| Variant ID: vg0132054062 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 32054062 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GAACATCAATGCTCATAGCATTGTCTATATTACTCAAGGTCATGCCGGGTTCAAGTTGTCAACAACAATGGAAAGACAGTGTTTGATGGAGAGGTTCGTC[C/G]
TGGGCAGCTGCTAATTATACCACAACACCATGTAGTTGTGAAAAAAGCACAAAGAGAAGGATGCTTATATATTGCATTCAAAACCAACCCTAATTCCATT
AATGGAATTAGGGTTGGTTTTGAATGCAATATATAAGCATCCTTCTCTTTGTGCTTTTTTCACAACTACATGGTGTTGTGGTATAATTAGCAGCTGCCCA[G/C]
GACGAACCTCTCCATCAAACACTGTCTTTCCATTGTTGTTGACAACTTGAACCCGGCATGACCTTGAGTAATATAGACAATGCTATGAGCATTGATGTTC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.00% | 0.80% | 0.23% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 96.80% | 2.50% | 0.73% | 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 | 93.70% | 5.00% | 1.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0132054062 | C -> G | LOC_Os01g55630.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:45.497; most accessible tissue: Callus, score: 84.144 | N | N | N | N |
| vg0132054062 | C -> G | LOC_Os01g55620.1 | upstream_gene_variant ; 3296.0bp to feature; MODIFIER | silent_mutation | Average:45.497; most accessible tissue: Callus, score: 84.144 | N | N | N | N |
| vg0132054062 | C -> G | LOC_Os01g55640.1 | upstream_gene_variant ; 3093.0bp to feature; MODIFIER | silent_mutation | Average:45.497; most accessible tissue: Callus, score: 84.144 | N | N | N | N |
| vg0132054062 | C -> G | LOC_Os01g55650.1 | downstream_gene_variant ; 3321.0bp to feature; MODIFIER | silent_mutation | Average:45.497; most accessible tissue: Callus, score: 84.144 | N | N | N | N |