Search for Variation information by Variation ID:
Detailed information for vg0814381647:
| Variant ID: vg0814381647 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 14381647 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CGGGGAGGCTCGCGACGAGGCCGCGGGCACATCGCCTGGGCCCACCTCCCCGGGCGACGCCCAGGATCAAACGGGTTCGGGGGACATCCCCGAGCCCAGC[A/G]
CGTCCTCCGGGGGGCCGAGCCGCATCGCCTTCTCTCCAAGGCGGCTCTTCTCCTCATCTTCCGTCGCCCCGCTGAGCGCCGAGCCCATTCTGCAGGCCTT
Reverse complement sequence
AAGGCCTGCAGAATGGGCTCGGCGCTCAGCGGGGCGACGGAAGATGAGGAGAAGAGCCGCCTTGGAGAGAAGGCGATGCGGCTCGGCCCCCCGGAGGACG[T/C]
GCTGGGCTCGGGGATGTCCCCCGAACCCGTTTGATCCTGGGCGTCGCCCGGGGAGGTGGGCCCAGGCGATGTGCCCGCGGCCTCGTCGCGAGCCTCCCCG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 0.80% | 0.70% | 1.71% | 96.80% | NA |
| All Indica | 2759 | 0.10% | 1.10% | 1.56% | 97.25% | NA |
| All Japonica | 1512 | 2.20% | 0.00% | 2.45% | 95.30% | NA |
| Aus | 269 | 0.40% | 0.00% | 0.37% | 99.26% | NA |
| Indica I | 595 | 0.20% | 0.20% | 0.84% | 98.82% | NA |
| Indica II | 465 | 0.00% | 0.20% | 0.43% | 99.35% | NA |
| Indica III | 913 | 0.10% | 2.20% | 2.63% | 95.07% | NA |
| Indica Intermediate | 786 | 0.00% | 1.10% | 1.53% | 97.33% | NA |
| Temperate Japonica | 767 | 3.50% | 0.00% | 3.52% | 92.96% | NA |
| Tropical Japonica | 504 | 1.00% | 0.00% | 0.99% | 98.02% | NA |
| Japonica Intermediate | 241 | 0.80% | 0.00% | 2.07% | 97.10% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 2.20% | 0.00% | 0.00% | 97.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0814381647 | A -> G | LOC_Os08g23760.1 | missense_variant ; p.Thr558Ala; MODERATE | nonsynonymous_codon ; T558A | Average:25.733; most accessible tissue: Minghui63 panicle, score: 50.413 | benign  |
-0.128 |
TOLERATED | 0.32 |
| vg0814381647 | A -> DEL | LOC_Os08g23760.1 | N | frameshift_variant | Average:25.733; most accessible tissue: Minghui63 panicle, score: 50.413 | N | N | N | N |