Search for Variation information by Variation ID:
Detailed information for vg0814381605:
| Variant ID: vg0814381605 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 14381605 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 76. )
Flanking Sequence (100 bp) in Reference Genome:
AACTGGGCCCACTCCTTCGGGCAACCCTCAGGCGACAGCCTCCGGGGAGGCTCGCGACGAGGCCGCGGGCACATCGCCTGGGCCCACCTCCCCGGGCGAC[G/A]
CCCAGGATCAAACGGGTTCGGGGGACATCCCCGAGCCCAGCACGTCCTCCGGGGGGCCGAGCCGCATCGCCTTCTCTCCAAGGCGGCTCTTCTCCTCATC
Reverse complement sequence
GATGAGGAGAAGAGCCGCCTTGGAGAGAAGGCGATGCGGCTCGGCCCCCCGGAGGACGTGCTGGGCTCGGGGATGTCCCCCGAACCCGTTTGATCCTGGG[C/T]
GTCGCCCGGGGAGGTGGGCCCAGGCGATGTGCCCGCGGCCTCGTCGCGAGCCTCCCCGGAGGCTGTCGCCTGAGGGTTGCCCGAAGGAGTGGGCCCAGTT
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 | 1.40% | 0.50% | 2.37% | 95.70% | NA |
| All Indica | 2759 | 0.30% | 0.90% | 2.86% | 95.94% | NA |
| All Japonica | 1512 | 3.60% | 0.00% | 2.12% | 94.25% | NA |
| Aus | 269 | 0.40% | 0.00% | 0.37% | 99.26% | NA |
| Indica I | 595 | 0.50% | 0.00% | 1.34% | 98.15% | NA |
| Indica II | 465 | 0.20% | 0.40% | 1.51% | 97.85% | NA |
| Indica III | 913 | 0.30% | 1.60% | 4.38% | 93.65% | NA |
| Indica Intermediate | 786 | 0.10% | 1.00% | 3.05% | 95.80% | NA |
| Temperate Japonica | 767 | 5.30% | 0.00% | 3.39% | 91.26% | NA |
| Tropical Japonica | 504 | 1.80% | 0.00% | 0.60% | 97.62% | NA |
| Japonica Intermediate | 241 | 2.10% | 0.00% | 1.24% | 96.68% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0814381605 | G -> A | LOC_Os08g23760.1 | missense_variant ; p.Ala544Thr; MODERATE | nonsynonymous_codon ; A544T | Average:25.733; most accessible tissue: Minghui63 panicle, score: 50.413 | benign  |
1.244 |
TOLERATED | 0.05 |
| vg0814381605 | G -> DEL | LOC_Os08g23760.1 | N | frameshift_variant | Average:25.733; most accessible tissue: Minghui63 panicle, score: 50.413 | N | N | N | N |