Search for Variation information by Variation ID:
Detailed information for vg0300825584:
| Variant ID: vg0300825584 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 825584 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTTAGGGATGTGCAATGCGTCACCGGTTGCATGGCCGCCCTAAGTCGGTTCATATCGAGGCTGGGAGAGAAGGCGTTACCCTTATTTAAGCTTCTCAAAC[G/A]
CTCCGGACCGTTTACCTGGACGGAGGAAGCCGAAAATGCCCTCACTCAGTTGAAGGCATGTCTAAGCTCTCCCCCAGTTCTGGTCGCCCCGGAGCCAGAC
Reverse complement sequence
GTCTGGCTCCGGGGCGACCAGAACTGGGGGAGAGCTTAGACATGCCTTCAACTGAGTGAGGGCATTTTCGGCTTCCTCCGTCCAGGTAAACGGTCCGGAG[C/T]
GTTTGAGAAGCTTAAATAAGGGTAACGCCTTCTCTCCCAGCCTCGATATGAACCGACTTAGGGCGGCCATGCAACCGGTGACGCATTGCACATCCCTAAG
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 | 17.70% | 0.90% | 2.58% | 78.84% | NA |
| All Indica | 2759 | 7.80% | 1.50% | 4.06% | 86.66% | NA |
| All Japonica | 1512 | 37.60% | 0.00% | 0.53% | 61.84% | NA |
| Aus | 269 | 5.20% | 0.00% | 0.00% | 94.80% | NA |
| Indica I | 595 | 4.20% | 3.70% | 3.36% | 88.74% | NA |
| Indica II | 465 | 9.00% | 1.70% | 6.67% | 82.58% | NA |
| Indica III | 913 | 9.60% | 0.10% | 2.85% | 87.40% | NA |
| Indica Intermediate | 786 | 7.60% | 1.30% | 4.45% | 86.64% | NA |
| Temperate Japonica | 767 | 60.80% | 0.00% | 0.78% | 38.46% | NA |
| Tropical Japonica | 504 | 6.90% | 0.00% | 0.20% | 92.86% | NA |
| Japonica Intermediate | 241 | 28.20% | 0.00% | 0.41% | 71.37% | NA |
| VI/Aromatic | 96 | 21.90% | 0.00% | 1.04% | 77.08% | NA |
| Intermediate | 90 | 20.00% | 0.00% | 1.11% | 78.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0300825584 | G -> A | LOC_Os03g02350.1 | missense_variant ; p.Arg1088His; MODERATE | nonsynonymous_codon ; R1088H | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.909 |
DELETERIOUS | 0.01 |
| vg0300825584 | G -> DEL | LOC_Os03g02350.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |