| Variant ID: vg1124756834 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 24756834 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GGACGTCCGACGTGAGGTTCAAGGTCGGCGGCGAGACGTTCCCGGCGCACCGGTGCGTCCTCGCGGCGCGGTCGCCGGTGTTCAGGGCGGAGCTCCTCGG[C/A]
CCCATGAGGGAGCACGCCGCGACGACCATCCGCGTCGACGACATGGACGCCTCCGTGTTCGCCGCTCTGCTGCGCTTCGTCTACACCGACGAGCTGCCGG
CCGGCAGCTCGTCGGTGTAGACGAAGCGCAGCAGAGCGGCGAACACGGAGGCGTCCATGTCGTCGACGCGGATGGTCGTCGCGGCGTGCTCCCTCATGGG[G/T]
CCGAGGAGCTCCGCCCTGAACACCGGCGACCGCGCCGCGAGGACGCACCGGTGCGCCGGGAACGTCTCGCCGCCGACCTTGAACCTCACGTCGGACGTCC
| 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 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.50% | 2.50% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.00% | 2.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1124756834 | C -> A | LOC_Os11g41300.1 | synonymous_variant ; p.Gly223Gly; LOW | N | Average:76.064; most accessible tissue: Minghui63 flag leaf, score: 87.326 | N | N | N | N |
| vg1124756834 | C -> A | LOC_Os11g41310.1 | upstream_gene_variant ; 1878.0bp to feature; MODIFIER | N | Average:76.064; most accessible tissue: Minghui63 flag leaf, score: 87.326 | N | N | N | N |