Search for Variation information by Variation ID:
Detailed information for vg0322194093:
| Variant ID: vg0322194093 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 22194093 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ACGGGGAGAAGTCAGGGTCCCTGGCCTGGTAGCTTGCCAGTACGAGCTCCACCGCCCCCCGGGCGAGGTCCCTCGAGGATGACTTGATCGTCTCCTCGAG[C/G]
TCCTCGGGGAGCCGCTGGAGGGCCCCGGCCATCTCTGAGAGGCACTGGGCGAGGCCCCCCTGGTTGGCGGCGTACTTCGCGTGCCGCCCGCCCCAGAGAC
Reverse complement sequence
GTCTCTGGGGCGGGCGGCACGCGAAGTACGCCGCCAACCAGGGGGGCCTCGCCCAGTGCCTCTCAGAGATGGCCGGGGCCCTCCAGCGGCTCCCCGAGGA[G/C]
CTCGAGGAGACGATCAAGTCATCCTCGAGGGACCTCGCCCGGGGGGCGGTGGAGCTCGTACTGGCAAGCTACCAGGCCAGGGACCCTGACTTCTCCCCGT
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 39.70% | 0.00% | 0.78% | 59.54% | NA |
| All Indica | 2759 | 43.90% | 0.00% | 0.54% | 55.56% | NA |
| All Japonica | 1512 | 32.50% | 0.00% | 0.93% | 66.60% | NA |
| Aus | 269 | 43.90% | 0.00% | 2.23% | 53.90% | NA |
| Indica I | 595 | 21.80% | 0.20% | 0.67% | 77.31% | NA |
| Indica II | 465 | 29.90% | 0.00% | 0.86% | 69.25% | NA |
| Indica III | 913 | 70.80% | 0.00% | 0.22% | 29.03% | NA |
| Indica Intermediate | 786 | 37.50% | 0.00% | 0.64% | 61.83% | NA |
| Temperate Japonica | 767 | 15.50% | 0.00% | 0.78% | 83.70% | NA |
| Tropical Japonica | 504 | 58.10% | 0.00% | 0.99% | 40.87% | NA |
| Japonica Intermediate | 241 | 32.80% | 0.00% | 1.24% | 65.98% | NA |
| VI/Aromatic | 96 | 25.00% | 0.00% | 2.08% | 72.92% | NA |
| Intermediate | 90 | 34.40% | 0.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0322194093 | C -> DEL | LOC_Os03g39930.1 | N | frameshift_variant | Average:6.269; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |
| vg0322194093 | C -> G | LOC_Os03g39930.1 | missense_variant ; p.Glu343Asp; MODERATE | nonsynonymous_codon ; E343D | Average:6.269; most accessible tissue: Zhenshan97 flower, score: 9.663 | benign  |
1.376 |
DELETERIOUS | 0.00 |