Search for Variation information by Variation ID:
Detailed information for vg0725421257:
| Variant ID: vg0725421257 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 25421257 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CAGCCTGAAGCGCACCCTGAGGCGTGCTGCCGTCGCCGTAGACGAGGAGGCGACGCTCCCCATCTCGCCGTTCTCCTGCATCACCTGCGACTGGTGATGC[C/T]
ACGGATTTGTCGACCCTCTGAAGCGCCTCCCCCTGCTTAGGGCTTTGGCGCGGAGGAGGTGGAGGAGTACGAGCTCGACGGCGTGGATTCGGCTCCCCGT
Reverse complement sequence
ACGGGGAGCCGAATCCACGCCGTCGAGCTCGTACTCCTCCACCTCCTCCGCGCCAAAGCCCTAAGCAGGGGGAGGCGCTTCAGAGGGTCGACAAATCCGT[G/A]
GCATCACCAGTCGCAGGTGATGCAGGAGAACGGCGAGATGGGGAGCGTCGCCTCCTCGTCTACGGCGACGGCAGCACGCCTCAGGGTGCGCTTCAGGCTG
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 | 23.50% | 0.40% | 2.14% | 73.97% | NA |
| All Indica | 2759 | 3.80% | 0.60% | 1.70% | 93.87% | NA |
| All Japonica | 1512 | 59.80% | 0.00% | 2.51% | 37.70% | NA |
| Aus | 269 | 1.90% | 0.00% | 1.12% | 97.03% | NA |
| Indica I | 595 | 5.20% | 0.00% | 0.50% | 94.29% | NA |
| Indica II | 465 | 4.10% | 0.00% | 0.00% | 95.91% | NA |
| Indica III | 913 | 2.60% | 1.50% | 3.07% | 92.77% | NA |
| Indica Intermediate | 786 | 4.10% | 0.30% | 2.04% | 93.64% | NA |
| Temperate Japonica | 767 | 89.40% | 0.00% | 0.39% | 10.17% | NA |
| Tropical Japonica | 504 | 13.30% | 0.00% | 6.55% | 80.16% | NA |
| Japonica Intermediate | 241 | 62.70% | 0.00% | 0.83% | 36.51% | NA |
| VI/Aromatic | 96 | 66.70% | 1.00% | 5.21% | 27.08% | NA |
| Intermediate | 90 | 34.40% | 2.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0725421257 | C -> DEL | LOC_Os07g42460.1 | N | frameshift_variant | Average:6.77; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |
| vg0725421257 | C -> T | LOC_Os07g42460.1 | synonymous_variant ; p.Val51Val; LOW | nonsynonymous_codon ; V51A | Average:6.77; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | benign  |
-0.241 |
TOLERATED | 1.00 |