| Variant ID: vg1225603256 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 25603256 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AAGAACGCTAAGAATGCATCCCACAAAGAGAGTAGTGGCTTCCTCGAATTGCTTCTGCTGTTCAGCAGTAAGAACTCCTTCAGGTTTGCCAGTACTCACC[C/T]
AGAAGCATTTCATAGCTGTCAGCCACAGAGTGACCCTGATCTGCCATCTCTTAAAATGCACACCGGTGAATTTATCCGGCCTCAGTGCATCGGCAAAACC
GGTTTTGCCGATGCACTGAGGCCGGATAAATTCACCGGTGTGCATTTTAAGAGATGGCAGATCAGGGTCACTCTGTGGCTGACAGCTATGAAATGCTTCT[G/A]
GGTGAGTACTGGCAAACCTGAAGGAGTTCTTACTGCTGAACAGCAGAAGCAATTCGAGGAAGCCACTACTCTCTTTGTGGGATGCATTCTTAGCGTTCTT
| 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 | 74.90% | 1.50% | 8.65% | 14.90% | NA |
| All Indica | 2759 | 67.50% | 2.60% | 14.39% | 15.51% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 8.60% | 0.00% | 2.23% | 89.22% | NA |
| Indica I | 595 | 91.10% | 0.00% | 4.54% | 4.37% | NA |
| Indica II | 465 | 38.30% | 5.80% | 26.67% | 29.25% | NA |
| Indica III | 913 | 73.20% | 3.50% | 11.28% | 12.05% | NA |
| Indica Intermediate | 786 | 60.30% | 1.70% | 18.19% | 19.85% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 76.00% | 0.00% | 1.04% | 22.92% | NA |
| Intermediate | 90 | 78.90% | 0.00% | 5.56% | 15.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1225603256 | C -> DEL | LOC_Os12g41280.1 | N | frameshift_variant | Average:15.427; most accessible tissue: Zhenshan97 flag leaf, score: 26.688 | N | N | N | N |
| vg1225603256 | C -> T | LOC_Os12g41280.1 | stop_gained ; p.Trp36*; HIGH | stop_gained | Average:15.427; most accessible tissue: Zhenshan97 flag leaf, score: 26.688 | N | N | N | N |