| Variant ID: vg1218481261 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18481261 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ACCCCCTAGTCGTCCTCTACCCATCCCCTCAAGTCCCGTCCGCCGCCATCGCCGGAAACGCTCTCCCCGCGAGCTCCCTCTCTCTCCACCTCCGGCAGCC[G/A]
CTCCAGCTGCCGTGCGCCGTCGCCCCGGCCGTCGCCGGTCAGCGCCGCCACTTCCCTCGGCTCCGCAAAGTCGAGCTCTACCCCGGCCACCCGTTCTTTT
AAAAGAACGGGTGGCCGGGGTAGAGCTCGACTTTGCGGAGCCGAGGGAAGTGGCGGCGCTGACCGGCGACGGCCGGGGCGACGGCGCACGGCAGCTGGAG[C/T]
GGCTGCCGGAGGTGGAGAGAGAGGGAGCTCGCGGGGAGAGCGTTTCCGGCGATGGCGGCGGACGGGACTTGAGGGGATGGGTAGAGGACGACTAGGGGGT
| 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 | 17.30% | 2.30% | 5.18% | 75.29% | NA |
| All Indica | 2759 | 6.30% | 3.30% | 6.31% | 84.16% | NA |
| All Japonica | 1512 | 36.60% | 0.50% | 0.79% | 62.04% | NA |
| Aus | 269 | 19.00% | 2.20% | 17.47% | 61.34% | NA |
| Indica I | 595 | 5.90% | 1.30% | 4.71% | 88.07% | NA |
| Indica II | 465 | 8.60% | 3.70% | 5.81% | 81.94% | NA |
| Indica III | 913 | 4.20% | 4.50% | 7.89% | 83.46% | NA |
| Indica Intermediate | 786 | 7.60% | 3.10% | 5.98% | 83.33% | NA |
| Temperate Japonica | 767 | 59.70% | 0.00% | 0.78% | 39.50% | NA |
| Tropical Japonica | 504 | 6.70% | 1.40% | 0.40% | 91.47% | NA |
| Japonica Intermediate | 241 | 25.70% | 0.40% | 1.66% | 72.20% | NA |
| VI/Aromatic | 96 | 10.40% | 1.00% | 5.21% | 83.33% | NA |
| Intermediate | 90 | 31.10% | 2.20% | 7.78% | 58.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218481261 | G -> DEL | N | N | silent_mutation | Average:36.941; most accessible tissue: Minghui63 young leaf, score: 65.161 | N | N | N | N |
| vg1218481261 | G -> A | LOC_Os12g30770.1 | upstream_gene_variant ; 1948.0bp to feature; MODIFIER | silent_mutation | Average:36.941; most accessible tissue: Minghui63 young leaf, score: 65.161 | N | N | N | N |
| vg1218481261 | G -> A | LOC_Os12g30790.1 | downstream_gene_variant ; 3645.0bp to feature; MODIFIER | silent_mutation | Average:36.941; most accessible tissue: Minghui63 young leaf, score: 65.161 | N | N | N | N |
| vg1218481261 | 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 |