| Variant ID: vg1218481387 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18481387 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CGGCCGTCGCCGGTCAGCGCCGCCACTTCCCTCGGCTCCGCAAAGTCGAGCTCTACCCCGGCCACCCGTTCTTTTGCGCTGAACCCCGCCGGAAGTCGCC[G/A]
TCACCGTGAAGGCCGAACCGTTGCCATGTTTTGATCTCCAACGAAGCTTTGCCGTCGACTCCGTGGTCGCCGGACCTCGCCGTATCCACTGTCGGCATCG
CGATGCCGACAGTGGATACGGCGAGGTCCGGCGACCACGGAGTCGACGGCAAAGCTTCGTTGGAGATCAAAACATGGCAACGGTTCGGCCTTCACGGTGA[C/T]
GGCGACTTCCGGCGGGGTTCAGCGCAAAAGAACGGGTGGCCGGGGTAGAGCTCGACTTTGCGGAGCCGAGGGAAGTGGCGGCGCTGACCGGCGACGGCCG
| 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 | 13.20% | 0.30% | 2.88% | 83.62% | NA |
| All Indica | 2759 | 2.30% | 0.50% | 2.97% | 94.20% | NA |
| All Japonica | 1512 | 35.10% | 0.00% | 0.60% | 64.29% | NA |
| Aus | 269 | 1.50% | 0.00% | 13.38% | 85.13% | NA |
| Indica I | 595 | 3.50% | 0.00% | 1.85% | 94.62% | NA |
| Indica II | 465 | 3.00% | 0.00% | 2.58% | 94.41% | NA |
| Indica III | 913 | 0.40% | 1.60% | 3.07% | 94.85% | NA |
| Indica Intermediate | 786 | 3.10% | 0.00% | 3.94% | 93.00% | NA |
| Temperate Japonica | 767 | 59.70% | 0.00% | 0.39% | 39.90% | NA |
| Tropical Japonica | 504 | 3.00% | 0.00% | 0.60% | 96.43% | NA |
| Japonica Intermediate | 241 | 24.10% | 0.00% | 1.24% | 74.69% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 5.21% | 94.79% | NA |
| Intermediate | 90 | 26.70% | 1.10% | 4.44% | 67.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218481387 | G -> DEL | N | N | silent_mutation | Average:25.353; most accessible tissue: Minghui63 young leaf, score: 44.63 | N | N | N | N |
| vg1218481387 | G -> A | LOC_Os12g30780.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:25.353; most accessible tissue: Minghui63 young leaf, score: 44.63 | N | N | N | N |
| vg1218481387 | G -> A | LOC_Os12g30770.1 | upstream_gene_variant ; 2074.0bp to feature; MODIFIER | silent_mutation | Average:25.353; most accessible tissue: Minghui63 young leaf, score: 44.63 | N | N | N | N |
| vg1218481387 | G -> A | LOC_Os12g30790.1 | downstream_gene_variant ; 3519.0bp to feature; MODIFIER | silent_mutation | Average:25.353; most accessible tissue: Minghui63 young leaf, score: 44.63 | N | N | N | N |