| Variant ID: vg1218481269 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18481269 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GTCGTCCTCTACCCATCCCCTCAAGTCCCGTCCGCCGCCATCGCCGGAAACGCTCTCCCCGCGAGCTCCCTCTCTCTCCACCTCCGGCAGCCGCTCCAGC[T/C]
GCCGTGCGCCGTCGCCCCGGCCGTCGCCGGTCAGCGCCGCCACTTCCCTCGGCTCCGCAAAGTCGAGCTCTACCCCGGCCACCCGTTCTTTTGCGCTGAA
TTCAGCGCAAAAGAACGGGTGGCCGGGGTAGAGCTCGACTTTGCGGAGCCGAGGGAAGTGGCGGCGCTGACCGGCGACGGCCGGGGCGACGGCGCACGGC[A/G]
GCTGGAGCGGCTGCCGGAGGTGGAGAGAGAGGGAGCTCGCGGGGAGAGCGTTTCCGGCGATGGCGGCGGACGGGACTTGAGGGGATGGGTAGAGGACGAC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 13.20% | 3.20% | 6.69% | 76.91% | NA |
| All Indica | 2759 | 2.90% | 4.10% | 6.78% | 86.23% | NA |
| All Japonica | 1512 | 34.60% | 1.10% | 1.79% | 62.57% | NA |
| Aus | 269 | 0.70% | 4.50% | 31.23% | 63.57% | NA |
| Indica I | 595 | 2.40% | 1.50% | 5.71% | 90.42% | NA |
| Indica II | 465 | 4.30% | 4.30% | 6.67% | 84.73% | NA |
| Indica III | 913 | 2.00% | 5.80% | 7.23% | 84.99% | NA |
| Indica Intermediate | 786 | 3.40% | 4.10% | 7.12% | 85.37% | NA |
| Temperate Japonica | 767 | 58.80% | 0.10% | 1.17% | 39.90% | NA |
| Tropical Japonica | 504 | 3.00% | 2.60% | 2.58% | 91.87% | NA |
| Japonica Intermediate | 241 | 23.70% | 0.80% | 2.07% | 73.44% | NA |
| VI/Aromatic | 96 | 0.00% | 4.20% | 7.29% | 88.54% | NA |
| Intermediate | 90 | 22.20% | 5.60% | 12.22% | 60.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218481269 | T -> C | LOC_Os12g30770.1 | upstream_gene_variant ; 1956.0bp to feature; MODIFIER | silent_mutation | Average:36.941; most accessible tissue: Minghui63 young leaf, score: 65.161 | N | N | N | N |
| vg1218481269 | T -> C | LOC_Os12g30790.1 | downstream_gene_variant ; 3637.0bp to feature; MODIFIER | silent_mutation | Average:36.941; most accessible tissue: Minghui63 young leaf, score: 65.161 | N | N | N | N |
| vg1218481269 | T -> C | LOC_Os12g30780.1 | intron_variant ; MODIFIER | silent_mutation | Average:36.941; most accessible tissue: Minghui63 young leaf, score: 65.161 | N | N | N | N |
| vg1218481269 | T -> DEL | N | N | silent_mutation | Average:36.941; most accessible tissue: Minghui63 young leaf, score: 65.161 | N | N | N | N |