| Variant ID: vg1105159831 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5159831 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CGTCGGCTTCCTTCTTTTTGTCGCTCGCAGGCCTCCCCTTTCGGGTGGCCAGCGAAACGCCTTCGACGGCGAGGACATGACCCTCGTCGTCGGAATGGGC[T/C]
GACCTCTTCTTCCTCCTCCTGTCACGCCGCCCTGTCCGAGCAGCAGATCCGGGGACGGCCGAAGCTGCCACACCGGAACCGGAGGGGTTCCAGGTCCATG
CATGGACCTGGAACCCCTCCGGTTCCGGTGTGGCAGCTTCGGCCGTCCCCGGATCTGCTGCTCGGACAGGGCGGCGTGACAGGAGGAGGAAGAAGAGGTC[A/G]
GCCCATTCCGACGACGAGGGTCATGTCCTCGCCGTCGAAGGCGTTTCGCTGGCCACCCGAAAGGGGAGGCCTGCGAGCGACAAAAAGAAGGAAGCCGACG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 48.70% | 0.10% | 17.52% | 33.69% | NA |
| All Indica | 2759 | 29.90% | 0.10% | 24.86% | 45.20% | NA |
| All Japonica | 1512 | 85.20% | 0.20% | 4.37% | 10.25% | NA |
| Aus | 269 | 27.90% | 0.40% | 20.07% | 51.67% | NA |
| Indica I | 595 | 19.20% | 0.00% | 11.60% | 69.24% | NA |
| Indica II | 465 | 16.60% | 0.00% | 22.37% | 61.08% | NA |
| Indica III | 913 | 39.00% | 0.20% | 40.20% | 20.59% | NA |
| Indica Intermediate | 786 | 35.20% | 0.00% | 18.58% | 46.18% | NA |
| Temperate Japonica | 767 | 89.70% | 0.40% | 1.04% | 8.87% | NA |
| Tropical Japonica | 504 | 80.80% | 0.00% | 8.13% | 11.11% | NA |
| Japonica Intermediate | 241 | 80.10% | 0.00% | 7.05% | 12.86% | NA |
| VI/Aromatic | 96 | 70.80% | 0.00% | 11.46% | 17.71% | NA |
| Intermediate | 90 | 50.00% | 0.00% | 12.22% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105159831 | T -> DEL | LOC_Os11g09660.1 | N | frameshift_variant | Average:5.072; most accessible tissue: Callus, score: 8.148 | N | N | N | N |
| vg1105159831 | T -> C | LOC_Os11g09660.1 | synonymous_variant ; p.Ser430Ser; LOW | synonymous_codon | Average:5.072; most accessible tissue: Callus, score: 8.148 | N | N | N | N |