| Variant ID: vg0302880430 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 2880430 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GGCGCCGGCGCCGGCGGCGAGCCGGCGAAGAAGTCGACGGCGATGAAGAGCCAATCCTTCAGCATGGCGGGCCAGCCGCAACAGTAGACGAAGAAGAAGA[A/C]
GAAGAAGAAGAAGAAGAAGAAGATGCCGCGCTGCTAGCTGAGCCGTTCGCACGGCGGCCTGATCGAGCGCGCATTGCCATTTATCGTTTTTGATTTTCTC
GAGAAAATCAAAAACGATAAATGGCAATGCGCGCTCGATCAGGCCGCCGTGCGAACGGCTCAGCTAGCAGCGCGGCATCTTCTTCTTCTTCTTCTTCTTC[T/G]
TCTTCTTCTTCGTCTACTGTTGCGGCTGGCCCGCCATGCTGAAGGATTGGCTCTTCATCGCCGTCGACTTCTTCGCCGGCTCGCCGCCGGCGCCGGCGCC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.60% | 0.20% | 0.19% | 0.00% | NA |
| All Indica | 2759 | 99.40% | 0.30% | 0.29% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 98.90% | 0.70% | 0.37% | 0.00% | NA |
| Indica I | 595 | 99.00% | 0.20% | 0.84% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.20% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.40% | 0.40% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0302880430 | A -> C | LOC_Os03g05770.1 | 3_prime_UTR_variant ; 14.0bp to feature; MODIFIER | N | Average:69.932; most accessible tissue: Callus, score: 83.477 | N | N | N | N |
| vg0302880430 | A -> C | LOC_Os03g05760.1 | downstream_gene_variant ; 5000.0bp to feature; MODIFIER | N | Average:69.932; most accessible tissue: Callus, score: 83.477 | N | N | N | N |
| vg0302880430 | A -> C | LOC_Os03g05780.1 | downstream_gene_variant ; 2575.0bp to feature; MODIFIER | N | Average:69.932; most accessible tissue: Callus, score: 83.477 | N | N | N | N |