Search for Variation information by Variation ID:
Detailed information for vg0334132528:
| Variant ID: vg0334132528 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 34132528 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GTAGATGGATCGGCAATGGATGTACGCTGACCGGCGGTCCAAAGAGTTTATTGACGGCGTGCACTATTTTTTAAGAGTGGCCGAAGCTAACAGGCAAAGG[G/A]
GTTTTATTTGTTGTCCATGCAATAAGTGTAAGAATCAGAAGGAGTATTCTGCATCCAGGACTATTCATTTCCACTTGTTTGAGTCGGGGTTCATGCCAAG
Reverse complement sequence
CTTGGCATGAACCCCGACTCAAACAAGTGGAAATGAATAGTCCTGGATGCAGAATACTCCTTCTGATTCTTACACTTATTGCATGGACAACAAATAAAAC[C/T]
CCTTTGCCTGTTAGCTTCGGCCACTCTTAAAAAATAGTGCACGCCGTCAATAAACTCTTTGGACCGCCGGTCAGCGTACATCCATTGCCGATCCATCTAC
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 | 46.30% | 0.00% | 2.37% | 51.31% | NA |
| All Indica | 2759 | 18.30% | 0.00% | 3.55% | 78.11% | NA |
| All Japonica | 1512 | 97.90% | 0.10% | 0.20% | 1.85% | NA |
| Aus | 269 | 22.30% | 0.00% | 3.72% | 73.98% | NA |
| Indica I | 595 | 15.00% | 0.00% | 1.51% | 83.53% | NA |
| Indica II | 465 | 5.60% | 0.00% | 2.15% | 92.26% | NA |
| Indica III | 913 | 28.70% | 0.00% | 5.81% | 65.50% | NA |
| Indica Intermediate | 786 | 16.40% | 0.00% | 3.31% | 80.28% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.13% | 0.26% | NA |
| Tropical Japonica | 504 | 94.80% | 0.00% | 0.40% | 4.76% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.40% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 94.80% | 0.00% | 0.00% | 5.21% | NA |
| Intermediate | 90 | 56.70% | 0.00% | 1.11% | 42.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0334132528 | G -> A | LOC_Os03g60010.1 | missense_variant ; p.Gly33Ser; MODERATE | nonsynonymous_codon ; G33S | Average:12.835; most accessible tissue: Zhenshan97 root, score: 20.427 | benign  |
1.152 |
DELETERIOUS | 0.03 |
| vg0334132528 | G -> DEL | LOC_Os03g60010.1 | N | frameshift_variant | Average:12.835; most accessible tissue: Zhenshan97 root, score: 20.427 | N | N | N | N |