Search for Variation information by Variation ID:
Detailed information for vg0725421246:
| Variant ID: vg0725421246 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 25421246 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GAGCGCGCCAGCAGCCTGAAGCGCACCCTGAGGCGTGCTGCCGTCGCCGTAGACGAGGAGGCGACGCTCCCCATCTCGCCGTTCTCCTGCATCACCTGCG[A/G]
CTGGTGATGCCACGGATTTGTCGACCCTCTGAAGCGCCTCCCCCTGCTTAGGGCTTTGGCGCGGAGGAGGTGGAGGAGTACGAGCTCGACGGCGTGGATT
Reverse complement sequence
AATCCACGCCGTCGAGCTCGTACTCCTCCACCTCCTCCGCGCCAAAGCCCTAAGCAGGGGGAGGCGCTTCAGAGGGTCGACAAATCCGTGGCATCACCAG[T/C]
CGCAGGTGATGCAGGAGAACGGCGAGATGGGGAGCGTCGCCTCCTCGTCTACGGCGACGGCAGCACGCCTCAGGGTGCGCTTCAGGCTGCTGGCGCGCTC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 25.90% | 0.50% | 1.67% | 71.86% | NA |
| All Indica | 2759 | 6.90% | 0.10% | 2.03% | 91.05% | NA |
| All Japonica | 1512 | 61.10% | 1.50% | 0.86% | 36.51% | NA |
| Aus | 269 | 3.00% | 0.00% | 1.49% | 95.54% | NA |
| Indica I | 595 | 6.40% | 0.00% | 0.84% | 92.77% | NA |
| Indica II | 465 | 4.50% | 0.20% | 0.65% | 94.62% | NA |
| Indica III | 913 | 8.10% | 0.10% | 3.72% | 88.06% | NA |
| Indica Intermediate | 786 | 7.10% | 0.00% | 1.78% | 91.09% | NA |
| Temperate Japonica | 767 | 89.60% | 0.00% | 0.52% | 9.91% | NA |
| Tropical Japonica | 504 | 15.90% | 4.60% | 1.79% | 77.78% | NA |
| Japonica Intermediate | 241 | 65.10% | 0.00% | 0.00% | 34.85% | NA |
| VI/Aromatic | 96 | 75.00% | 0.00% | 2.08% | 22.92% | NA |
| Intermediate | 90 | 36.70% | 0.00% | 4.44% | 58.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0725421246 | A -> DEL | LOC_Os07g42460.1 | N | frameshift_variant | Average:6.77; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |
| vg0725421246 | A -> G | LOC_Os07g42460.1 | missense_variant ; p.Val55Ala; MODERATE | nonsynonymous_codon ; V55A | Average:6.77; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | benign  |
0.417 |
TOLERATED | 0.51 |