Search for Variation information by Variation ID:
Detailed information for vg0322194110:
| Variant ID: vg0322194110 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 22194110 |
| Reference Allele: G | Alternative Allele: C,T |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TCCCTGGCCTGGTAGCTTGCCAGTACGAGCTCCACCGCCCCCCGGGCGAGGTCCCTCGAGGATGACTTGATCGTCTCCTCGAGCTCCTCGGGGAGCCGCT[G/C,T]
GAGGGCCCCGGCCATCTCTGAGAGGCACTGGGCGAGGCCCCCCTGGTTGGCGGCGTACTTCGCGTGCCGCCCGCCCCAGAGACCCGCCTGCCGCCCGGCG
Reverse complement sequence
CGCCGGGCGGCAGGCGGGTCTCTGGGGCGGGCGGCACGCGAAGTACGCCGCCAACCAGGGGGGCCTCGCCCAGTGCCTCTCAGAGATGGCCGGGGCCCTC[C/G,A]
AGCGGCTCCCCGAGGAGCTCGAGGAGACGATCAAGTCATCCTCGAGGGACCTCGCCCGGGGGGCGGTGGAGCTCGTACTGGCAAGCTACCAGGCCAGGGA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 20.70% | 0.50% | 10.62% | 68.15% | T: 0.02% |
| All Indica | 2759 | 16.90% | 0.70% | 14.39% | 67.96% | T: 0.04% |
| All Japonica | 1512 | 29.70% | 0.10% | 1.65% | 68.52% | NA |
| Aus | 269 | 17.10% | 0.40% | 21.93% | 60.59% | NA |
| Indica I | 595 | 12.30% | 0.00% | 6.05% | 81.68% | NA |
| Indica II | 465 | 3.70% | 0.20% | 10.11% | 86.02% | NA |
| Indica III | 913 | 28.30% | 1.90% | 25.74% | 44.03% | T: 0.11% |
| Indica Intermediate | 786 | 15.10% | 0.10% | 10.05% | 74.68% | NA |
| Temperate Japonica | 767 | 15.50% | 0.00% | 0.78% | 83.70% | NA |
| Tropical Japonica | 504 | 53.20% | 0.40% | 2.38% | 44.05% | NA |
| Japonica Intermediate | 241 | 25.70% | 0.00% | 2.90% | 71.37% | NA |
| VI/Aromatic | 96 | 3.10% | 0.00% | 13.54% | 83.33% | NA |
| Intermediate | 90 | 16.70% | 0.00% | 8.89% | 74.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0322194110 | G -> C | LOC_Os03g39930.1 | missense_variant ; p.Gln338Glu; MODERATE | nonsynonymous_codon ; Q338E | Average:6.269; most accessible tissue: Zhenshan97 flower, score: 9.663 | benign  |
0.055 |
TOLERATED | 0.31 |
| vg0322194110 | G -> DEL | LOC_Os03g39930.1 | N | frameshift_variant | Average:6.269; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |
| vg0322194110 | G -> T | LOC_Os03g39930.1 | missense_variant ; p.Gln338Lys; MODERATE | nonsynonymous_codon ; Q338K | Average:6.269; most accessible tissue: Zhenshan97 flower, score: 9.663 | benign |
-0.183 |
TOLERATED | 0.07 |