Search for Variation information by Variation ID:
Detailed information for vg0908137400:
| Variant ID: vg0908137400 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 8137400 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CGAAGGATCCGCGACTTCGACATCCACGGGTGATGAGGAAGGGCGGCGAGATGGGGAGCGTCGCCTCCTCGTCTACGGCGACGGCAGCACGCCCCAGGGC[G/A]
CGCTCCAAGCTGCGGGCGCGCTCCTACGTCACCCGCCCATTGTCCCTGACCCAGAGTCTCCAGCCCAACGTTGGCTGGACGACGTGGCCAACTTGGTCAT
Reverse complement sequence
ATGACCAAGTTGGCCACGTCGTCCAGCCAACGTTGGGCTGGAGACTCTGGGTCAGGGACAATGGGCGGGTGACGTAGGAGCGCGCCCGCAGCTTGGAGCG[C/T]
GCCCTGGGGCGTGCTGCCGTCGCCGTAGACGAGGAGGCGACGCTCCCCATCTCGCCGCCCTTCCTCATCACCCGTGGATGTCGAAGTCGCGGATCCTTCG
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 | 41.00% | 0.20% | 5.95% | 52.90% | NA |
| All Indica | 2759 | 34.30% | 0.00% | 6.02% | 59.70% | NA |
| All Japonica | 1512 | 54.70% | 0.60% | 3.11% | 41.60% | NA |
| Aus | 269 | 8.90% | 0.00% | 23.05% | 68.03% | NA |
| Indica I | 595 | 12.30% | 0.00% | 5.71% | 82.02% | NA |
| Indica II | 465 | 67.10% | 0.00% | 2.80% | 30.11% | NA |
| Indica III | 913 | 30.90% | 0.00% | 8.21% | 60.90% | NA |
| Indica Intermediate | 786 | 35.50% | 0.00% | 5.60% | 58.91% | NA |
| Temperate Japonica | 767 | 82.30% | 1.20% | 3.91% | 12.65% | NA |
| Tropical Japonica | 504 | 23.80% | 0.00% | 2.98% | 73.21% | NA |
| Japonica Intermediate | 241 | 31.50% | 0.00% | 0.83% | 67.63% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 0.00% | 13.54% | NA |
| Intermediate | 90 | 62.20% | 0.00% | 6.67% | 31.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0908137400 | G -> DEL | LOC_Os09g13850.1 | N | frameshift_variant | Average:28.376; most accessible tissue: Minghui63 flag leaf, score: 61.847 | N | N | N | N |
| vg0908137400 | G -> A | LOC_Os09g13850.1 | missense_variant ; p.Ala81Thr; MODERATE | nonsynonymous_codon ; A81T | Average:28.376; most accessible tissue: Minghui63 flag leaf, score: 61.847 | benign  |
0.574 |
DELETERIOUS | 0.04 |