Search for Variation information by Variation ID:
Detailed information for vg0221509038:
| Variant ID: vg0221509038 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21509038 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCCCGTTGTCCCTGACCCGGAGTCTCCAGCCCAACGTTGGCTGGACGACGTGGCCAACTTGGTCATGACGGCACGGCAGCGCCTAGGTGCTGGTGGGCGG[T/C]
CCTCCGCCACCAAGACCTCTGGCGCTACTACCACCGGCTCCGTGTCGTCAAGGCGGAGGGCGCGGCGAGCGGCGGCTGTTGCTCGCCATTCGGCCGCCAC
Reverse complement sequence
GTGGCGGCCGAATGGCGAGCAACAGCCGCCGCTCGCCGCGCCCTCCGCCTTGACGACACGGAGCCGGTGGTAGTAGCGCCAGAGGTCTTGGTGGCGGAGG[A/G]
CCGCCCACCAGCACCTAGGCGCTGCCGTGCCGTCATGACCAAGTTGGCCACGTCGTCCAGCCAACGTTGGGCTGGAGACTCCGGGTCAGGGACAACGGGC
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 35.30% | 0.20% | 0.38% | 64.07% | NA |
| All Indica | 2759 | 2.50% | 0.40% | 0.43% | 96.70% | 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 | 2.50% | 0.00% | 0.34% | 97.14% | NA |
| Indica II | 465 | 2.40% | 1.50% | 0.22% | 95.91% | NA |
| Indica III | 913 | 1.80% | 0.10% | 0.44% | 97.70% | NA |
| Indica Intermediate | 786 | 3.30% | 0.40% | 0.64% | 95.67% | 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% | 4.44% | 38.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221509038 | T -> DEL | LOC_Os02g35800.1 | N | frameshift_variant | Average:10.913; most accessible tissue: Callus, score: 25.55 | N | N | N | N |
| vg0221509038 | T -> C | LOC_Os02g35800.1 | missense_variant ; p.Ser126Pro; MODERATE | nonsynonymous_codon ; S126P | Average:10.913; most accessible tissue: Callus, score: 25.55 | possibly damaging  |
1.817 |
DELETERIOUS | 0.00 |