Search for Variation information by Variation ID:
Detailed information for vg0725421247:
| Variant ID: vg0725421247 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 25421247 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AGCGCGCCAGCAGCCTGAAGCGCACCCTGAGGCGTGCTGCCGTCGCCGTAGACGAGGAGGCGACGCTCCCCATCTCGCCGTTCTCCTGCATCACCTGCGA[C/T]
TGGTGATGCCACGGATTTGTCGACCCTCTGAAGCGCCTCCCCCTGCTTAGGGCTTTGGCGCGGAGGAGGTGGAGGAGTACGAGCTCGACGGCGTGGATTC
Reverse complement sequence
GAATCCACGCCGTCGAGCTCGTACTCCTCCACCTCCTCCGCGCCAAAGCCCTAAGCAGGGGGAGGCGCTTCAGAGGGTCGACAAATCCGTGGCATCACCA[G/A]
TCGCAGGTGATGCAGGAGAACGGCGAGATGGGGAGCGTCGCCTCCTCGTCTACGGCGACGGCAGCACGCCTCAGGGTGCGCTTCAGGCTGCTGGCGCGCT
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 | 24.30% | 0.40% | 1.69% | 73.64% | NA |
| All Indica | 2759 | 4.10% | 0.70% | 1.74% | 93.55% | NA |
| All Japonica | 1512 | 61.60% | 0.00% | 1.19% | 37.24% | NA |
| Aus | 269 | 1.90% | 0.00% | 1.12% | 97.03% | NA |
| Indica I | 595 | 5.20% | 0.00% | 0.84% | 93.95% | NA |
| Indica II | 465 | 4.30% | 0.00% | 0.22% | 95.48% | NA |
| Indica III | 913 | 3.10% | 1.80% | 3.07% | 92.11% | NA |
| Indica Intermediate | 786 | 4.20% | 0.30% | 1.78% | 93.77% | NA |
| Temperate Japonica | 767 | 89.40% | 0.00% | 0.39% | 10.17% | NA |
| Tropical Japonica | 504 | 18.50% | 0.00% | 2.78% | 78.77% | NA |
| Japonica Intermediate | 241 | 63.10% | 0.00% | 0.41% | 36.51% | NA |
| VI/Aromatic | 96 | 69.80% | 0.00% | 3.12% | 27.08% | NA |
| Intermediate | 90 | 35.60% | 1.10% | 8.89% | 54.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0725421247 | C -> DEL | LOC_Os07g42460.1 | N | frameshift_variant | Average:6.77; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |
| vg0725421247 | C -> T | LOC_Os07g42460.1 | missense_variant ; p.Val55Ile; MODERATE | nonsynonymous_codon ; V55I | Average:6.77; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | benign  |
0.505 |
TOLERATED | 0.48 |