Search for Variation information by Variation ID:
Detailed information for vg0321793120:
| Variant ID: vg0321793120 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 21793120 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTCCCTCGCCGGAGCAGGTGGACTGGGCGGAAGGTGCAGTGATCTCCGCCCAGTCGGCGGCGGATAACATGGCGTCCTATGTGCTGGATCTCAGGAGGGG[C/T]
CTGGCCGTGTTCGCCGGGACAGGGAGGCCCGAGGAGGCGGTGCTCAGGAAGCACGTCGCGTGGGCCGACGCGCGCCGCGCGGAGGCGGTGGAGATCGCCT
Reverse complement sequence
AGGCGATCTCCACCGCCTCCGCGCGGCGCGCGTCGGCCCACGCGACGTGCTTCCTGAGCACCGCCTCCTCGGGCCTCCCTGTCCCGGCGAACACGGCCAG[G/A]
CCCCTCCTGAGATCCAGCACATAGGACGCCATGTTATCCGCCGCCGACTGGGCGGAGATCACTGCACCTTCCGCCCAGTCCACCTGCTCCGGCGAGGGAG
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 | 80.30% | 1.70% | 12.78% | 5.21% | NA |
| All Indica | 2759 | 70.20% | 2.80% | 20.95% | 6.05% | NA |
| All Japonica | 1512 | 93.40% | 0.30% | 1.19% | 5.16% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 31.40% | 4.20% | 55.46% | 8.91% | NA |
| Indica II | 465 | 90.10% | 1.50% | 7.53% | 0.86% | NA |
| Indica III | 913 | 74.90% | 3.30% | 13.14% | 8.65% | NA |
| Indica Intermediate | 786 | 82.30% | 1.90% | 11.83% | 3.94% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.13% | 0.26% | NA |
| Tropical Japonica | 504 | 95.20% | 0.20% | 1.19% | 3.37% | NA |
| Japonica Intermediate | 241 | 69.70% | 1.20% | 4.56% | 24.48% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 88.90% | 1.10% | 8.89% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0321793120 | C -> T | LOC_Os03g39240.1 | synonymous_variant ; p.Gly87Gly; LOW | nonsynonymous_codon ; G87A | Average:66.032; most accessible tissue: Zhenshan97 flower, score: 78.317 | benign  |
0.2 |
TOLERATED | 0.33 |
| vg0321793120 | C -> DEL | LOC_Os03g39240.1 | N | frameshift_variant | Average:66.032; most accessible tissue: Zhenshan97 flower, score: 78.317 | N | N | N | N |