Search for Variation information by Variation ID:
Detailed information for vg0300825644:
| Variant ID: vg0300825644 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 825644 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.86, G: 0.14, others allele: 0.00, population size: 92. )
Flanking Sequence (100 bp) in Reference Genome:
CTGGGAGAGAAGGCGTTACCCTTATTTAAGCTTCTCAAACGCTCCGGACCGTTTACCTGGACGGAGGAAGCCGAAAATGCCCTCACTCAGTTGAAGGCAT[G/A]
TCTAAGCTCTCCCCCAGTTCTGGTCGCCCCGGAGCCAGACGAGCCCTTGTTACTCTACTTAGCGGCGACCCCGCAAGTAGTTAGTGCGGCATTGGTTGTG
Reverse complement sequence
CACAACCAATGCCGCACTAACTACTTGCGGGGTCGCCGCTAAGTAGAGTAACAAGGGCTCGTCTGGCTCCGGGGCGACCAGAACTGGGGGAGAGCTTAGA[C/T]
ATGCCTTCAACTGAGTGAGGGCATTTTCGGCTTCCTCCGTCCAGGTAAACGGTCCGGAGCGTTTGAGAAGCTTAAATAAGGGTAACGCCTTCTCTCCCAG
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 | 13.10% | 3.20% | 0.95% | 82.84% | NA |
| All Indica | 2759 | 1.10% | 4.70% | 1.38% | 92.82% | NA |
| All Japonica | 1512 | 37.30% | 0.20% | 0.33% | 62.17% | NA |
| Aus | 269 | 1.50% | 1.50% | 0.00% | 97.03% | NA |
| Indica I | 595 | 0.50% | 4.20% | 2.02% | 93.28% | NA |
| Indica II | 465 | 4.50% | 4.90% | 1.29% | 89.25% | NA |
| Indica III | 913 | 0.30% | 5.00% | 0.77% | 93.87% | NA |
| Indica Intermediate | 786 | 0.50% | 4.50% | 1.65% | 93.38% | NA |
| Temperate Japonica | 767 | 61.10% | 0.00% | 0.13% | 38.72% | NA |
| Tropical Japonica | 504 | 6.20% | 0.20% | 0.40% | 93.25% | NA |
| Japonica Intermediate | 241 | 26.60% | 0.80% | 0.83% | 71.78% | NA |
| VI/Aromatic | 96 | 4.20% | 12.50% | 1.04% | 82.29% | NA |
| Intermediate | 90 | 15.60% | 1.10% | 1.11% | 82.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0300825644 | G -> A | LOC_Os03g02350.1 | missense_variant ; p.Cys1108Tyr; MODERATE | nonsynonymous_codon ; C1108Y | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
-1.152 |
TOLERATED | 1.00 |
| vg0300825644 | G -> DEL | LOC_Os03g02350.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |