| Variant ID: vg1105183812 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5183812 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GATTACATTGATTGGATCTGGGTTGGCTTCTAAGAACAATATGCCTGAGACGTTCTATTCAGCCAGAGATTCACATGGGACTAAATCCCATCCTGACCAT[A/G]
AGATGCGTGACTTCGGTGCAGACTTTTTTCTTTGGGCATGTGATATTACTGATGTTTGGGGTCTTAGGGGCTGTTTGGTTTCCAGGGACTTATTCCAATT
AATTGGAATAAGTCCCTGGAAACCAAACAGCCCCTAAGACCCCAAACATCAGTAATATCACATGCCCAAAGAAAAAAGTCTGCACCGAAGTCACGCATCT[T/C]
ATGGTCAGGATGGGATTTAGTCCCATGTGAATCTCTGGCTGAATAGAACGTCTCAGGCATATTGTTCTTAGAAGCCAACCCAGATCCAATCAATGTAATC
| 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 | 67.80% | 0.30% | 1.59% | 30.32% | NA |
| All Indica | 2759 | 51.00% | 0.00% | 1.78% | 47.23% | NA |
| All Japonica | 1512 | 98.30% | 0.30% | 0.40% | 1.06% | NA |
| Aus | 269 | 68.40% | 0.00% | 1.86% | 29.74% | NA |
| Indica I | 595 | 29.20% | 0.00% | 3.03% | 67.73% | NA |
| Indica II | 465 | 22.40% | 0.00% | 1.72% | 75.91% | NA |
| Indica III | 913 | 73.20% | 0.00% | 0.99% | 25.85% | NA |
| Indica Intermediate | 786 | 58.70% | 0.00% | 1.78% | 39.57% | NA |
| Temperate Japonica | 767 | 97.00% | 0.40% | 0.78% | 1.83% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.40% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 69.80% | 7.30% | 14.58% | 8.33% | NA |
| Intermediate | 90 | 68.90% | 1.10% | 1.11% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105183812 | A -> DEL | LOC_Os11g09710.1 | N | frameshift_variant | Average:18.184; most accessible tissue: Callus, score: 89.679 | N | N | N | N |
| vg1105183812 | A -> G | LOC_Os11g09710.1 | missense_variant ; p.Lys296Glu; MODERATE | nonsynonymous_codon ; K296E | Average:18.184; most accessible tissue: Callus, score: 89.679 | unknown | unknown | TOLERATED | 0.15 |