Search for Variation information by Variation ID:
Detailed information for vg0612160212:
| Variant ID: vg0612160212 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 12160212 |
| Reference Allele: C | Alternative Allele: T,A |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TTGTCGGCATAACTCTTATGTCGAGACTGAGCCACTCGCAATCTTTATTGAATGATCTTTACCTTTTCTTCTGCTTCCCTTAGGATATCCGTCCCAAAAA[C/T,A]
CTGACGTTCTCCCGTTTGATCCCACAAAAGCGGAGTGCGGCACTTTCGACCATACAGTGCTTCGTAAGGAGCCATCTGTAAACTAGTTTGATAACTGTTG
Reverse complement sequence
CAACAGTTATCAAACTAGTTTACAGATGGCTCCTTACGAAGCACTGTATGGTCGAAAGTGCCGCACTCCGCTTTTGTGGGATCAAACGGGAGAACGTCAG[G/A,T]
TTTTTGGGACGGATATCCTAAGGGAAGCAGAAGAAAAGGTAAAGATCATTCAATAAAGATTGCGAGTGGCTCAGTCTCGACATAAGAGTTATGCCGACAA
Allele Frequencies:
| 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 | 82.40% | 0.20% | 5.84% | 11.45% | A: 0.06% |
| All Indica | 2759 | 77.70% | 0.40% | 7.36% | 14.50% | A: 0.11% |
| All Japonica | 1512 | 92.10% | 0.00% | 0.73% | 7.21% | NA |
| Aus | 269 | 74.00% | 0.00% | 18.96% | 7.06% | NA |
| Indica I | 595 | 71.90% | 0.20% | 11.43% | 16.13% | A: 0.34% |
| Indica II | 465 | 72.90% | 0.00% | 10.32% | 16.56% | A: 0.22% |
| Indica III | 913 | 84.60% | 0.70% | 3.18% | 11.61% | NA |
| Indica Intermediate | 786 | 76.80% | 0.40% | 7.38% | 15.39% | NA |
| Temperate Japonica | 767 | 96.00% | 0.00% | 0.26% | 3.78% | NA |
| Tropical Japonica | 504 | 85.50% | 0.00% | 1.59% | 12.90% | NA |
| Japonica Intermediate | 241 | 93.40% | 0.00% | 0.41% | 6.22% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 6.25% | 1.04% | NA |
| Intermediate | 90 | 81.10% | 0.00% | 5.56% | 13.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0612160212 | C -> T | LOC_Os06g21050.1 | missense_variant ; p.Val1226Ile; MODERATE | nonsynonymous_codon ; V1226I | Average:4.878; most accessible tissue: Callus, score: 8.991 | benign  |
0.525 |
DELETERIOUS | 0.02 |
| vg0612160212 | C -> A | LOC_Os06g21050.1 | missense_variant ; p.Val1226Phe; MODERATE | nonsynonymous_codon ; V1226F | Average:4.878; most accessible tissue: Callus, score: 8.991 | benign |
0.727 |
DELETERIOUS | 0.00 |
| vg0612160212 | C -> DEL | LOC_Os06g21050.1 | N | frameshift_variant | Average:4.878; most accessible tissue: Callus, score: 8.991 | N | N | N | N |