| Variant ID: vg1105183667 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5183667 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GTAACAATGTTCTTCTTATTACTCGATTGTTGGCGAGTGGGTATCCCTTGACAGCTGGAATGCTTCATGGCACCTTATATTGGTATCTTAAAGGTGACCA[A/G]
TACTATTATGCTCCTAAATGTGCAACTACTGCTGATGCTCACGCGATTACATTGATTGGATCTGGGTTGGCTTCTAAGAACAATATGCCTGAGACGTTCT
AGAACGTCTCAGGCATATTGTTCTTAGAAGCCAACCCAGATCCAATCAATGTAATCGCGTGAGCATCAGCAGTAGTTGCACATTTAGGAGCATAATAGTA[T/C]
TGGTCACCTTTAAGATACCAATATAAGGTGCCATGAAGCATTCCAGCTGTCAAGGGATACCCACTCGCCAACAATCGAGTAATAAGAAGAACATTGTTAC
| 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 | 64.20% | 4.20% | 0.78% | 30.87% | NA |
| All Indica | 2759 | 49.30% | 1.50% | 1.20% | 47.99% | NA |
| All Japonica | 1512 | 97.60% | 1.20% | 0.07% | 1.12% | NA |
| Aus | 269 | 22.30% | 45.00% | 0.74% | 31.97% | NA |
| Indica I | 595 | 27.70% | 0.30% | 2.18% | 69.75% | NA |
| Indica II | 465 | 22.40% | 0.00% | 1.51% | 76.13% | NA |
| Indica III | 913 | 72.00% | 1.50% | 0.55% | 25.96% | NA |
| Indica Intermediate | 786 | 55.20% | 3.30% | 1.02% | 40.46% | NA |
| Temperate Japonica | 767 | 97.90% | 0.00% | 0.13% | 1.96% | NA |
| Tropical Japonica | 504 | 96.80% | 3.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.80% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 78.10% | 13.50% | 0.00% | 8.33% | NA |
| Intermediate | 90 | 68.90% | 3.30% | 1.11% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105183667 | A -> DEL | LOC_Os11g09710.1 | N | frameshift_variant | Average:13.071; most accessible tissue: Callus, score: 83.164 | N | N | N | N |
| vg1105183667 | A -> G | LOC_Os11g09710.1 | synonymous_variant ; p.Gln247Gln; LOW | synonymous_codon | Average:13.071; most accessible tissue: Callus, score: 83.164 | N | N | N | N |