Search for Variation information by Variation ID:
Detailed information for vg0725421252:
| Variant ID: vg0725421252 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 25421252 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCCAGCAGCCTGAAGCGCACCCTGAGGCGTGCTGCCGTCGCCGTAGACGAGGAGGCGACGCTCCCCATCTCGCCGTTCTCCTGCATCACCTGCGACTGGT[G/A]
ATGCCACGGATTTGTCGACCCTCTGAAGCGCCTCCCCCTGCTTAGGGCTTTGGCGCGGAGGAGGTGGAGGAGTACGAGCTCGACGGCGTGGATTCGGCTC
Reverse complement sequence
GAGCCGAATCCACGCCGTCGAGCTCGTACTCCTCCACCTCCTCCGCGCCAAAGCCCTAAGCAGGGGGAGGCGCTTCAGAGGGTCGACAAATCCGTGGCAT[C/T]
ACCAGTCGCAGGTGATGCAGGAGAACGGCGAGATGGGGAGCGTCGCCTCCTCGTCTACGGCGACGGCAGCACGCCTCAGGGTGCGCTTCAGGCTGCTGGC
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 | 24.30% | 0.40% | 1.74% | 73.59% | NA |
| All Indica | 2759 | 4.10% | 0.60% | 1.81% | 93.48% | NA |
| All Japonica | 1512 | 61.60% | 0.00% | 1.12% | 37.30% | 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 | 3.20% | 1.50% | 3.18% | 92.11% | NA |
| Indica Intermediate | 786 | 4.30% | 0.30% | 1.91% | 93.51% | NA |
| Temperate Japonica | 767 | 89.40% | 0.00% | 0.39% | 10.17% | NA |
| Tropical Japonica | 504 | 18.50% | 0.00% | 2.58% | 78.97% | 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% | 10.00% | 53.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0725421252 | G -> DEL | LOC_Os07g42460.1 | N | frameshift_variant | Average:6.77; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |
| vg0725421252 | G -> A | LOC_Os07g42460.1 | missense_variant ; p.Ser53Leu; MODERATE | nonsynonymous_codon ; S53L | Average:6.77; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | possibly damaging  |
1.896 |
DELETERIOUS | 0.01 |