Search for Variation information by Variation ID:
Detailed information for vg0725421381:
| Variant ID: vg0725421381 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 25421381 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CGCCTCCCCCTGCTTAGGGCTTTGGCGCGGAGGAGGTGGAGGAGTACGAGCTCGACGGCGTGGATTCGGCTCCCCGTCGTCGCCGCTCACACTCGGAGAG[A/T]
GGTCGTGCGCTTTTCCTTGCTCGGCCATTAGGCTGAACAAGAAAAACTTGGCACACACGGAAGAGTCTGAGAGCTCAGAAAACACACGCTGAGCCCCCTA
Reverse complement sequence
TAGGGGGCTCAGCGTGTGTTTTCTGAGCTCTCAGACTCTTCCGTGTGTGCCAAGTTTTTCTTGTTCAGCCTAATGGCCGAGCAAGGAAAAGCGCACGACC[T/A]
CTCTCCGAGTGTGAGCGGCGACGACGGGGAGCCGAATCCACGCCGTCGAGCTCGTACTCCTCCACCTCCTCCGCGCCAAAGCCCTAAGCAGGGGGAGGCG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 23.70% | 0.30% | 1.67% | 74.27% | NA |
| All Indica | 2759 | 4.20% | 0.60% | 2.14% | 93.08% | NA |
| All Japonica | 1512 | 60.20% | 0.00% | 0.26% | 39.55% | NA |
| Aus | 269 | 2.20% | 0.00% | 1.12% | 96.65% | NA |
| Indica I | 595 | 4.90% | 2.00% | 1.51% | 91.60% | NA |
| Indica II | 465 | 3.90% | 0.00% | 0.43% | 95.70% | NA |
| Indica III | 913 | 3.80% | 0.10% | 2.96% | 93.10% | NA |
| Indica Intermediate | 786 | 4.30% | 0.40% | 2.67% | 92.62% | NA |
| Temperate Japonica | 767 | 89.70% | 0.00% | 0.26% | 10.04% | NA |
| Tropical Japonica | 504 | 13.30% | 0.00% | 0.20% | 86.51% | NA |
| Japonica Intermediate | 241 | 64.30% | 0.00% | 0.41% | 35.27% | NA |
| VI/Aromatic | 96 | 63.50% | 0.00% | 4.17% | 32.29% | NA |
| Intermediate | 90 | 31.10% | 0.00% | 10.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0725421381 | A -> DEL | LOC_Os07g42460.1 | N | frameshift_variant | Average:7.82; most accessible tissue: Zhenshan97 flag leaf, score: 13.342 | N | N | N | N |
| vg0725421381 | A -> T | LOC_Os07g42460.1 | missense_variant ; p.Leu10His; MODERATE | nonsynonymous_codon ; L10H | Average:7.82; most accessible tissue: Zhenshan97 flag leaf, score: 13.342 | probably damaging  |
3.24 |
DELETERIOUS | 0.01 |