| Variant ID: vg1105161082 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5161082 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 112. )
CCCTCTCGAGCGCCTCCTCCCGCCTAGGACTTTGGCGTGGAGGGGGCGGTGGAGTACGAGCTCGACGGCGTGGGTTTGGCTCCCCGTCGTCACCGCTAAC[A/G]
CTCGGAGAGAGGTTGTGCGCCTTTGCTTGTTCAGCCATTGGGCTGAACAGGAAAAGCTTGGCGCACACGAAAGAGTGCGAGAGCTTAGAAGAACACACGC
GCGTGTGTTCTTCTAAGCTCTCGCACTCTTTCGTGTGCGCCAAGCTTTTCCTGTTCAGCCCAATGGCTGAACAAGCAAAGGCGCACAACCTCTCTCCGAG[T/C]
GTTAGCGGTGACGACGGGGAGCCAAACCCACGCCGTCGAGCTCGTACTCCACCGCCCCCTCCACGCCAAAGTCCTAGGCGGGAGGAGGCGCTCGAGAGGG
| 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 | 40.50% | 28.80% | 17.39% | 13.39% | NA |
| All Indica | 2759 | 17.50% | 40.30% | 23.99% | 18.23% | NA |
| All Japonica | 1512 | 90.10% | 0.30% | 3.24% | 6.35% | NA |
| Aus | 269 | 3.30% | 74.30% | 20.82% | 1.49% | NA |
| Indica I | 595 | 9.70% | 37.80% | 33.95% | 18.49% | NA |
| Indica II | 465 | 12.50% | 39.10% | 20.22% | 28.17% | NA |
| Indica III | 913 | 19.30% | 46.00% | 21.03% | 13.69% | NA |
| Indica Intermediate | 786 | 24.30% | 36.10% | 22.14% | 17.43% | NA |
| Temperate Japonica | 767 | 89.40% | 0.10% | 1.96% | 8.47% | NA |
| Tropical Japonica | 504 | 93.70% | 0.40% | 2.98% | 2.98% | NA |
| Japonica Intermediate | 241 | 84.60% | 0.80% | 7.88% | 6.64% | NA |
| VI/Aromatic | 96 | 20.80% | 25.00% | 36.46% | 17.71% | NA |
| Intermediate | 90 | 42.20% | 21.10% | 22.22% | 14.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105161082 | A -> DEL | LOC_Os11g09660.1 | N | frameshift_variant | Average:5.487; most accessible tissue: Zhenshan97 flag leaf, score: 9.474 | N | N | N | N |
| vg1105161082 | A -> G | LOC_Os11g09660.1 | synonymous_variant ; p.Ser13Ser; LOW | synonymous_codon | Average:5.487; most accessible tissue: Zhenshan97 flag leaf, score: 9.474 | N | N | N | N |