| Variant ID: vg1105161067 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5161067 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TCGCGGATCCTTCGACCCTCTCGAGCGCCTCCTCCCGCCTAGGACTTTGGCGTGGAGGGGGCGGTGGAGTACGAGCTCGACGGCGTGGGTTTGGCTCCCC[G/A]
TCGTCACCGCTAACACTCGGAGAGAGGTTGTGCGCCTTTGCTTGTTCAGCCATTGGGCTGAACAGGAAAAGCTTGGCGCACACGAAAGAGTGCGAGAGCT
AGCTCTCGCACTCTTTCGTGTGCGCCAAGCTTTTCCTGTTCAGCCCAATGGCTGAACAAGCAAAGGCGCACAACCTCTCTCCGAGTGTTAGCGGTGACGA[C/T]
GGGGAGCCAAACCCACGCCGTCGAGCTCGTACTCCACCGCCCCCTCCACGCCAAAGTCCTAGGCGGGAGGAGGCGCTCGAGAGGGTCGAAGGATCCGCGA
| 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 | 83.10% | 0.10% | 2.14% | 14.64% | NA |
| All Indica | 2759 | 77.10% | 0.00% | 3.01% | 19.90% | NA |
| All Japonica | 1512 | 92.10% | 0.00% | 0.99% | 6.94% | NA |
| Aus | 269 | 91.80% | 1.50% | 0.37% | 6.32% | NA |
| Indica I | 595 | 63.50% | 0.00% | 9.08% | 27.39% | NA |
| Indica II | 465 | 71.40% | 0.00% | 0.65% | 27.96% | NA |
| Indica III | 913 | 88.30% | 0.00% | 0.55% | 11.17% | NA |
| Indica Intermediate | 786 | 77.70% | 0.00% | 2.67% | 19.59% | NA |
| Temperate Japonica | 767 | 91.40% | 0.00% | 0.26% | 8.34% | NA |
| Tropical Japonica | 504 | 96.60% | 0.00% | 0.00% | 3.37% | NA |
| Japonica Intermediate | 241 | 84.60% | 0.00% | 5.39% | 9.96% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 0.00% | 7.29% | NA |
| Intermediate | 90 | 82.20% | 0.00% | 2.22% | 15.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105161067 | G -> A | LOC_Os11g09660.1 | synonymous_variant ; p.Asp18Asp; LOW | synonymous_codon | Average:5.942; most accessible tissue: Callus, score: 11.873 | N | N | N | N |
| vg1105161067 | G -> DEL | LOC_Os11g09660.1 | N | frameshift_variant | Average:5.942; most accessible tissue: Callus, score: 11.873 | N | N | N | N |