| Variant ID: vg0415575714 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 15575714 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCTCTCCTCCACAACCGCCTCACACTTATCCTCTCAGATCGATCTCCCTCTTCTCCCTCTCAGATCGATCTCCCTCTCCTCCTCCCCCTCCGCCACCTCC[A/C]
CTACCTCCTCCCCCTCCGCCTCCTCCCCTTCCTCCTCCCATCCCCGGCCCTCTCCTCCCCGTCCTCCCTTCCCATCGCTCAGATCGATCTCCCTCTCCTC
GAGGAGAGGGAGATCGATCTGAGCGATGGGAAGGGAGGACGGGGAGGAGAGGGCCGGGGATGGGAGGAGGAAGGGGAGGAGGCGGAGGGGGAGGAGGTAG[T/G]
GGAGGTGGCGGAGGGGGAGGAGGAGAGGGAGATCGATCTGAGAGGGAGAAGAGGGAGATCGATCTGAGAGGATAAGTGTGAGGCGGTTGTGGAGGAGAGG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 60.70% | 10.40% | 5.61% | 23.32% | NA |
| All Indica | 2759 | 64.40% | 10.60% | 7.36% | 17.62% | NA |
| All Japonica | 1512 | 62.60% | 12.10% | 3.44% | 21.89% | NA |
| Aus | 269 | 3.00% | 0.40% | 0.37% | 96.28% | NA |
| Indica I | 595 | 73.40% | 8.90% | 6.72% | 10.92% | NA |
| Indica II | 465 | 54.00% | 8.60% | 7.96% | 29.46% | NA |
| Indica III | 913 | 64.20% | 11.80% | 7.23% | 16.76% | NA |
| Indica Intermediate | 786 | 64.10% | 11.60% | 7.63% | 16.67% | NA |
| Temperate Japonica | 767 | 50.60% | 6.00% | 2.87% | 40.55% | NA |
| Tropical Japonica | 504 | 74.60% | 20.60% | 3.57% | 1.19% | NA |
| Japonica Intermediate | 241 | 75.50% | 13.70% | 4.98% | 5.81% | NA |
| VI/Aromatic | 96 | 79.20% | 9.40% | 2.08% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0415575714 | A -> C | LOC_Os04g26690.1 | intron_variant ; MODIFIER | silent_mutation | Average:40.858; most accessible tissue: Zhenshan97 flag leaf, score: 60.705 | N | N | N | N |
| vg0415575714 | A -> DEL | N | N | silent_mutation | Average:40.858; most accessible tissue: Zhenshan97 flag leaf, score: 60.705 | N | N | N | N |