Search for Variation information by Variation ID:
Detailed information for vg0609244062:
| Variant ID: vg0609244062 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 9244062 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GACTTGTCGACCCTCTCAAGCGCCTCCCCCTGCTTAGGGCTTTGGCGCGGAGGAGGTGGAGGAGTACGAGCTCGACGGCGTGGATTCGGCTCCCCGTCGT[C/T]
GCCGCTCACACTCGGCGAGAGGTCGTGCGTTTTTCCTTGCTCGGCCATTAGGCTGAACAAGAAAAACTTGGGGCACACGGAAGAGTCTGAGAGCTCTGAA
Reverse complement sequence
TTCAGAGCTCTCAGACTCTTCCGTGTGCCCCAAGTTTTTCTTGTTCAGCCTAATGGCCGAGCAAGGAAAAACGCACGACCTCTCGCCGAGTGTGAGCGGC[G/A]
ACGACGGGGAGCCGAATCCACGCCGTCGAGCTCGTACTCCTCCACCTCCTCCGCGCCAAAGCCCTAAGCAGGGGGAGGCGCTTGAGAGGGTCGACAAGTC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 12.50% | 0.30% | 2.77% | 84.43% | NA |
| All Indica | 2759 | 1.20% | 0.00% | 1.34% | 97.46% | NA |
| All Japonica | 1512 | 36.30% | 0.80% | 4.83% | 58.07% | NA |
| Aus | 269 | 0.40% | 0.00% | 3.72% | 95.91% | NA |
| Indica I | 595 | 2.20% | 0.00% | 1.18% | 96.64% | NA |
| Indica II | 465 | 0.60% | 0.00% | 1.08% | 98.28% | NA |
| Indica III | 913 | 0.50% | 0.00% | 0.88% | 98.58% | NA |
| Indica Intermediate | 786 | 1.50% | 0.00% | 2.16% | 96.31% | NA |
| Temperate Japonica | 767 | 67.50% | 0.70% | 5.74% | 26.08% | NA |
| Tropical Japonica | 504 | 1.40% | 0.80% | 2.38% | 95.44% | NA |
| Japonica Intermediate | 241 | 10.00% | 1.20% | 7.05% | 81.74% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 5.21% | 94.79% | NA |
| Intermediate | 90 | 11.10% | 0.00% | 6.67% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0609244062 | C -> T | LOC_Os06g16230.1 | missense_variant ; p.Asp17Asn; MODERATE | nonsynonymous_codon ; D17N | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | possibly damaging  |
1.641 |
DELETERIOUS | 0.00 |
| vg0609244062 | C -> DEL | LOC_Os06g16230.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |