| Variant ID: vg1101752255 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1752255 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 327. )
GTCTGGAAATACGATTCTACTTTTACATCGATAGCAAATACAACGGATCTGTTGGTGAACCGAAACATAAATAGCATCATCAGCAGCTTTGAACCTGCTG[C/A]
TGCTTGGGCAGCGCGTAGCGGCAGAGAGGGCAGAGGCAGCTATCCCTGAGCCAACGGAAGAGGCAGTTCTCGTGGAAGGAGTGGTTACACGGCATCGTCC
GGACGATGCCGTGTAACCACTCCTTCCACGAGAACTGCCTCTTCCGTTGGCTCAGGGATAGCTGCCTCTGCCCTCTCTGCCGCTACGCGCTGCCCAAGCA[G/T]
CAGCAGGTTCAAAGCTGCTGATGATGCTATTTATGTTTCGGTTCACCAACAGATCCGTTGTATTTGCTATCGATGTAAAAGTAGAATCGTATTTCCAGAC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 98.70% | 1.30% | 0.00% | 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 | 97.50% | 2.50% | 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 | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1101752255 | C -> A | LOC_Os11g04280.1 | missense_variant ; p.Gln212His; MODERATE | N | Average:43.426; most accessible tissue: Callus, score: 67.863 | N | N | N | N |
| vg1101752255 | C -> A | LOC_Os11g04270.1 | upstream_gene_variant ; 1371.0bp to feature; MODIFIER | N | Average:43.426; most accessible tissue: Callus, score: 67.863 | N | N | N | N |
| vg1101752255 | C -> A | LOC_Os11g04240.1 | downstream_gene_variant ; 3431.0bp to feature; MODIFIER | N | Average:43.426; most accessible tissue: Callus, score: 67.863 | N | N | N | N |
| vg1101752255 | C -> A | LOC_Os11g04267.1 | downstream_gene_variant ; 4691.0bp to feature; MODIFIER | N | Average:43.426; most accessible tissue: Callus, score: 67.863 | N | N | N | N |