Search for Variation information by Variation ID:
Detailed information for vg0607893841:
| Variant ID: vg0607893841 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 7893841 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 93. )
Flanking Sequence (100 bp) in Reference Genome:
GCGAGTTTTCACTCACCCATCTTGTTCGTCTTCTGGTCTTTTCTTTTGTTTCAGCGAGATCCCGTCGCGTCCCTCCCGCCATTCCAAGTCCGGCCAGTCT[G/A]
AGGCCGAGGATCCGGCGACCGCAGAGGCCCGCAGGCGGCAAGCTGACCGGCGAGAGGCCGCGGATCGCCTACGGGAAGCCGAGGAGGCCGCCCAGGAGGC
Reverse complement sequence
GCCTCCTGGGCGGCCTCCTCGGCTTCCCGTAGGCGATCCGCGGCCTCTCGCCGGTCAGCTTGCCGCCTGCGGGCCTCTGCGGTCGCCGGATCCTCGGCCT[C/T]
AGACTGGCCGGACTTGGAATGGCGGGAGGGACGCGACGGGATCTCGCTGAAACAAAAGAAAAGACCAGAAGACGAACAAGATGGGTGAGTGAAAACTCGC
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 | 6.60% | 0.20% | 0.97% | 92.26% | NA |
| All Indica | 2759 | 0.10% | 0.30% | 0.51% | 99.13% | NA |
| All Japonica | 1512 | 19.70% | 0.00% | 0.40% | 79.89% | NA |
| Aus | 269 | 0.00% | 0.40% | 8.92% | 90.71% | NA |
| Indica I | 595 | 0.00% | 0.20% | 0.17% | 99.66% | NA |
| Indica II | 465 | 0.20% | 0.00% | 0.00% | 99.78% | NA |
| Indica III | 913 | 0.00% | 0.50% | 0.99% | 98.47% | NA |
| Indica Intermediate | 786 | 0.10% | 0.30% | 0.51% | 99.11% | NA |
| Temperate Japonica | 767 | 34.20% | 0.00% | 0.26% | 65.58% | NA |
| Tropical Japonica | 504 | 2.20% | 0.00% | 0.79% | 97.02% | NA |
| Japonica Intermediate | 241 | 10.40% | 0.00% | 0.00% | 89.63% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 2.08% | 96.88% | NA |
| Intermediate | 90 | 11.10% | 0.00% | 0.00% | 88.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0607893841 | G -> A | LOC_Os06g14150.1 | missense_variant ; p.Glu437Lys; MODERATE | nonsynonymous_codon ; E437K | Average:7.489; most accessible tissue: Callus, score: 21.67 | benign  |
1.285 |
DELETERIOUS | 0.02 |
| vg0607893841 | G -> DEL | LOC_Os06g14150.1 | N | frameshift_variant | Average:7.489; most accessible tissue: Callus, score: 21.67 | N | N | N | N |