Search for Variation information by Variation ID:
Detailed information for vg0221509060:
| Variant ID: vg0221509060 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21509060 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TCTCCAGCCCAACGTTGGCTGGACGACGTGGCCAACTTGGTCATGACGGCACGGCAGCGCCTAGGTGCTGGTGGGCGGTCCTCCGCCACCAAGACCTCTG[G/A]
CGCTACTACCACCGGCTCCGTGTCGTCAAGGCGGAGGGCGCGGCGAGCGGCGGCTGTTGCTCGCCATTCGGCCGCCACTCCTTCGTCAGCGCCTCCGACC
Reverse complement sequence
GGTCGGAGGCGCTGACGAAGGAGTGGCGGCCGAATGGCGAGCAACAGCCGCCGCTCGCCGCGCCCTCCGCCTTGACGACACGGAGCCGGTGGTAGTAGCG[C/T]
CAGAGGTCTTGGTGGCGGAGGACCGCCCACCAGCACCTAGGCGCTGCCGTGCCGTCATGACCAAGTTGGCCACGTCGTCCAGCCAACGTTGGGCTGGAGA
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 | 35.40% | 0.20% | 0.59% | 63.80% | NA |
| All Indica | 2759 | 2.60% | 0.40% | 0.72% | 96.30% | NA |
| All Japonica | 1512 | 96.50% | 0.00% | 0.07% | 3.44% | NA |
| Aus | 269 | 1.50% | 0.00% | 0.00% | 98.51% | NA |
| Indica I | 595 | 2.40% | 0.00% | 0.50% | 97.14% | NA |
| Indica II | 465 | 2.40% | 1.50% | 0.43% | 95.70% | NA |
| Indica III | 913 | 2.00% | 0.10% | 0.99% | 96.93% | NA |
| Indica Intermediate | 786 | 3.60% | 0.40% | 0.76% | 95.29% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.00% | 1.43% | NA |
| Tropical Japonica | 504 | 93.10% | 0.00% | 0.20% | 6.75% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 0.00% | 2.90% | NA |
| VI/Aromatic | 96 | 90.60% | 0.00% | 1.04% | 8.33% | NA |
| Intermediate | 90 | 56.70% | 0.00% | 6.67% | 36.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221509060 | G -> A | LOC_Os02g35800.1 | missense_variant ; p.Gly133Asp; MODERATE | nonsynonymous_codon ; G133D | Average:10.345; most accessible tissue: Callus, score: 25.55 | possibly damaging  |
1.911 |
DELETERIOUS | 0.01 |
| vg0221509060 | G -> DEL | LOC_Os02g35800.1 | N | frameshift_variant | Average:10.345; most accessible tissue: Callus, score: 25.55 | N | N | N | N |