| Variant ID: vg1218481382 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18481382 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CGCCCCGGCCGTCGCCGGTCAGCGCCGCCACTTCCCTCGGCTCCGCAAAGTCGAGCTCTACCCCGGCCACCCGTTCTTTTGCGCTGAACCCCGCCGGAAG[T/C]
CGCCGTCACCGTGAAGGCCGAACCGTTGCCATGTTTTGATCTCCAACGAAGCTTTGCCGTCGACTCCGTGGTCGCCGGACCTCGCCGTATCCACTGTCGG
CCGACAGTGGATACGGCGAGGTCCGGCGACCACGGAGTCGACGGCAAAGCTTCGTTGGAGATCAAAACATGGCAACGGTTCGGCCTTCACGGTGACGGCG[A/G]
CTTCCGGCGGGGTTCAGCGCAAAAGAACGGGTGGCCGGGGTAGAGCTCGACTTTGCGGAGCCGAGGGAAGTGGCGGCGCTGACCGGCGACGGCCGGGGCG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 13.20% | 0.40% | 2.96% | 83.47% | NA |
| All Indica | 2759 | 2.30% | 0.60% | 3.15% | 93.95% | NA |
| All Japonica | 1512 | 35.10% | 0.00% | 0.60% | 64.29% | NA |
| Aus | 269 | 1.50% | 0.00% | 13.75% | 84.76% | NA |
| Indica I | 595 | 3.50% | 0.00% | 1.85% | 94.62% | NA |
| Indica II | 465 | 3.00% | 0.00% | 3.01% | 93.98% | NA |
| Indica III | 913 | 0.40% | 1.80% | 3.29% | 94.52% | NA |
| Indica Intermediate | 786 | 3.20% | 0.00% | 4.07% | 92.75% | NA |
| Temperate Japonica | 767 | 59.70% | 0.00% | 0.26% | 40.03% | NA |
| Tropical Japonica | 504 | 3.00% | 0.00% | 0.79% | 96.23% | NA |
| Japonica Intermediate | 241 | 24.10% | 0.00% | 1.24% | 74.69% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 4.17% | 95.83% | NA |
| Intermediate | 90 | 27.80% | 1.10% | 3.33% | 67.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218481382 | T -> C | LOC_Os12g30770.1 | upstream_gene_variant ; 2069.0bp to feature; MODIFIER | silent_mutation | Average:25.92; most accessible tissue: Minghui63 young leaf, score: 44.63 | N | N | N | N |
| vg1218481382 | T -> C | LOC_Os12g30790.1 | downstream_gene_variant ; 3524.0bp to feature; MODIFIER | silent_mutation | Average:25.92; most accessible tissue: Minghui63 young leaf, score: 44.63 | N | N | N | N |
| vg1218481382 | T -> C | LOC_Os12g30780.1 | intron_variant ; MODIFIER | silent_mutation | Average:25.92; most accessible tissue: Minghui63 young leaf, score: 44.63 | N | N | N | N |
| vg1218481382 | T -> DEL | N | N | silent_mutation | Average:25.92; most accessible tissue: Minghui63 young leaf, score: 44.63 | N | N | N | N |