf, score: 61.322 | N | N | N | N |