| Variant ID: vg1223515300 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 23515300 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CGGGTACGTTCGATCTTCAGCTATTGATTCTGAATATGTTTGCTATGTATTTGTCAACATAAACTGTCATAAGCTTTGATGATTTTGATGTACTTTCCAT[C/G]
ATAGAAGAATACTATGTTAGCCCCAATAGTTCTGCTTACAATTGATTTGAAGTTATATTCAGTTGAAGCCATCCATAAGACAAAAAAAAAGTTGTCATTT
AAATGACAACTTTTTTTTTGTCTTATGGATGGCTTCAACTGAATATAACTTCAAATCAATTGTAAGCAGAACTATTGGGGCTAACATAGTATTCTTCTAT[G/C]
ATGGAAAGTACATCAAAATCATCAAAGCTTATGACAGTTTATGTTGACAAATACATAGCAAACATATTCAGAATCAATAGCTGAAGATCGAACGTACCCG
| 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 | 98.70% | 0.90% | 0.40% | 0.00% | NA |
| All Indica | 2759 | 98.30% | 1.10% | 0.65% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 97.80% | 1.90% | 0.37% | 0.00% | NA |
| Indica I | 595 | 98.20% | 0.30% | 1.51% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.70% | 0.80% | 0.55% | 0.00% | NA |
| Indica Intermediate | 786 | 97.20% | 2.30% | 0.51% | 0.00% | NA |
| Temperate Japonica | 767 | 99.50% | 0.50% | 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 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1223515300 | C -> G | LOC_Os12g38310.1 | upstream_gene_variant ; 1352.0bp to feature; MODIFIER | silent_mutation | Average:61.732; most accessible tissue: Minghui63 root, score: 88.578 | N | N | N | N |
| vg1223515300 | C -> G | LOC_Os12g38280.1 | downstream_gene_variant ; 4719.0bp to feature; MODIFIER | silent_mutation | Average:61.732; most accessible tissue: Minghui63 root, score: 88.578 | N | N | N | N |
| vg1223515300 | C -> G | LOC_Os12g38290.1 | downstream_gene_variant ; 1823.0bp to feature; MODIFIER | silent_mutation | Average:61.732; most accessible tissue: Minghui63 root, score: 88.578 | N | N | N | N |
| vg1223515300 | C -> G | LOC_Os12g38320.1 | downstream_gene_variant ; 4668.0bp to feature; MODIFIER | silent_mutation | Average:61.732; most accessible tissue: Minghui63 root, score: 88.578 | N | N | N | N |
| vg1223515300 | C -> G | LOC_Os12g38300.1 | intron_variant ; MODIFIER | silent_mutation | Average:61.732; most accessible tissue: Minghui63 root, score: 88.578 | N | N | N | N |