Search for Variation information by Variation ID:
Detailed information for vg0322194096:
| Variant ID: vg0322194096 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 22194096 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGGAGAAGTCAGGGTCCCTGGCCTGGTAGCTTGCCAGTACGAGCTCCACCGCCCCCCGGGCGAGGTCCCTCGAGGATGACTTGATCGTCTCCTCGAGCTC[C/A]
TCGGGGAGCCGCTGGAGGGCCCCGGCCATCTCTGAGAGGCACTGGGCGAGGCCCCCCTGGTTGGCGGCGTACTTCGCGTGCCGCCCGCCCCAGAGACCCG
Reverse complement sequence
CGGGTCTCTGGGGCGGGCGGCACGCGAAGTACGCCGCCAACCAGGGGGGCCTCGCCCAGTGCCTCTCAGAGATGGCCGGGGCCCTCCAGCGGCTCCCCGA[G/T]
GAGCTCGAGGAGACGATCAAGTCATCCTCGAGGGACCTCGCCCGGGGGGCGGTGGAGCTCGTACTGGCAAGCTACCAGGCCAGGGACCCTGACTTCTCCC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 35.00% | 0.10% | 4.82% | 60.16% | NA |
| All Indica | 2759 | 36.90% | 0.00% | 6.56% | 56.54% | NA |
| All Japonica | 1512 | 31.20% | 0.20% | 1.92% | 66.67% | NA |
| Aus | 269 | 41.60% | 0.00% | 4.09% | 54.28% | NA |
| Indica I | 595 | 19.70% | 0.00% | 2.18% | 78.15% | NA |
| Indica II | 465 | 19.80% | 0.00% | 10.54% | 69.68% | NA |
| Indica III | 913 | 62.30% | 0.00% | 7.56% | 30.12% | NA |
| Indica Intermediate | 786 | 30.50% | 0.00% | 6.36% | 63.10% | NA |
| Temperate Japonica | 767 | 15.50% | 0.00% | 0.78% | 83.70% | NA |
| Tropical Japonica | 504 | 56.50% | 0.40% | 1.98% | 41.07% | NA |
| Japonica Intermediate | 241 | 28.20% | 0.40% | 5.39% | 65.98% | NA |
| VI/Aromatic | 96 | 24.00% | 0.00% | 3.12% | 72.92% | NA |
| Intermediate | 90 | 30.00% | 0.00% | 4.44% | 65.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0322194096 | C -> A | LOC_Os03g39930.1 | missense_variant ; p.Glu342Asp; MODERATE | nonsynonymous_codon ; E342D | Average:6.269; most accessible tissue: Zhenshan97 flower, score: 9.663 | benign  |
1.274 |
DELETERIOUS | 0.01 |
| vg0322194096 | C -> DEL | LOC_Os03g39930.1 | N | frameshift_variant | Average:6.269; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |