| Variant ID: vg1105160887 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5160887 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AGTTGGCCACGTCGTCCAGCCAACGTTGGGCTGGAGACTCCGGGTCAGGGACAATGGGCGGGTGACGTAGGAGCGCGCCCGCAGCTTGGAGCGCGCCCTG[G/C]
GGCGTGCTGCCGTCGCCGTAGACGAGGAGGCGACGCTCCCCACCTCGCCGCCCTTCCCCATCACCCGTGGATGTCGAAGTCGCGGATCCTTCGACCCTCT
AGAGGGTCGAAGGATCCGCGACTTCGACATCCACGGGTGATGGGGAAGGGCGGCGAGGTGGGGAGCGTCGCCTCCTCGTCTACGGCGACGGCAGCACGCC[C/G]
CAGGGCGCGCTCCAAGCTGCGGGCGCGCTCCTACGTCACCCGCCCATTGTCCCTGACCCGGAGTCTCCAGCCCAACGTTGGCTGGACGACGTGGCCAACT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 33.50% | 0.10% | 15.59% | 50.76% | NA |
| All Indica | 2759 | 10.00% | 0.20% | 19.83% | 69.95% | NA |
| All Japonica | 1512 | 83.90% | 0.00% | 4.30% | 11.84% | NA |
| Aus | 269 | 0.70% | 0.00% | 29.00% | 70.26% | NA |
| Indica I | 595 | 5.70% | 0.00% | 6.22% | 88.07% | NA |
| Indica II | 465 | 5.40% | 1.10% | 14.19% | 79.35% | NA |
| Indica III | 913 | 8.50% | 0.00% | 35.05% | 56.41% | NA |
| Indica Intermediate | 786 | 17.70% | 0.10% | 15.78% | 66.41% | NA |
| Temperate Japonica | 767 | 88.50% | 0.00% | 0.65% | 10.82% | NA |
| Tropical Japonica | 504 | 79.40% | 0.00% | 8.13% | 12.50% | NA |
| Japonica Intermediate | 241 | 78.40% | 0.00% | 7.88% | 13.69% | NA |
| VI/Aromatic | 96 | 7.30% | 0.00% | 38.54% | 54.17% | NA |
| Intermediate | 90 | 34.40% | 0.00% | 11.11% | 54.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105160887 | G -> DEL | LOC_Os11g09660.1 | N | frameshift_variant | Average:6.486; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1105160887 | G -> C | LOC_Os11g09660.1 | synonymous_variant ; p.Pro78Pro; LOW | synonymous_codon | Average:6.486; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |