Search for Variation information by Variation ID:
Detailed information for vg0329362446:
| Variant ID: vg0329362446 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 29362446 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGAGGAGAAATGAGGTTTCCCCGGGATGGTTCTGTCCCCCCCATCTTGCGGAGCCGTTTCTTCTTCCGCTCCCCCTCGGGCTGCGGCGTCGGCGCGGCCC[C/T]
CTCCGGGCGCCTGCTGCTGACACGCGCCGCCCCGCCCCCTCGGGGAGGAGATGGGGAGGAAGTACCCTCTTGCTTTCTCTTCCCTCGGGCGTCGGCAGGG
Reverse complement sequence
CCCTGCCGACGCCCGAGGGAAGAGAAAGCAAGAGGGTACTTCCTCCCCATCTCCTCCCCGAGGGGGCGGGGCGGCGCGTGTCAGCAGCAGGCGCCCGGAG[G/A]
GGGCCGCGCCGACGCCGCAGCCCGAGGGGGAGCGGAAGAAGAAACGGCTCCGCAAGATGGGGGGGACAGAACCATCCCGGGGAAACCTCATTTCTCCTCC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.80% | 0.10% | 1.50% | 41.58% | NA |
| All Indica | 2759 | 38.10% | 0.00% | 1.67% | 60.24% | NA |
| All Japonica | 1512 | 98.90% | 0.30% | 0.40% | 0.40% | NA |
| Aus | 269 | 4.10% | 0.00% | 4.46% | 91.45% | NA |
| Indica I | 595 | 53.40% | 0.00% | 0.67% | 45.88% | NA |
| Indica II | 465 | 38.10% | 0.00% | 0.65% | 61.29% | NA |
| Indica III | 913 | 28.70% | 0.00% | 2.30% | 69.00% | NA |
| Indica Intermediate | 786 | 37.40% | 0.00% | 2.29% | 60.31% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.13% | 0.26% | NA |
| Tropical Japonica | 504 | 97.40% | 1.00% | 0.99% | 0.60% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 71.90% | 0.00% | 2.08% | 26.04% | NA |
| Intermediate | 90 | 65.60% | 0.00% | 5.56% | 28.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0329362446 | C -> T | LOC_Os03g51320.1 | missense_variant ; p.Gly338Arg; MODERATE | nonsynonymous_codon ; G338R | Average:26.118; most accessible tissue: Zhenshan97 root, score: 59.664 | probably damaging  |
2.607 |
DELETERIOUS | 0.01 |
| vg0329362446 | C -> DEL | LOC_Os03g51320.1 | N | frameshift_variant | Average:26.118; most accessible tissue: Zhenshan97 root, score: 59.664 | N | N | N | N |