Search for Variation information by Variation ID:
Detailed information for vg0327370661:
| Variant ID: vg0327370661 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 27370661 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CATCTTGAACACCGGCGAGCGCGCGGCGAGCACGGCGCGGTGTGCATGAAACGTCTCGCTGCCGACGGAGAACAACACGTCCGAGCCGTCGGCACGGTCC[G/A]
CGATGTCGTCGAGCTGGCCGTTGAGGTTCGACCGCGGGATGGGTATAGTGCCGTCGTCATCACCGGCATATAATATATATTTAAGAAAAGTAAAAATAGG
Reverse complement sequence
CCTATTTTTACTTTTCTTAAATATATATTATATGCCGGTGATGACGACGGCACTATACCCATCCCGCGGTCGAACCTCAACGGCCAGCTCGACGACATCG[C/T]
GGACCGTGCCGACGGCTCGGACGTGTTGTTCTCCGTCGGCAGCGAGACGTTTCATGCACACCGCGCCGTGCTCGCCGCGCGCTCGCCGGTGTTCAAGATG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 65.80% | 34.00% | 0.15% | 0.06% | NA |
| All Indica | 2759 | 98.30% | 1.40% | 0.14% | 0.07% | NA |
| All Japonica | 1512 | 1.30% | 98.50% | 0.13% | 0.07% | NA |
| Aus | 269 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.00% | 0.80% | 0.17% | 0.00% | NA |
| Indica II | 465 | 98.50% | 1.10% | 0.00% | 0.43% | NA |
| Indica III | 913 | 98.50% | 1.30% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 97.60% | 2.30% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 0.70% | 99.10% | 0.13% | 0.13% | NA |
| Tropical Japonica | 504 | 1.80% | 98.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 2.50% | 97.50% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 57.30% | 42.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 63.30% | 35.60% | 1.11% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0327370661 | G -> A | LOC_Os03g48120.1 | missense_variant ; p.Ala44Val; MODERATE | nonsynonymous_codon ; A44V | Average:77.914; most accessible tissue: Zhenshan97 panicle, score: 88.35 | benign  |
-0.134 |
TOLERATED | 0.36 |
| vg0327370661 | G -> DEL | LOC_Os03g48120.1 | N | frameshift_variant | Average:77.914; most accessible tissue: Zhenshan97 panicle, score: 88.35 | N | N | N | N |