Search for Variation information by Variation ID:
Detailed information for vg0910657428:
| Variant ID: vg0910657428 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 10657428 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GTCGCCCAGGGCAACCTCCTTGACTGGGACCTCGTCGCACGTGACCATCCGCTGCCTTGGGGCGGCCGGGACGGAGGTGCTGAGCCTCTCGTCGCCACCC[G/T]
CGGGCTTGGACGCCGCGGCGAGATGGTCCGCGCGCTGCTCCATACAAGCAAGCGCGACTTTGAGGTCGCCATGGTCGGTGATGGGGCCACCGGGTCCCGG
Reverse complement sequence
CCGGGACCCGGTGGCCCCATCACCGACCATGGCGACCTCAAAGTCGCGCTTGCTTGTATGGAGCAGCGCGCGGACCATCTCGCCGCGGCGTCCAAGCCCG[C/A]
GGGTGGCGACGAGAGGCTCAGCACCTCCGTCCCGGCCGCCCCAAGGCAGCGGATGGTCACGTGCGACGAGGTCCCAGTCAAGGAGGTTGCCCTGGGCGAC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 27.30% | 0.60% | 39.55% | 32.54% | NA |
| All Indica | 2759 | 15.00% | 1.00% | 51.03% | 32.95% | NA |
| All Japonica | 1512 | 53.80% | 0.00% | 15.48% | 30.75% | NA |
| Aus | 269 | 4.80% | 0.00% | 64.31% | 30.86% | NA |
| Indica I | 595 | 33.90% | 0.00% | 31.43% | 34.62% | NA |
| Indica II | 465 | 13.80% | 0.60% | 36.56% | 49.03% | NA |
| Indica III | 913 | 1.80% | 1.80% | 77.33% | 19.17% | NA |
| Indica Intermediate | 786 | 16.90% | 1.00% | 43.89% | 38.17% | NA |
| Temperate Japonica | 767 | 70.30% | 0.00% | 10.95% | 18.77% | NA |
| Tropical Japonica | 504 | 35.30% | 0.00% | 22.02% | 42.66% | NA |
| Japonica Intermediate | 241 | 39.80% | 0.00% | 16.18% | 43.98% | NA |
| VI/Aromatic | 96 | 29.20% | 0.00% | 22.92% | 47.92% | NA |
| Intermediate | 90 | 25.60% | 0.00% | 35.56% | 38.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0910657428 | G -> DEL | LOC_Os09g17420.1 | N | frameshift_variant | Average:8.619; most accessible tissue: Callus, score: 24.426 | N | N | N | N |
| vg0910657428 | G -> T | LOC_Os09g17420.1 | missense_variant ; p.Ala148Glu; MODERATE | nonsynonymous_codon ; A148E | Average:8.619; most accessible tissue: Callus, score: 24.426 | benign  |
0.645 |
TOLERATED | 1.00 |