Search for Variation information by Variation ID:
Detailed information for vg0137499394:
| Variant ID: vg0137499394 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 37499394 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTCGGCCTGGCGAGCCCGGGCGGCCTCCTGGGCGGCCTCCTCGGCTTCCCGTAGGCGATCCGCGGCCTCTCGCCGGTCAGATTCCCGCCTGAGGGCCTCT[G/A]
CGGCCGCCGGATCCTCGGCCTCAGACTGGCCGGACTTGGAATGGCGGGAGGGACGCGACGGGATCTCGCTGAAACAAAAGAAAAAACCAGAAGACGAACA
Reverse complement sequence
TGTTCGTCTTCTGGTTTTTTCTTTTGTTTCAGCGAGATCCCGTCGCGTCCCTCCCGCCATTCCAAGTCCGGCCAGTCTGAGGCCGAGGATCCGGCGGCCG[C/T]
AGAGGCCCTCAGGCGGGAATCTGACCGGCGAGAGGCCGCGGATCGCCTACGGGAAGCCGAGGAGGCCGCCCAGGAGGCCGCCCGGGCTCGCCAGGCCGAG
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 | 34.60% | 1.20% | 0.34% | 63.82% | NA |
| All Indica | 2759 | 2.10% | 0.00% | 0.25% | 97.61% | NA |
| All Japonica | 1512 | 94.00% | 3.80% | 0.13% | 2.05% | NA |
| Aus | 269 | 1.50% | 0.00% | 2.60% | 95.91% | NA |
| Indica I | 595 | 1.20% | 0.00% | 0.17% | 98.66% | NA |
| Indica II | 465 | 1.10% | 0.00% | 0.22% | 98.71% | NA |
| Indica III | 913 | 0.80% | 0.00% | 0.33% | 98.90% | NA |
| Indica Intermediate | 786 | 5.10% | 0.00% | 0.25% | 94.66% | NA |
| Temperate Japonica | 767 | 97.50% | 0.70% | 0.13% | 1.69% | NA |
| Tropical Japonica | 504 | 93.80% | 3.60% | 0.00% | 2.58% | NA |
| Japonica Intermediate | 241 | 83.40% | 14.10% | 0.41% | 2.07% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 63.30% | 1.10% | 0.00% | 35.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0137499394 | G -> A | LOC_Os01g64610.1 | missense_variant ; p.Ala410Val; MODERATE | nonsynonymous_codon ; A410V | Average:5.749; most accessible tissue: Minghui63 young leaf, score: 9.976 | benign  |
1.126 |
DELETERIOUS | 0.02 |
| vg0137499394 | G -> DEL | LOC_Os01g64610.1 | N | frameshift_variant | Average:5.749; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |