| Variant ID: vg1218481219 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18481219 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TCGATGTGGGCTCGATCCCGGCCTCCCATGGCTATATAAAGGACCCCCTAGTCGTCCTCTACCCATCCCCTCAAGTCCCGTCCGCCGCCATCGCCGGAAA[C/T]
GCTCTCCCCGCGAGCTCCCTCTCTCTCCACCTCCGGCAGCCGCTCCAGCTGCCGTGCGCCGTCGCCCCGGCCGTCGCCGGTCAGCGCCGCCACTTCCCTC
GAGGGAAGTGGCGGCGCTGACCGGCGACGGCCGGGGCGACGGCGCACGGCAGCTGGAGCGGCTGCCGGAGGTGGAGAGAGAGGGAGCTCGCGGGGAGAGC[G/A]
TTTCCGGCGATGGCGGCGGACGGGACTTGAGGGGATGGGTAGAGGACGACTAGGGGGTCCTTTATATAGCCATGGGAGGCCGGGATCGAGCCCACATCGA
| 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 | 18.00% | 0.20% | 8.23% | 73.51% | NA |
| All Indica | 2759 | 7.80% | 0.00% | 8.92% | 83.29% | NA |
| All Japonica | 1512 | 37.00% | 0.00% | 0.99% | 61.97% | NA |
| Aus | 269 | 16.40% | 2.60% | 39.03% | 42.01% | NA |
| Indica I | 595 | 6.20% | 0.00% | 5.88% | 87.90% | NA |
| Indica II | 465 | 13.80% | 0.00% | 4.95% | 81.29% | NA |
| Indica III | 913 | 3.60% | 0.00% | 12.71% | 83.68% | NA |
| Indica Intermediate | 786 | 10.30% | 0.00% | 9.16% | 80.53% | NA |
| Temperate Japonica | 767 | 60.50% | 0.00% | 0.52% | 38.98% | NA |
| Tropical Japonica | 504 | 6.70% | 0.00% | 1.39% | 91.87% | NA |
| Japonica Intermediate | 241 | 25.70% | 0.00% | 1.66% | 72.61% | NA |
| VI/Aromatic | 96 | 1.00% | 3.10% | 16.67% | 79.17% | NA |
| Intermediate | 90 | 36.70% | 0.00% | 7.78% | 55.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218481219 | C -> DEL | N | N | silent_mutation | Average:36.852; most accessible tissue: Minghui63 young leaf, score: 64.378 | N | N | N | N |
| vg1218481219 | C -> T | LOC_Os12g30770.1 | upstream_gene_variant ; 1906.0bp to feature; MODIFIER | silent_mutation | Average:36.852; most accessible tissue: Minghui63 young leaf, score: 64.378 | N | N | N | N |
| vg1218481219 | C -> T | LOC_Os12g30790.1 | downstream_gene_variant ; 3687.0bp to feature; MODIFIER | silent_mutation | Average:36.852; most accessible tissue: Minghui63 young leaf, score: 64.378 | N | N | N | N |
| vg1218481219 | C -> T | LOC_Os12g30780.1 | intron_variant ; MODIFIER | silent_mutation | Average:36.852; most accessible tissue: Minghui63 young leaf, score: 64.378 | N | N | N | N |