| Variant ID: vg1126362910 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26362910 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CTCCCAGCAGGGAGCGCCCAGCCAGCAAGTGGTGCTCCGTCCACAACACCTCCCTCCACGATCTTGCGGACTGTCGCGCAGTCAAAAACTTGGCTGAGCG[A/G]
ACGAGGAAGTGGGAGGAGGACAGGAGGCAGGAACGCCGTGAGGGCAAGTCTGCGGCAGTTCCCTCCGGTAAACGGCGAAGTGAGGCCAGACAGAAGGCCC
GGGCCTTCTGTCTGGCCTCACTTCGCCGTTTACCGGAGGGAACTGCCGCAGACTTGCCCTCACGGCGTTCCTGCCTCCTGTCCTCCTCCCACTTCCTCGT[T/C]
CGCTCAGCCAAGTTTTTGACTGCGCGACAGTCCGCAAGATCGTGGAGGGAGGTGTTGTGGACGGAGCACCACTTGCTGGCTGGGCGCTCCCTGCTGGGAG
| 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 | 6.70% | 0.20% | 16.06% | 77.00% | NA |
| All Indica | 2759 | 1.40% | 0.30% | 10.22% | 88.04% | NA |
| All Japonica | 1512 | 17.80% | 0.00% | 25.79% | 56.42% | NA |
| Aus | 269 | 0.00% | 0.00% | 21.93% | 78.07% | NA |
| Indica I | 595 | 1.00% | 1.20% | 5.55% | 92.27% | NA |
| Indica II | 465 | 2.20% | 0.00% | 2.80% | 95.05% | NA |
| Indica III | 913 | 0.90% | 0.20% | 16.76% | 82.15% | NA |
| Indica Intermediate | 786 | 1.90% | 0.00% | 10.56% | 87.53% | NA |
| Temperate Japonica | 767 | 30.40% | 0.00% | 13.82% | 55.80% | NA |
| Tropical Japonica | 504 | 1.20% | 0.00% | 42.06% | 56.75% | NA |
| Japonica Intermediate | 241 | 12.40% | 0.00% | 29.88% | 57.68% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 18.75% | 81.25% | NA |
| Intermediate | 90 | 11.10% | 1.10% | 11.11% | 76.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126362910 | A -> DEL | LOC_Os11g43670.1 | N | frameshift_variant | Average:13.073; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg1126362910 | A -> G | LOC_Os11g43670.1 | synonymous_variant ; p.Arg497Arg; LOW | synonymous_codon | Average:13.073; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |