| Variant ID: vg0234179687 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 34179687 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GCAATCACGTGGTTAACTGCTTCAAACCCACGGATTGCACAGTGGAAAAGGTATTGTTGTGCATCGGGTGAGCCCCCACGTAAGTTTTTAACCGATGCAG[A/G]
CCATCAGTGGAATGCCACTTATTTTATTTTAAAGGTTGTATTACCTTACAAGGATTTACTTACTGTTTTCCTTCAAACACGTAATGGCCCAAAAAACAGT
ACTGTTTTTTGGGCCATTACGTGTTTGAAGGAAAACAGTAAGTAAATCCTTGTAAGGTAATACAACCTTTAAAATAAAATAAGTGGCATTCCACTGATGG[T/C]
CTGCATCGGTTAAAAACTTACGTGGGGGCTCACCCGATGCACAACAATACCTTTTCCACTGTGCAATCCGTGGGTTTGAAGCAGTTAACCACGTGATTGC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 45.20% | 0.10% | 8.42% | 46.25% | NA |
| All Indica | 2759 | 20.90% | 0.00% | 9.17% | 69.88% | NA |
| All Japonica | 1512 | 97.00% | 0.40% | 0.40% | 2.25% | NA |
| Aus | 269 | 3.70% | 0.00% | 44.98% | 51.30% | NA |
| Indica I | 595 | 17.80% | 0.00% | 3.53% | 78.66% | NA |
| Indica II | 465 | 12.70% | 0.00% | 7.53% | 79.78% | NA |
| Indica III | 913 | 27.30% | 0.00% | 12.38% | 60.35% | NA |
| Indica Intermediate | 786 | 20.90% | 0.00% | 10.69% | 68.45% | NA |
| Temperate Japonica | 767 | 97.10% | 0.00% | 0.39% | 2.48% | NA |
| Tropical Japonica | 504 | 97.80% | 1.20% | 0.40% | 0.60% | NA |
| Japonica Intermediate | 241 | 94.60% | 0.00% | 0.41% | 4.98% | NA |
| VI/Aromatic | 96 | 29.20% | 0.00% | 12.50% | 58.33% | NA |
| Intermediate | 90 | 60.00% | 0.00% | 6.67% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0234179687 | A -> G | LOC_Os02g55840.1 | upstream_gene_variant ; 2398.0bp to feature; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179687 | A -> G | LOC_Os02g55840.2 | upstream_gene_variant ; 2398.0bp to feature; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179687 | A -> G | LOC_Os02g55840.5 | upstream_gene_variant ; 2398.0bp to feature; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179687 | A -> G | LOC_Os02g55840.4 | upstream_gene_variant ; 2398.0bp to feature; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179687 | A -> G | LOC_Os02g55840.3 | upstream_gene_variant ; 2398.0bp to feature; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179687 | A -> G | LOC_Os02g55840.6 | upstream_gene_variant ; 2400.0bp to feature; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179687 | A -> G | LOC_Os02g55830.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179687 | A -> DEL | N | N | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |