Search for Variation information by Variation ID:
Detailed information for vg0612160258:
| Variant ID: vg0612160258 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 12160258 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ATTGAATGATCTTTACCTTTTCTTCTGCTTCCCTTAGGATATCCGTCCCAAAAACCTGACGTTCTCCCGTTTGATCCCACAAAAGCGGAGTGCGGCACTT[T/C]
CGACCATACAGTGCTTCGTAAGGAGCCATCTGTAAACTAGTTTGATAACTGTTGTTGTATGAAAATTCTGCATAAGGTAGATTCTTATCCCAACTTCCAC
Reverse complement sequence
GTGGAAGTTGGGATAAGAATCTACCTTATGCAGAATTTTCATACAACAACAGTTATCAAACTAGTTTACAGATGGCTCCTTACGAAGCACTGTATGGTCG[A/G]
AAGTGCCGCACTCCGCTTTTGTGGGATCAAACGGGAGAACGTCAGGTTTTTGGGACGGATATCCTAAGGGAAGCAGAAGAAAAGGTAAAGATCATTCAAT
Allele Frequencies:
| 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 | 38.00% | 0.20% | 24.61% | 37.24% | NA |
| All Indica | 2759 | 11.00% | 0.30% | 34.25% | 54.44% | NA |
| All Japonica | 1512 | 87.40% | 0.00% | 3.84% | 8.73% | NA |
| Aus | 269 | 20.80% | 0.00% | 49.81% | 29.37% | NA |
| Indica I | 595 | 14.60% | 0.20% | 19.83% | 65.38% | NA |
| Indica II | 465 | 11.20% | 0.40% | 26.02% | 62.37% | NA |
| Indica III | 913 | 6.40% | 0.10% | 52.25% | 41.29% | NA |
| Indica Intermediate | 786 | 13.60% | 0.50% | 29.13% | 56.74% | NA |
| Temperate Japonica | 767 | 95.20% | 0.00% | 0.26% | 4.56% | NA |
| Tropical Japonica | 504 | 73.40% | 0.00% | 10.91% | 15.67% | NA |
| Japonica Intermediate | 241 | 92.10% | 0.00% | 0.41% | 7.47% | NA |
| VI/Aromatic | 96 | 70.80% | 0.00% | 12.50% | 16.67% | NA |
| Intermediate | 90 | 50.00% | 0.00% | 15.56% | 34.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0612160258 | T -> C | LOC_Os06g21050.1 | synonymous_variant ; p.Arg1210Arg; LOW | synonymous_codon | Average:4.878; most accessible tissue: Callus, score: 8.991 | N | N | N | N |
| vg0612160258 | T -> C | LOC_Os06g21050.1 | synonymous_variant ; p.Arg1210Arg; LOW | nonsynonymous_codon ; R1210W | Average:4.878; most accessible tissue: Callus, score: 8.991 | benign  |
1.375 |
DELETERIOUS | 0.00 |
| vg0612160258 | T -> DEL | LOC_Os06g21050.1 | N | frameshift_variant | Average:4.878; most accessible tissue: Callus, score: 8.991 | N | N | N | N |