| Variant ID: vg1218481288 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18481288 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTCAAGTCCCGTCCGCCGCCATCGCCGGAAACGCTCTCCCCGCGAGCTCCCTCTCTCTCCACCTCCGGCAGCCGCTCCAGCTGCCGTGCGCCGTCGCCCC[G/A]
GCCGTCGCCGGTCAGCGCCGCCACTTCCCTCGGCTCCGCAAAGTCGAGCTCTACCCCGGCCACCCGTTCTTTTGCGCTGAACCCCGCCGGAAGTCGCCGT
ACGGCGACTTCCGGCGGGGTTCAGCGCAAAAGAACGGGTGGCCGGGGTAGAGCTCGACTTTGCGGAGCCGAGGGAAGTGGCGGCGCTGACCGGCGACGGC[C/T]
GGGGCGACGGCGCACGGCAGCTGGAGCGGCTGCCGGAGGTGGAGAGAGAGGGAGCTCGCGGGGAGAGCGTTTCCGGCGATGGCGGCGGACGGGACTTGAG
| 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 | 32.20% | 0.20% | 9.33% | 58.34% | NA |
| All Indica | 2759 | 26.00% | 0.30% | 12.58% | 61.11% | NA |
| All Japonica | 1512 | 39.00% | 0.00% | 2.38% | 58.66% | NA |
| Aus | 269 | 59.90% | 0.00% | 6.32% | 33.83% | NA |
| Indica I | 595 | 16.10% | 0.00% | 6.89% | 76.97% | NA |
| Indica II | 465 | 28.60% | 0.00% | 9.46% | 61.94% | NA |
| Indica III | 913 | 30.00% | 0.70% | 17.96% | 51.37% | NA |
| Indica Intermediate | 786 | 27.40% | 0.30% | 12.47% | 59.92% | NA |
| Temperate Japonica | 767 | 60.60% | 0.00% | 0.65% | 38.72% | NA |
| Tropical Japonica | 504 | 10.30% | 0.00% | 4.17% | 85.52% | NA |
| Japonica Intermediate | 241 | 29.90% | 0.00% | 4.15% | 65.98% | NA |
| VI/Aromatic | 96 | 13.50% | 0.00% | 30.21% | 56.25% | NA |
| Intermediate | 90 | 43.30% | 0.00% | 13.33% | 43.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218481288 | G -> DEL | N | N | silent_mutation | Average:36.772; most accessible tissue: Minghui63 young leaf, score: 65.161 | N | N | N | N |
| vg1218481288 | G -> A | LOC_Os12g30770.1 | upstream_gene_variant ; 1975.0bp to feature; MODIFIER | silent_mutation | Average:36.772; most accessible tissue: Minghui63 young leaf, score: 65.161 | N | N | N | N |
| vg1218481288 | G -> A | LOC_Os12g30790.1 | downstream_gene_variant ; 3618.0bp to feature; MODIFIER | silent_mutation | Average:36.772; most accessible tissue: Minghui63 young leaf, score: 65.161 | N | N | N | N |
| vg1218481288 | G -> A | LOC_Os12g30780.1 | intron_variant ; MODIFIER | silent_mutation | Average:36.772; most accessible tissue: Minghui63 young leaf, score: 65.161 | N | N | N | N |