| Variant ID: vg1218481270 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18481270 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TCGTCCTCTACCCATCCCCTCAAGTCCCGTCCGCCGCCATCGCCGGAAACGCTCTCCCCGCGAGCTCCCTCTCTCTCCACCTCCGGCAGCCGCTCCAGCT[G/A]
CCGTGCGCCGTCGCCCCGGCCGTCGCCGGTCAGCGCCGCCACTTCCCTCGGCTCCGCAAAGTCGAGCTCTACCCCGGCCACCCGTTCTTTTGCGCTGAAC
GTTCAGCGCAAAAGAACGGGTGGCCGGGGTAGAGCTCGACTTTGCGGAGCCGAGGGAAGTGGCGGCGCTGACCGGCGACGGCCGGGGCGACGGCGCACGG[C/T]
AGCTGGAGCGGCTGCCGGAGGTGGAGAGAGAGGGAGCTCGCGGGGAGAGCGTTTCCGGCGATGGCGGCGGACGGGACTTGAGGGGATGGGTAGAGGACGA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 18.20% | 2.30% | 5.59% | 73.89% | NA |
| All Indica | 2759 | 7.60% | 3.30% | 7.14% | 81.88% | NA |
| All Japonica | 1512 | 36.80% | 0.50% | 0.79% | 61.84% | NA |
| Aus | 269 | 20.40% | 2.20% | 15.61% | 61.71% | NA |
| Indica I | 595 | 5.70% | 1.30% | 5.38% | 87.56% | NA |
| Indica II | 465 | 11.00% | 3.70% | 4.95% | 80.43% | NA |
| Indica III | 913 | 6.40% | 4.80% | 9.09% | 79.74% | NA |
| Indica Intermediate | 786 | 8.70% | 2.90% | 7.51% | 80.92% | NA |
| Temperate Japonica | 767 | 59.80% | 0.00% | 0.78% | 39.37% | NA |
| Tropical Japonica | 504 | 6.70% | 1.40% | 0.40% | 91.47% | NA |
| Japonica Intermediate | 241 | 26.60% | 0.40% | 1.66% | 71.37% | NA |
| VI/Aromatic | 96 | 9.40% | 1.00% | 7.29% | 82.29% | NA |
| Intermediate | 90 | 32.20% | 2.20% | 6.67% | 58.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218481270 | G -> DEL | N | N | silent_mutation | Average:36.941; most accessible tissue: Minghui63 young leaf, score: 65.161 | N | N | N | N |
| vg1218481270 | G -> A | LOC_Os12g30770.1 | upstream_gene_variant ; 1957.0bp to feature; MODIFIER | silent_mutation | Average:36.941; most accessible tissue: Minghui63 young leaf, score: 65.161 | N | N | N | N |
| vg1218481270 | G -> A | LOC_Os12g30790.1 | downstream_gene_variant ; 3636.0bp to feature; MODIFIER | silent_mutation | Average:36.941; most accessible tissue: Minghui63 young leaf, score: 65.161 | N | N | N | N |
| vg1218481270 | G -> A | LOC_Os12g30780.1 | intron_variant ; MODIFIER | silent_mutation | Average:36.941; most accessible tissue: Minghui63 young leaf, score: 65.161 | N | N | N | N |