Search for Variation information by Variation ID:
Detailed information for vg0300824531:
| Variant ID: vg0300824531 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 824531 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGCCCCGGTGGCCCCATCTCTGTCCATGGCGACCTCAAAGTCGCGCTCGCTTGTCTGGAGCAGCGCGCGGACCACCTCGTCGCTGCGTCCAAGCCCGAGG[G/A]
TGGCGACGAGAGGCTTGGCGCCTCCGCCCCCGCCACCCCGAGGCAGCGGATGATCACAGGCGACGAGGTCCCGGTCAAGGAGGTTGCCCTGGGCGACGGC
Reverse complement sequence
GCCGTCGCCCAGGGCAACCTCCTTGACCGGGACCTCGTCGCCTGTGATCATCCGCTGCCTCGGGGTGGCGGGGGCGGAGGCGCCAAGCCTCTCGTCGCCA[C/T]
CCTCGGGCTTGGACGCAGCGACGAGGTGGTCCGCGCGCTGCTCCAGACAAGCGAGCGCGACTTTGAGGTCGCCATGGACAGAGATGGGGCCACCGGGGCC
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 | 13.10% | 0.40% | 0.68% | 85.84% | NA |
| All Indica | 2759 | 1.10% | 0.10% | 0.07% | 98.77% | NA |
| All Japonica | 1512 | 37.30% | 0.00% | 0.20% | 62.50% | NA |
| Aus | 269 | 1.90% | 4.80% | 8.18% | 85.13% | NA |
| Indica I | 595 | 0.30% | 0.00% | 0.00% | 99.66% | NA |
| Indica II | 465 | 4.30% | 0.00% | 0.00% | 95.70% | NA |
| Indica III | 913 | 0.40% | 0.20% | 0.00% | 99.34% | NA |
| Indica Intermediate | 786 | 0.50% | 0.00% | 0.25% | 99.24% | NA |
| Temperate Japonica | 767 | 60.90% | 0.00% | 0.00% | 39.11% | NA |
| Tropical Japonica | 504 | 6.30% | 0.00% | 0.00% | 93.65% | NA |
| Japonica Intermediate | 241 | 27.00% | 0.00% | 1.24% | 71.78% | NA |
| VI/Aromatic | 96 | 4.20% | 4.20% | 5.21% | 86.46% | NA |
| Intermediate | 90 | 16.70% | 0.00% | 0.00% | 83.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0300824531 | G -> A | LOC_Os03g02350.1 | missense_variant ; p.Gly761Asp; MODERATE | nonsynonymous_codon ; G761D | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.417 |
DELETERIOUS | 0.03 |
| vg0300824531 | G -> DEL | LOC_Os03g02350.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |