| Variant ID: vg1105159876 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5159876 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TGGCCAGCGAAACGCCTTCGACGGCGAGGACATGACCCTCGTCGTCGGAATGGGCTGACCTCTTCTTCCTCCTCCTGTCACGCCGCCCTGTCCGAGCAGC[A/G]
GATCCGGGGACGGCCGAAGCTGCCACACCGGAACCGGAGGGGTTCCAGGTCCATGCCTCTTCCTTACGAGCCACTCGGTCCGCGAGCTGAAAAAGCTCCG
CGGAGCTTTTTCAGCTCGCGGACCGAGTGGCTCGTAAGGAAGAGGCATGGACCTGGAACCCCTCCGGTTCCGGTGTGGCAGCTTCGGCCGTCCCCGGATC[T/C]
GCTGCTCGGACAGGGCGGCGTGACAGGAGGAGGAAGAAGAGGTCAGCCCATTCCGACGACGAGGGTCATGTCCTCGCCGTCGAAGGCGTTTCGCTGGCCA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 32.20% | 0.60% | 16.99% | 50.15% | NA |
| All Indica | 2759 | 9.60% | 0.40% | 22.25% | 67.67% | NA |
| All Japonica | 1512 | 80.40% | 0.70% | 3.17% | 15.81% | NA |
| Aus | 269 | 0.70% | 2.60% | 38.29% | 58.36% | NA |
| Indica I | 595 | 6.10% | 0.00% | 9.58% | 84.37% | NA |
| Indica II | 465 | 4.70% | 0.60% | 12.90% | 81.72% | NA |
| Indica III | 913 | 8.10% | 0.40% | 38.99% | 52.46% | NA |
| Indica Intermediate | 786 | 17.00% | 0.60% | 17.94% | 64.38% | NA |
| Temperate Japonica | 767 | 82.70% | 1.30% | 5.61% | 10.43% | NA |
| Tropical Japonica | 504 | 78.20% | 0.00% | 0.79% | 21.03% | NA |
| Japonica Intermediate | 241 | 77.60% | 0.00% | 0.41% | 21.99% | NA |
| VI/Aromatic | 96 | 7.30% | 0.00% | 31.25% | 61.46% | NA |
| Intermediate | 90 | 36.70% | 1.10% | 8.89% | 53.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105159876 | A -> DEL | LOC_Os11g09660.1 | N | frameshift_variant | Average:5.639; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |
| vg1105159876 | A -> G | LOC_Os11g09660.1 | synonymous_variant ; p.Ser415Ser; LOW | synonymous_codon | Average:5.639; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |