Search for Variation information by Variation ID:
Detailed information for vg0125111997:
| Variant ID: vg0125111997 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 25111997 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GAAGAAGGGCAGACGTGCGGCGTGCTAAACTGACACGTGGTGGACAAGAATGACCGGTCTGTGACTGGTCTGACGCCGGTCACGTCATCGGCAGACAACC[G/A]
AGCTCCCACGTTGCATCTGCTTCCGGCGGAGTGGAGGTAGATATGACCCATCCCATCGGAGGGTCATTCGGACAGCAGCCATTGCAAATCTTCACCCATT
Reverse complement sequence
AATGGGTGAAGATTTGCAATGGCTGCTGTCCGAATGACCCTCCGATGGGATGGGTCATATCTACCTCCACTCCGCCGGAAGCAGATGCAACGTGGGAGCT[C/T]
GGTTGTCTGCCGATGACGTGACCGGCGTCAGACCAGTCACAGACCGGTCATTCTTGTCCACCACGTGTCAGTTTAGCACGCCGCACGTCTGCCCTTCTTC
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 | 49.90% | 0.30% | 5.44% | 44.39% | NA |
| All Indica | 2759 | 39.10% | 0.30% | 7.72% | 52.85% | NA |
| All Japonica | 1512 | 74.50% | 0.10% | 0.73% | 24.74% | NA |
| Aus | 269 | 4.80% | 1.90% | 10.41% | 82.90% | NA |
| Indica I | 595 | 33.60% | 0.00% | 14.96% | 51.43% | NA |
| Indica II | 465 | 60.00% | 0.00% | 5.16% | 34.84% | NA |
| Indica III | 913 | 31.00% | 0.30% | 4.60% | 64.07% | NA |
| Indica Intermediate | 786 | 40.50% | 0.60% | 7.38% | 51.53% | NA |
| Temperate Japonica | 767 | 98.20% | 0.00% | 0.13% | 1.69% | NA |
| Tropical Japonica | 504 | 44.00% | 0.00% | 0.99% | 54.96% | NA |
| Japonica Intermediate | 241 | 62.70% | 0.40% | 2.07% | 34.85% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 1.04% | 12.50% | NA |
| Intermediate | 90 | 61.10% | 0.00% | 4.44% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0125111997 | G -> A | LOC_Os01g43830.1 | missense_variant ; p.Arg18Trp; MODERATE | nonsynonymous_codon ; R18W | Average:6.081; most accessible tissue: Callus, score: 10.3 | probably damaging  |
3.422 |
TOLERATED | 0.22 |
| vg0125111997 | G -> DEL | LOC_Os01g43830.1 | N | frameshift_variant | Average:6.081; most accessible tissue: Callus, score: 10.3 | N | N | N | N |