Search for Variation information by Variation ID:
Detailed information for vg0612160226:
| Variant ID: vg0612160226 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 12160226 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTTATGTCGAGACTGAGCCACTCGCAATCTTTATTGAATGATCTTTACCTTTTCTTCTGCTTCCCTTAGGATATCCGTCCCAAAAACCTGACGTTCTCCC[G/A]
TTTGATCCCACAAAAGCGGAGTGCGGCACTTTCGACCATACAGTGCTTCGTAAGGAGCCATCTGTAAACTAGTTTGATAACTGTTGTTGTATGAAAATTC
Reverse complement sequence
GAATTTTCATACAACAACAGTTATCAAACTAGTTTACAGATGGCTCCTTACGAAGCACTGTATGGTCGAAAGTGCCGCACTCCGCTTTTGTGGGATCAAA[C/T]
GGGAGAACGTCAGGTTTTTGGGACGGATATCCTAAGGGAAGCAGAAGAAAAGGTAAAGATCATTCAATAAAGATTGCGAGTGGCTCAGTCTCGACATAAG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 84.00% | 0.30% | 5.12% | 10.58% | NA |
| All Indica | 2759 | 80.40% | 0.20% | 6.27% | 13.12% | NA |
| All Japonica | 1512 | 92.20% | 0.00% | 0.79% | 7.01% | NA |
| Aus | 269 | 70.30% | 4.10% | 18.59% | 7.06% | NA |
| Indica I | 595 | 76.80% | 0.00% | 8.91% | 14.29% | NA |
| Indica II | 465 | 76.10% | 0.00% | 9.46% | 14.41% | NA |
| Indica III | 913 | 86.30% | 0.10% | 2.85% | 10.73% | NA |
| Indica Intermediate | 786 | 78.90% | 0.50% | 6.36% | 14.25% | NA |
| Temperate Japonica | 767 | 96.00% | 0.00% | 0.26% | 3.78% | NA |
| Tropical Japonica | 504 | 85.90% | 0.00% | 1.79% | 12.30% | 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 | 85.60% | 0.00% | 1.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0612160226 | G -> A | LOC_Os06g21050.1 | missense_variant ; p.Thr1221Met; MODERATE | nonsynonymous_codon ; T1221M | Average:4.878; most accessible tissue: Callus, score: 8.991 | probably damaging  |
2.558 |
DELETERIOUS | 0.01 |
| vg0612160226 | G -> DEL | LOC_Os06g21050.1 | N | frameshift_variant | Average:4.878; most accessible tissue: Callus, score: 8.991 | N | N | N | N |