| Variant ID: vg1218481214 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18481214 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TCCCGTCGATGTGGGCTCGATCCCGGCCTCCCATGGCTATATAAAGGACCCCCTAGTCGTCCTCTACCCATCCCCTCAAGTCCCGTCCGCCGCCATCGCC[G/T]
GAAACGCTCTCCCCGCGAGCTCCCTCTCTCTCCACCTCCGGCAGCCGCTCCAGCTGCCGTGCGCCGTCGCCCCGGCCGTCGCCGGTCAGCGCCGCCACTT
AAGTGGCGGCGCTGACCGGCGACGGCCGGGGCGACGGCGCACGGCAGCTGGAGCGGCTGCCGGAGGTGGAGAGAGAGGGAGCTCGCGGGGAGAGCGTTTC[C/A]
GGCGATGGCGGCGGACGGGACTTGAGGGGATGGGTAGAGGACGACTAGGGGGTCCTTTATATAGCCATGGGAGGCCGGGATCGAGCCCACATCGACGGGA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 16.60% | 0.60% | 4.13% | 78.67% | NA |
| All Indica | 2759 | 5.60% | 1.00% | 4.64% | 88.76% | NA |
| All Japonica | 1512 | 36.80% | 0.00% | 0.93% | 62.30% | NA |
| Aus | 269 | 11.20% | 0.00% | 17.84% | 71.00% | NA |
| Indica I | 595 | 5.00% | 0.70% | 4.71% | 89.58% | NA |
| Indica II | 465 | 8.80% | 0.00% | 3.23% | 87.96% | NA |
| Indica III | 913 | 2.20% | 1.90% | 5.37% | 90.58% | NA |
| Indica Intermediate | 786 | 8.00% | 0.90% | 4.58% | 86.51% | NA |
| Temperate Japonica | 767 | 60.00% | 0.00% | 0.39% | 39.63% | NA |
| Tropical Japonica | 504 | 6.20% | 0.00% | 1.39% | 92.46% | NA |
| Japonica Intermediate | 241 | 27.00% | 0.00% | 1.66% | 71.37% | NA |
| VI/Aromatic | 96 | 11.50% | 1.00% | 3.12% | 84.38% | NA |
| Intermediate | 90 | 36.70% | 0.00% | 2.22% | 61.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218481214 | G -> DEL | N | N | silent_mutation | Average:36.69; most accessible tissue: Minghui63 young leaf, score: 64.378 | N | N | N | N |
| vg1218481214 | G -> T | LOC_Os12g30770.1 | upstream_gene_variant ; 1901.0bp to feature; MODIFIER | silent_mutation | Average:36.69; most accessible tissue: Minghui63 young leaf, score: 64.378 | N | N | N | N |
| vg1218481214 | G -> T | LOC_Os12g30790.1 | downstream_gene_variant ; 3692.0bp to feature; MODIFIER | silent_mutation | Average:36.69; most accessible tissue: Minghui63 young leaf, score: 64.378 | N | N | N | N |
| vg1218481214 | G -> T | LOC_Os12g30780.1 | intron_variant ; MODIFIER | silent_mutation | Average:36.69; most accessible tissue: Minghui63 young leaf, score: 64.378 | N | N | N | N |