Search for Variation information by Variation ID:
Detailed information for vg0814381584:
| Variant ID: vg0814381584 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 14381584 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 78. )
Flanking Sequence (100 bp) in Reference Genome:
AACAGCTGCTGCTGGCGCGTCAACTGGGCCCACTCCTTCGGGCAACCCTCAGGCGACAGCCTCCGGGGAGGCTCGCGACGAGGCCGCGGGCACATCGCCT[G/A]
GGCCCACCTCCCCGGGCGACGCCCAGGATCAAACGGGTTCGGGGGACATCCCCGAGCCCAGCACGTCCTCCGGGGGGCCGAGCCGCATCGCCTTCTCTCC
Reverse complement sequence
GGAGAGAAGGCGATGCGGCTCGGCCCCCCGGAGGACGTGCTGGGCTCGGGGATGTCCCCCGAACCCGTTTGATCCTGGGCGTCGCCCGGGGAGGTGGGCC[C/T]
AGGCGATGTGCCCGCGGCCTCGTCGCGAGCCTCCCCGGAGGCTGTCGCCTGAGGGTTGCCCGAAGGAGTGGGCCCAGTTGACGCGCCAGCAGCAGCTGTT
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 | 1.70% | 0.50% | 1.88% | 95.87% | NA |
| All Indica | 2759 | 0.10% | 0.90% | 1.81% | 97.21% | NA |
| All Japonica | 1512 | 5.00% | 0.00% | 2.51% | 92.46% | NA |
| Aus | 269 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Indica I | 595 | 0.30% | 0.00% | 0.84% | 98.82% | NA |
| Indica II | 465 | 0.00% | 0.40% | 0.86% | 98.71% | NA |
| Indica III | 913 | 0.10% | 1.50% | 2.30% | 96.06% | NA |
| Indica Intermediate | 786 | 0.00% | 1.00% | 2.54% | 96.44% | NA |
| Temperate Japonica | 767 | 7.60% | 0.00% | 3.00% | 89.44% | NA |
| Tropical Japonica | 504 | 2.60% | 0.00% | 1.59% | 95.83% | NA |
| Japonica Intermediate | 241 | 2.10% | 0.00% | 2.90% | 95.02% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 3.30% | 0.00% | 1.11% | 95.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0814381584 | G -> A | LOC_Os08g23760.1 | missense_variant ; p.Gly537Arg; MODERATE | nonsynonymous_codon ; G537R | Average:25.733; most accessible tissue: Minghui63 panicle, score: 50.413 | probably damaging  |
2.607 |
DELETERIOUS | 0.01 |
| vg0814381584 | G -> DEL | LOC_Os08g23760.1 | N | frameshift_variant | Average:25.733; most accessible tissue: Minghui63 panicle, score: 50.413 | N | N | N | N |