Search for Variation information by Variation ID:
Detailed information for vg0908137347:
| Variant ID: vg0908137347 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 8137347 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CCACCGCCCCCTCCACGCCAAAGTCCTAGGCGGGAGGAGGCGCTCGAGAGGGTCGAAGGATCCGCGACTTCGACATCCACGGGTGATGAGGAAGGGCGGC[G/A]
AGATGGGGAGCGTCGCCTCCTCGTCTACGGCGACGGCAGCACGCCCCAGGGCGCGCTCCAAGCTGCGGGCGCGCTCCTACGTCACCCGCCCATTGTCCCT
Reverse complement sequence
AGGGACAATGGGCGGGTGACGTAGGAGCGCGCCCGCAGCTTGGAGCGCGCCCTGGGGCGTGCTGCCGTCGCCGTAGACGAGGAGGCGACGCTCCCCATCT[C/T]
GCCGCCCTTCCTCATCACCCGTGGATGTCGAAGTCGCGGATCCTTCGACCCTCTCGAGCGCCTCCTCCCGCCTAGGACTTTGGCGTGGAGGGGGCGGTGG
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 | 41.90% | 0.20% | 7.05% | 50.83% | NA |
| All Indica | 2759 | 34.30% | 0.00% | 6.13% | 59.59% | NA |
| All Japonica | 1512 | 57.70% | 0.60% | 6.61% | 35.05% | NA |
| Aus | 269 | 8.60% | 0.00% | 20.07% | 71.38% | NA |
| Indica I | 595 | 11.90% | 0.00% | 6.22% | 81.85% | NA |
| Indica II | 465 | 67.10% | 0.00% | 2.80% | 30.11% | NA |
| Indica III | 913 | 31.20% | 0.00% | 7.78% | 61.01% | NA |
| Indica Intermediate | 786 | 35.40% | 0.00% | 6.11% | 58.52% | NA |
| Temperate Japonica | 767 | 84.20% | 1.20% | 2.74% | 11.86% | NA |
| Tropical Japonica | 504 | 28.40% | 0.00% | 12.90% | 58.73% | NA |
| Japonica Intermediate | 241 | 34.90% | 0.00% | 5.81% | 59.34% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 1.04% | 12.50% | NA |
| Intermediate | 90 | 63.30% | 0.00% | 10.00% | 26.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0908137347 | G -> DEL | LOC_Os09g13850.1 | N | frameshift_variant | Average:25.698; most accessible tissue: Minghui63 flag leaf, score: 54.348 | N | N | N | N |
| vg0908137347 | G -> A | LOC_Os09g13850.1 | missense_variant ; p.Arg63Gln; MODERATE | nonsynonymous_codon ; R63Q | Average:25.698; most accessible tissue: Minghui63 flag leaf, score: 54.348 | possibly damaging  |
1.549 |
DELETERIOUS | 0.03 |