Search for Variation information by Variation ID:
Detailed information for vg0435226174:
| Variant ID: vg0435226174 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 35226174 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GTGCGCCAAGCTTTTCCTGTTCAGCCCAATGGCCGAACAAGCAAAGGCGCACAACCTCTCTCCGAGTGTTAGCGGTGACGACGGGGAGCCAAACCCACGC[C/T]
GTCGAGCTCGTACTCCACCGCCCCCTCCACGCCAAAGTCCTAGGCGGGAGGAGGTGCTCGAGAGGGTCGAAGGATCCACGACTTCGACATCCACGGGTGA
Reverse complement sequence
TCACCCGTGGATGTCGAAGTCGTGGATCCTTCGACCCTCTCGAGCACCTCCTCCCGCCTAGGACTTTGGCGTGGAGGGGGCGGTGGAGTACGAGCTCGAC[G/A]
GCGTGGGTTTGGCTCCCCGTCGTCACCGCTAACACTCGGAGAGAGGTTGTGCGCCTTTGCTTGTTCGGCCATTGGGCTGAACAGGAAAAGCTTGGCGCAC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 67.40% | 0.10% | 11.91% | 20.59% | NA |
| All Indica | 2759 | 46.90% | 0.00% | 19.28% | 33.82% | NA |
| All Japonica | 1512 | 97.60% | 0.30% | 1.85% | 0.26% | NA |
| Aus | 269 | 92.20% | 0.00% | 0.00% | 7.81% | NA |
| Indica I | 595 | 29.10% | 0.00% | 26.39% | 44.54% | NA |
| Indica II | 465 | 37.40% | 0.00% | 24.52% | 38.06% | NA |
| Indica III | 913 | 58.80% | 0.00% | 13.69% | 27.49% | NA |
| Indica Intermediate | 786 | 52.00% | 0.10% | 17.30% | 30.53% | NA |
| Temperate Japonica | 767 | 98.40% | 0.70% | 0.91% | 0.00% | NA |
| Tropical Japonica | 504 | 97.00% | 0.00% | 2.38% | 0.60% | NA |
| Japonica Intermediate | 241 | 95.90% | 0.00% | 3.73% | 0.41% | NA |
| VI/Aromatic | 96 | 93.80% | 0.00% | 1.04% | 5.21% | NA |
| Intermediate | 90 | 86.70% | 0.00% | 2.22% | 11.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0435226174 | C -> DEL | LOC_Os04g59220.1 | N | frameshift_variant | Average:7.482; most accessible tissue: Zhenshan97 root, score: 10.511 | N | N | N | N |
| vg0435226174 | C -> T | LOC_Os04g59220.1 | missense_variant ; p.Arg25Cys; MODERATE | nonsynonymous_codon ; R25C | Average:7.482; most accessible tissue: Zhenshan97 root, score: 10.511 | probably damaging  |
2.882 |
DELETERIOUS | 0.00 |