| Variant ID: vg1105159758 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5159758 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GGCTCTGCTGGTAGCTCGCGGCTCGAAGGGCCGCGCGCCACCTTCGCTCTTCCAAGTAGCCGAGGTCAGGGAGCGTCGGCTTCCTTCTTTTTGTCGCTCG[C/T]
AGGCCTCCCCTTTCGGGTGGCCAGCGAAACGCCTTCGACGGCGAGGACATGACCCTCGTCGTCGGAATGGGCTGACCTCTTCTTCCTCCTCCTGTCACGC
GCGTGACAGGAGGAGGAAGAAGAGGTCAGCCCATTCCGACGACGAGGGTCATGTCCTCGCCGTCGAAGGCGTTTCGCTGGCCACCCGAAAGGGGAGGCCT[G/A]
CGAGCGACAAAAAGAAGGAAGCCGACGCTCCCTGACCTCGGCTACTTGGAAGAGCGAAGGTGGCGCGCGGCCCTTCGAGCCGCGAGCTACCAGCAGAGCC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 33.60% | 2.40% | 18.11% | 45.87% | NA |
| All Indica | 2759 | 12.00% | 0.00% | 20.88% | 67.16% | NA |
| All Japonica | 1512 | 77.80% | 7.50% | 10.38% | 4.30% | NA |
| Aus | 269 | 4.50% | 0.00% | 30.86% | 64.68% | NA |
| Indica I | 595 | 7.60% | 0.00% | 9.08% | 83.36% | NA |
| Indica II | 465 | 4.90% | 0.00% | 4.73% | 90.32% | NA |
| Indica III | 913 | 11.80% | 0.00% | 39.76% | 48.41% | NA |
| Indica Intermediate | 786 | 19.60% | 0.00% | 17.43% | 62.98% | NA |
| Temperate Japonica | 767 | 77.10% | 11.30% | 7.43% | 4.17% | NA |
| Tropical Japonica | 504 | 81.90% | 0.20% | 13.69% | 4.17% | NA |
| Japonica Intermediate | 241 | 71.40% | 10.80% | 12.86% | 4.98% | NA |
| VI/Aromatic | 96 | 35.40% | 0.00% | 29.17% | 35.42% | NA |
| Intermediate | 90 | 38.90% | 1.10% | 13.33% | 46.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105159758 | C -> T | LOC_Os11g09660.1 | missense_variant ; p.Ala455Thr; MODERATE | nonsynonymous_codon ; A455T | Average:5.323; most accessible tissue: Callus, score: 10.907 | unknown | unknown | DELETERIOUS | 0.00 |
| vg1105159758 | C -> DEL | LOC_Os11g09660.1 | N | frameshift_variant | Average:5.323; most accessible tissue: Callus, score: 10.907 | N | N | N | N |