| Variant ID: vg1218481384 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18481384 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCCCGGCCGTCGCCGGTCAGCGCCGCCACTTCCCTCGGCTCCGCAAAGTCGAGCTCTACCCCGGCCACCCGTTCTTTTGCGCTGAACCCCGCCGGAAGTC[G/A]
CCGTCACCGTGAAGGCCGAACCGTTGCCATGTTTTGATCTCCAACGAAGCTTTGCCGTCGACTCCGTGGTCGCCGGACCTCGCCGTATCCACTGTCGGCA
TGCCGACAGTGGATACGGCGAGGTCCGGCGACCACGGAGTCGACGGCAAAGCTTCGTTGGAGATCAAAACATGGCAACGGTTCGGCCTTCACGGTGACGG[C/T]
GACTTCCGGCGGGGTTCAGCGCAAAAGAACGGGTGGCCGGGGTAGAGCTCGACTTTGCGGAGCCGAGGGAAGTGGCGGCGCTGACCGGCGACGGCCGGGG
| 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 | 13.50% | 0.20% | 4.17% | 82.16% | NA |
| All Indica | 2759 | 3.10% | 0.00% | 2.68% | 94.24% | NA |
| All Japonica | 1512 | 34.50% | 0.50% | 0.07% | 64.88% | NA |
| Aus | 269 | 1.90% | 0.00% | 41.26% | 56.88% | NA |
| Indica I | 595 | 3.70% | 0.00% | 0.84% | 95.46% | NA |
| Indica II | 465 | 3.70% | 0.00% | 2.58% | 93.76% | NA |
| Indica III | 913 | 2.40% | 0.00% | 2.52% | 95.07% | NA |
| Indica Intermediate | 786 | 3.10% | 0.00% | 4.33% | 92.62% | NA |
| Temperate Japonica | 767 | 59.70% | 0.00% | 0.00% | 40.29% | NA |
| Tropical Japonica | 504 | 2.80% | 0.20% | 0.20% | 96.83% | NA |
| Japonica Intermediate | 241 | 20.70% | 2.90% | 0.00% | 76.35% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 4.17% | 95.83% | NA |
| Intermediate | 90 | 28.90% | 0.00% | 7.78% | 63.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218481384 | G -> DEL | N | N | silent_mutation | Average:25.353; most accessible tissue: Minghui63 young leaf, score: 44.63 | N | N | N | N |
| vg1218481384 | 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 |
| vg1218481384 | G -> A | LOC_Os12g30770.1 | upstream_gene_variant ; 2071.0bp to feature; MODIFIER | silent_mutation | Average:25.353; most accessible tissue: Minghui63 young leaf, score: 44.63 | N | N | N | N |
| vg1218481384 | G -> A | LOC_Os12g30790.1 | downstream_gene_variant ; 3522.0bp to feature; MODIFIER | silent_mutation | Average:25.353; most accessible tissue: Minghui63 young leaf, score: 44.63 | N | N | N | N |