Search for Variation information by Variation ID:
Detailed information for vg0221509287:
| Variant ID: vg0221509287 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21509287 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TGCCCGCATCAGTATCGAGCGCCGGCGTAATGGCCGACGTGCTGCCCACGCAACGGAGGGCGCCTCCTCGTCCGGAGTGTCACATCAACACGGACGCGGG[G/T]
ATCAGCCCTCCGTGCCCCCGGTTGGTGGTGTCGGCTGTAGAGCCTTTGTGGCGAGCCTTCGGAACGTCCGTTGGCCCCCAAGGTTCCGGCCCACCATCGC
Reverse complement sequence
GCGATGGTGGGCCGGAACCTTGGGGGCCAACGGACGTTCCGAAGGCTCGCCACAAAGGCTCTACAGCCGACACCACCAACCGGGGGCACGGAGGGCTGAT[C/A]
CCCGCGTCCGTGTTGATGTGACACTCCGGACGAGGAGGCGCCCTCCGTTGCGTGGGCAGCACGTCGGCCATTACGCCGGCGCTCGATACTGATGCGGGCA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 34.80% | 0.10% | 2.22% | 62.82% | NA |
| All Indica | 2759 | 2.80% | 0.00% | 2.54% | 94.67% | NA |
| All Japonica | 1512 | 94.40% | 0.20% | 2.12% | 3.24% | NA |
| Aus | 269 | 1.10% | 0.00% | 0.37% | 98.51% | NA |
| Indica I | 595 | 2.70% | 0.00% | 1.51% | 95.80% | NA |
| Indica II | 465 | 2.80% | 0.00% | 3.87% | 93.33% | NA |
| Indica III | 913 | 2.20% | 0.00% | 1.97% | 95.84% | NA |
| Indica Intermediate | 786 | 3.60% | 0.00% | 3.18% | 93.26% | NA |
| Temperate Japonica | 767 | 94.70% | 0.40% | 3.78% | 1.17% | NA |
| Tropical Japonica | 504 | 93.10% | 0.00% | 0.40% | 6.55% | NA |
| Japonica Intermediate | 241 | 96.70% | 0.00% | 0.41% | 2.90% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 1.04% | 7.29% | NA |
| Intermediate | 90 | 56.70% | 2.20% | 1.11% | 40.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221509287 | G -> T | LOC_Os02g35800.1 | missense_variant ; p.Asp209Tyr; MODERATE | nonsynonymous_codon ; D209Y | Average:5.563; most accessible tissue: Callus, score: 14.511 | benign  |
0.764 |
DELETERIOUS | 0.01 |
| vg0221509287 | G -> DEL | LOC_Os02g35800.1 | N | frameshift_variant | Average:5.563; most accessible tissue: Callus, score: 14.511 | N | N | N | N |