Search for Variation information by Variation ID:
Detailed information for vg0300826027:
| Variant ID: vg0300826027 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 826027 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGCCACTGTGGGAAGGCCGCACCTATCGCCCTTTGACCCCGAGGCTAACCCTGTGCTGACTCGACCCGGGAAAGAGCAGGGAGAAGAGGCCCCCGAGCCG[A/G]
ACGGAGGCCTAAGGCCCCTGACGACCGGAGTTGGCCCTTTGCCCGCTTGTCCGACGACGCCAGGAGCCCCCGACCCCCAGGACGGCCCCGAAGCCACTAT
Reverse complement sequence
ATAGTGGCTTCGGGGCCGTCCTGGGGGTCGGGGGCTCCTGGCGTCGTCGGACAAGCGGGCAAAGGGCCAACTCCGGTCGTCAGGGGCCTTAGGCCTCCGT[T/C]
CGGCTCGGGGGCCTCTTCTCCCTGCTCTTTCCCGGGTCGAGTCAGCACAGGGTTAGCCTCGGGGTCAAAGGGCGATAGGTGCGGCCTTCCCACAGTGGCC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 13.30% | 0.90% | 1.61% | 84.15% | NA |
| All Indica | 2759 | 1.50% | 1.50% | 2.21% | 94.78% | NA |
| All Japonica | 1512 | 37.20% | 0.00% | 0.33% | 62.43% | NA |
| Aus | 269 | 1.50% | 0.70% | 0.37% | 97.40% | NA |
| Indica I | 595 | 1.70% | 0.20% | 3.87% | 94.29% | NA |
| Indica II | 465 | 4.90% | 0.90% | 2.80% | 91.40% | NA |
| Indica III | 913 | 0.30% | 3.00% | 0.99% | 95.73% | NA |
| Indica Intermediate | 786 | 0.80% | 1.10% | 2.04% | 96.06% | NA |
| Temperate Japonica | 767 | 61.00% | 0.00% | 0.52% | 38.46% | NA |
| Tropical Japonica | 504 | 6.00% | 0.00% | 0.00% | 94.05% | NA |
| Japonica Intermediate | 241 | 27.00% | 0.00% | 0.41% | 72.61% | NA |
| VI/Aromatic | 96 | 7.30% | 0.00% | 8.33% | 84.38% | NA |
| Intermediate | 90 | 15.60% | 0.00% | 1.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0300826027 | A -> DEL | LOC_Os03g02350.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0300826027 | A -> G | LOC_Os03g02350.1 | missense_variant ; p.Asn1236Asp; MODERATE | nonsynonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
1.29 |
DELETERIOUS | 0.01 |