Search for Variation information by Variation ID:
Detailed information for vg0420967517:
| Variant ID: vg0420967517 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 20967517 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCTGGGGCGCGTGAAGAACACGTACGCCTCGGTGGCCGAGTACCTCGCTGTGTTCGAGCCGCTGCTGTTCGAGGAGGTGAAGGCGCAGATCGTCCAGGGG[C/T]
GCAGCGACGAGGAGGAAGGTGGGTGGGTGGGTGGCGCGCCCGATTTCGTGTTGCCCCCCCAATTTGCTGTCGGTTTATTTAACAGTGTGTGTGTGTGTGT
Reverse complement sequence
ACACACACACACACACTGTTAAATAAACCGACAGCAAATTGGGGGGGCAACACGAAATCGGGCGCGCCACCCACCCACCCACCTTCCTCCTCGTCGCTGC[G/A]
CCCCTGGACGATCTGCGCCTTCACCTCCTCGAACAGCAGCGGCTCGAACACAGCGAGGTACTCGGCCACCGAGGCGTACGTGTTCTTCACGCGCCCCAGC
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 | 83.60% | 0.30% | 4.46% | 11.64% | NA |
| All Indica | 2759 | 85.10% | 0.50% | 6.85% | 7.54% | NA |
| All Japonica | 1512 | 91.90% | 0.00% | 0.86% | 7.21% | NA |
| Aus | 269 | 27.90% | 0.00% | 0.00% | 72.12% | NA |
| Indica I | 595 | 95.30% | 2.00% | 2.52% | 0.17% | NA |
| Indica II | 465 | 75.70% | 0.00% | 15.48% | 8.82% | NA |
| Indica III | 913 | 85.30% | 0.00% | 5.15% | 9.53% | NA |
| Indica Intermediate | 786 | 82.60% | 0.40% | 7.00% | 10.05% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 79.40% | 0.00% | 2.38% | 18.25% | NA |
| Japonica Intermediate | 241 | 92.90% | 0.00% | 0.00% | 7.05% | NA |
| VI/Aromatic | 96 | 61.50% | 0.00% | 5.21% | 33.33% | NA |
| Intermediate | 90 | 87.80% | 0.00% | 4.44% | 7.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420967517 | C -> DEL | LOC_Os04g34670.1 | N | frameshift_variant | Average:53.716; most accessible tissue: Zhenshan97 panicle, score: 84.824 | N | N | N | N |
| vg0420967517 | C -> T | LOC_Os04g34670.1 | missense_variant ; p.Arg63Cys; MODERATE | nonsynonymous_codon ; R63C | Average:53.716; most accessible tissue: Zhenshan97 panicle, score: 84.824 | probably damaging  |
3.355 |
DELETERIOUS | 0.00 |