| Variant ID: vg1224818756 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 24818756 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CATAATCAGCATGCTCATCATCATCATCACTCTTCTCTTCCTCAATCATCTCATGTTTGACATGAGAGCGGCTGCTGTTTGGATCTTCAGGCTCCTTCCC[T/C]
GTTGAAAATGGATCATCTTTATCTGTTAGCAAAATAAACAAGTAGAACATTCTTGGCTTCAATATCGTTTAAGAGTAATTCACAACATCACAATCTCAGA
TCTGAGATTGTGATGTTGTGAATTACTCTTAAACGATATTGAAGCCAAGAATGTTCTACTTGTTTATTTTGCTAACAGATAAAGATGATCCATTTTCAAC[A/G]
GGGAAGGAGCCTGAAGATCCAAACAGCAGCCGCTCTCATGTCAAACATGAGATGATTGAGGAAGAGAAGAGTGATGATGATGATGAGCATGCTGATTATG
| 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 | 99.70% | 0.20% | 0.11% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.10% | 0.60% | 0.33% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 98.30% | 1.20% | 0.52% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1224818756 | T -> C | LOC_Os12g40120.1 | splice_acceptor_variant&intron_variant ; HIGH | N | Average:50.403; most accessible tissue: Callus, score: 88.891 | N | N | N | N |
| vg1224818756 | T -> C | LOC_Os12g40130.1 | upstream_gene_variant ; 2348.0bp to feature; MODIFIER | N | Average:50.403; most accessible tissue: Callus, score: 88.891 | N | N | N | N |
| vg1224818756 | T -> C | LOC_Os12g40140.1 | upstream_gene_variant ; 4514.0bp to feature; MODIFIER | N | Average:50.403; most accessible tissue: Callus, score: 88.891 | N | N | N | N |