Search for Variation information by Variation ID:
Detailed information for vg0329362085:
| Variant ID: vg0329362085 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 29362085 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TCACGGGTCGCCTCGGAGGATGTCGTCGCCTCGGCCTGGCGGAGTCCGGCCTCCTCCCGAGCGGCTTCCTCGGTCTGGCGAGCCTGGGCGGCCTCCCGAG[C/T]
GGCCTCCTCGGCTTCCCGAAGGCGATCCGCGGCTTCTCGCCGGTCAGATTCCCGCCTCCGGGCCTCTGTGGTCGCCGGGTCCTCGGCCTCAGACTGGCCG
Reverse complement sequence
CGGCCAGTCTGAGGCCGAGGACCCGGCGACCACAGAGGCCCGGAGGCGGGAATCTGACCGGCGAGAAGCCGCGGATCGCCTTCGGGAAGCCGAGGAGGCC[G/A]
CTCGGGAGGCCGCCCAGGCTCGCCAGACCGAGGAAGCCGCTCGGGAGGAGGCCGGACTCCGCCAGGCCGAGGCGACGACATCCTCCGAGGCGACCCGTGA
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 | 55.90% | 0.50% | 1.06% | 42.51% | NA |
| All Indica | 2759 | 37.90% | 0.00% | 0.83% | 61.25% | NA |
| All Japonica | 1512 | 97.90% | 1.50% | 0.07% | 0.46% | NA |
| Aus | 269 | 2.20% | 0.00% | 2.23% | 95.54% | NA |
| Indica I | 595 | 53.10% | 0.00% | 0.17% | 46.72% | NA |
| Indica II | 465 | 38.70% | 0.00% | 0.43% | 60.86% | NA |
| Indica III | 913 | 28.10% | 0.00% | 1.31% | 70.54% | NA |
| Indica Intermediate | 786 | 37.30% | 0.00% | 1.02% | 61.70% | NA |
| Temperate Japonica | 767 | 96.60% | 3.00% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 53.10% | 0.00% | 18.75% | 28.12% | NA |
| Intermediate | 90 | 65.60% | 1.10% | 2.22% | 31.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0329362085 | C -> T | LOC_Os03g51320.1 | missense_variant ; p.Ala427Thr; MODERATE | nonsynonymous_codon ; A427T | Average:29.123; most accessible tissue: Zhenshan97 flag leaf, score: 70.425 | benign  |
1.282 |
DELETERIOUS | 0.01 |
| vg0329362085 | C -> DEL | LOC_Os03g51320.1 | N | frameshift_variant | Average:29.123; most accessible tissue: Zhenshan97 flag leaf, score: 70.425 | N | N | N | N |