Search for Variation information by Variation ID:
Detailed information for vg0300826013:
| Variant ID: vg0300826013 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 826013 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CAGGAAGGCCCTGAGGCCACTGTGGGAAGGCCGCACCTATCGCCCTTTGACCCCGAGGCTAACCCTGTGCTGACTCGACCCGGGAAAGAGCAGGGAGAAG[A/T]
GGCCCCCGAGCCGAACGGAGGCCTAAGGCCCCTGACGACCGGAGTTGGCCCTTTGCCCGCTTGTCCGACGACGCCAGGAGCCCCCGACCCCCAGGACGGC
Reverse complement sequence
GCCGTCCTGGGGGTCGGGGGCTCCTGGCGTCGTCGGACAAGCGGGCAAAGGGCCAACTCCGGTCGTCAGGGGCCTTAGGCCTCCGTTCGGCTCGGGGGCC[T/A]
CTTCTCCCTGCTCTTTCCCGGGTCGAGTCAGCACAGGGTTAGCCTCGGGGTCAAAGGGCGATAGGTGCGGCCTTCCCACAGTGGCCTCAGGGCCTTCCTG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 14.60% | 1.00% | 1.69% | 82.63% | NA |
| All Indica | 2759 | 3.30% | 1.60% | 1.92% | 93.19% | NA |
| All Japonica | 1512 | 37.40% | 0.00% | 0.53% | 62.10% | NA |
| Aus | 269 | 1.50% | 1.50% | 0.00% | 97.03% | NA |
| Indica I | 595 | 4.90% | 0.00% | 2.69% | 92.44% | NA |
| Indica II | 465 | 7.30% | 0.90% | 2.58% | 89.25% | NA |
| Indica III | 913 | 0.50% | 3.20% | 1.31% | 94.96% | NA |
| Indica Intermediate | 786 | 2.90% | 1.40% | 1.65% | 94.02% | NA |
| Temperate Japonica | 767 | 61.10% | 0.00% | 0.39% | 38.46% | NA |
| Tropical Japonica | 504 | 6.20% | 0.00% | 0.60% | 93.25% | NA |
| Japonica Intermediate | 241 | 27.00% | 0.00% | 0.83% | 72.20% | NA |
| VI/Aromatic | 96 | 17.70% | 1.00% | 17.71% | 63.54% | NA |
| Intermediate | 90 | 16.70% | 0.00% | 2.22% | 81.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0300826013 | A -> T | LOC_Os03g02350.1 | missense_variant ; p.Glu1231Val; MODERATE | nonsynonymous_codon ; E1231V | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.34 |
DELETERIOUS | 0.00 |
| vg0300826013 | A -> DEL | LOC_Os03g02350.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |