Search for Variation information by Variation ID:
Detailed information for vg1105160525:
| Variant ID: vg1105160525 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5160525 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ACGGACGTTCCGAAGGCTCGCCACAAAGGCTCTACAGCCGACACCACCAACCGGGGGCACGAAGGGCTGATCCCCGCGTCCGTGTTGATGTGACACTCCG[G/A]
ACGAGGAGGCGCCCTCCGTTGCGTGGGCAGCACGTCGACCATTACGCCGGCGCTCGATACTGATGCGGGCATCCGGCCCCCCACGCAGATCTTCCTGGGT
Reverse complement sequence
ACCCAGGAAGATCTGCGTGGGGGGCCGGATGCCCGCATCAGTATCGAGCGCCGGCGTAATGGTCGACGTGCTGCCCACGCAACGGAGGGCGCCTCCTCGT[C/T]
CGGAGTGTCACATCAACACGGACGCGGGGATCAGCCCTTCGTGCCCCCGGTTGGTGGTGTCGGCTGTAGAGCCTTTGTGGCGAGCCTTCGGAACGTCCGT
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 | 10.70% | 0.80% | 18.35% | 70.10% | NA |
| All Indica | 2759 | 1.10% | 0.50% | 12.83% | 85.57% | NA |
| All Japonica | 1512 | 30.20% | 1.60% | 31.48% | 36.77% | NA |
| Aus | 269 | 0.70% | 0.00% | 2.97% | 96.28% | NA |
| Indica I | 595 | 2.20% | 0.00% | 4.71% | 93.11% | NA |
| Indica II | 465 | 1.10% | 0.20% | 5.81% | 92.90% | NA |
| Indica III | 913 | 0.10% | 0.70% | 18.18% | 81.05% | NA |
| Indica Intermediate | 786 | 1.40% | 0.90% | 16.92% | 80.79% | NA |
| Temperate Japonica | 767 | 34.80% | 0.70% | 18.90% | 45.63% | NA |
| Tropical Japonica | 504 | 15.10% | 3.40% | 51.59% | 29.96% | NA |
| Japonica Intermediate | 241 | 46.90% | 0.80% | 29.46% | 22.82% | NA |
| VI/Aromatic | 96 | 5.20% | 1.00% | 12.50% | 81.25% | NA |
| Intermediate | 90 | 15.60% | 0.00% | 18.89% | 65.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105160525 | G -> A | LOC_Os11g09660.1 | missense_variant ; p.Ser199Phe; MODERATE | nonsynonymous_codon ; S199F | Average:9.342; most accessible tissue: Zhenshan97 panicle, score: 16.188 | possibly damaging  |
1.806 |
DELETERIOUS | 0.00 |
| vg1105160525 | G -> DEL | LOC_Os11g09660.1 | N | frameshift_variant | Average:9.342; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |