Search for Variation information by Variation ID:
Detailed information for vg0322194053:
| Variant ID: vg0322194053 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 22194053 |
| Reference Allele: G | Alternative Allele: A,T |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CCATCCTCGGTTCCGGGAGGGAACTCTTCCAGCGCTGCCCACGGGGAGAAGTCAGGGTCCCTGGCCTGGTAGCTTGCCAGTACGAGCTCCACCGCCCCCC[G/A,T]
GGCGAGGTCCCTCGAGGATGACTTGATCGTCTCCTCGAGCTCCTCGGGGAGCCGCTGGAGGGCCCCGGCCATCTCTGAGAGGCACTGGGCGAGGCCCCCC
Reverse complement sequence
GGGGGGCCTCGCCCAGTGCCTCTCAGAGATGGCCGGGGCCCTCCAGCGGCTCCCCGAGGAGCTCGAGGAGACGATCAAGTCATCCTCGAGGGACCTCGCC[C/T,A]
GGGGGGCGGTGGAGCTCGTACTGGCAAGCTACCAGGCCAGGGACCCTGACTTCTCCCCGTGGGCAGCGCTGGAAGAGTTCCCTCCCGGAACCGAGGATGG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 39.10% | 0.20% | 1.44% | 59.08% | T: 0.19% |
| All Indica | 2759 | 43.60% | 0.40% | 1.09% | 54.98% | NA |
| All Japonica | 1512 | 30.70% | 0.00% | 2.31% | 66.47% | T: 0.53% |
| Aus | 269 | 46.10% | 0.00% | 0.74% | 53.16% | NA |
| Indica I | 595 | 22.00% | 0.00% | 0.84% | 77.14% | NA |
| Indica II | 465 | 28.60% | 1.30% | 1.72% | 68.39% | NA |
| Indica III | 913 | 70.60% | 0.10% | 0.77% | 28.48% | NA |
| Indica Intermediate | 786 | 37.30% | 0.40% | 1.27% | 61.07% | NA |
| Temperate Japonica | 767 | 15.30% | 0.00% | 1.17% | 83.57% | NA |
| Tropical Japonica | 504 | 53.40% | 0.00% | 4.37% | 40.67% | T: 1.59% |
| Japonica Intermediate | 241 | 32.40% | 0.00% | 1.66% | 65.98% | NA |
| VI/Aromatic | 96 | 27.10% | 0.00% | 1.04% | 71.88% | NA |
| Intermediate | 90 | 34.40% | 0.00% | 0.00% | 64.44% | T: 1.11% |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0322194053 | G -> T | LOC_Os03g39930.1 | synonymous_variant ; p.Arg357Arg; LOW | synonymous_codon | Average:6.522; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |
| vg0322194053 | G -> A | LOC_Os03g39930.1 | missense_variant ; p.Arg357Trp; MODERATE | nonsynonymous_codon ; R357W | Average:6.522; most accessible tissue: Zhenshan97 flower, score: 9.663 | probably damaging  |
3.14 |
DELETERIOUS | 0.01 |
| vg0322194053 | G -> DEL | LOC_Os03g39930.1 | N | frameshift_variant | Average:6.522; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |