Search for Variation information by Variation ID:
Detailed information for vg0612160260:
| Variant ID: vg0612160260 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 12160260 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TGAATGATCTTTACCTTTTCTTCTGCTTCCCTTAGGATATCCGTCCCAAAAACCTGACGTTCTCCCGTTTGATCCCACAAAAGCGGAGTGCGGCACTTTC[G/A]
ACCATACAGTGCTTCGTAAGGAGCCATCTGTAAACTAGTTTGATAACTGTTGTTGTATGAAAATTCTGCATAAGGTAGATTCTTATCCCAACTTCCACCA
Reverse complement sequence
TGGTGGAAGTTGGGATAAGAATCTACCTTATGCAGAATTTTCATACAACAACAGTTATCAAACTAGTTTACAGATGGCTCCTTACGAAGCACTGTATGGT[C/T]
GAAAGTGCCGCACTCCGCTTTTGTGGGATCAAACGGGAGAACGTCAGGTTTTTGGGACGGATATCCTAAGGGAAGCAGAAGAAAAGGTAAAGATCATTCA
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 | 37.60% | 0.10% | 23.55% | 38.68% | NA |
| All Indica | 2759 | 10.50% | 0.20% | 32.44% | 56.80% | NA |
| All Japonica | 1512 | 87.40% | 0.00% | 3.77% | 8.80% | NA |
| Aus | 269 | 19.70% | 0.00% | 50.56% | 29.74% | NA |
| Indica I | 595 | 14.50% | 0.20% | 18.49% | 66.89% | NA |
| Indica II | 465 | 10.30% | 0.40% | 24.09% | 65.16% | NA |
| Indica III | 913 | 5.70% | 0.00% | 49.18% | 45.13% | NA |
| Indica Intermediate | 786 | 13.40% | 0.40% | 28.50% | 57.76% | NA |
| Temperate Japonica | 767 | 95.20% | 0.00% | 0.39% | 4.43% | NA |
| Tropical Japonica | 504 | 73.40% | 0.00% | 10.52% | 16.07% | NA |
| Japonica Intermediate | 241 | 92.10% | 0.00% | 0.41% | 7.47% | NA |
| VI/Aromatic | 96 | 69.80% | 0.00% | 13.54% | 16.67% | NA |
| Intermediate | 90 | 51.10% | 0.00% | 13.33% | 35.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0612160260 | G -> A | LOC_Os06g21050.1 | stop_gained ; p.Arg1210*; HIGH | nonsynonymous_codon ; R1210W | Average:4.878; most accessible tissue: Callus, score: 8.991 | benign  |
1.375 |
DELETERIOUS | 0.00 |
| vg0612160260 | G -> DEL | LOC_Os06g21050.1 | N | frameshift_variant | Average:4.878; most accessible tissue: Callus, score: 8.991 | N | N | N | N |