Search for Variation information by Variation ID:
Detailed information for vg0807397578:
| Variant ID: vg0807397578 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 7397578 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 331. )
Flanking Sequence (100 bp) in Reference Genome:
CGATTGTATCCTATATCGCGGTGAGGAGTATGAGAACCTAGAAGCATGCCCTGTTTGCAAAGCACTACGATACAAGATTAGACGGGACGATCCAGGAGAA[G/A]
TTGACGGGCAGCTAACAAAGAAGAGAATTCCTGCTAAGGTGATGTGGTATTTCCCTATAATACCACGGCTAAGGCGTTTGTTCAGGAACAAGGGGAATGC
Reverse complement sequence
GCATTCCCCTTGTTCCTGAACAAACGCCTTAGCCGTGGTATTATAGGGAAATACCACATCACCTTAGCAGGAATTCTCTTCTTTGTTAGCTGCCCGTCAA[C/T]
TTCTCCTGGATCGTCCCGTCTAATCTTGTATCGTAGTGCTTTGCAAACAGGGCATGCTTCTAGGTTCTCATACTCCTCACCGCGATATAGGATACAATCG
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 | 0.20% | 0.20% | 1.90% | 97.76% | NA |
| All Indica | 2759 | 0.30% | 0.20% | 0.25% | 99.28% | NA |
| All Japonica | 1512 | 0.00% | 0.20% | 5.49% | 94.31% | NA |
| Aus | 269 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Indica I | 595 | 0.20% | 0.00% | 0.00% | 99.83% | NA |
| Indica II | 465 | 0.20% | 0.40% | 0.43% | 98.92% | NA |
| Indica III | 913 | 0.40% | 0.10% | 0.33% | 99.12% | NA |
| Indica Intermediate | 786 | 0.30% | 0.30% | 0.25% | 99.24% | NA |
| Temperate Japonica | 767 | 0.00% | 0.00% | 0.26% | 99.74% | NA |
| Tropical Japonica | 504 | 0.00% | 0.40% | 4.76% | 94.84% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.40% | 23.65% | 75.93% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0807397578 | G -> A | LOC_Os08g12500.1 | missense_variant ; p.Val254Ile; MODERATE | nonsynonymous_codon ; V254I | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
1.343 |
DELETERIOUS | 0.00 |
| vg0807397578 | G -> DEL | LOC_Os08g12500.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |