| Variant ID: vg1123252981 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 23252981 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CGCTCCAGTCGATCTTGGCCCATTCTTCGTTGATCAGAGCCTCGAGCTTGGCCTGATCGGCGAGGTAGCTCTCGCCGACGACGTAGCAGCCGTTGTCCTC[G/A]
ACCTGGCGGCTGACCTCGGCCTGGAACACGGCGAGGTCGTCGTCCAAAGCCTTGTGCAGGGCGGCCATCTTGTCGATCTCCCGGCGCTGCTCCGGCGAGA
TCTCGCCGGAGCAGCGCCGGGAGATCGACAAGATGGCCGCCCTGCACAAGGCTTTGGACGACGACCTCGCCGTGTTCCAGGCCGAGGTCAGCCGCCAGGT[C/T]
GAGGACAACGGCTGCTACGTCGTCGGCGAGAGCTACCTCGCCGATCAGGCCAAGCTCGAGGCTCTGATCAACGAAGAATGGGCCAAGATCGACTGGAGCG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.00% | 1.00% | 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 | 98.00% | 2.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1123252981 | G -> A | LOC_Os11g39060.1 | synonymous_variant ; p.Val97Val; LOW | N | Average:70.369; most accessible tissue: Callus, score: 83.174 | N | N | N | N |
| vg1123252981 | G -> A | LOC_Os11g39040.1 | upstream_gene_variant ; 4038.0bp to feature; MODIFIER | N | Average:70.369; most accessible tissue: Callus, score: 83.174 | N | N | N | N |
| vg1123252981 | G -> A | LOC_Os11g39050.1 | upstream_gene_variant ; 2466.0bp to feature; MODIFIER | N | Average:70.369; most accessible tissue: Callus, score: 83.174 | N | N | N | N |
| vg1123252981 | G -> A | LOC_Os11g39070.1 | downstream_gene_variant ; 2805.0bp to feature; MODIFIER | N | Average:70.369; most accessible tissue: Callus, score: 83.174 | N | N | N | N |