Search for Variation information by Variation ID:
Detailed information for vg0816115289:
| Variant ID: vg0816115289 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 16115289 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.04, others allele: 0.00, population size: 68. )
Flanking Sequence (100 bp) in Reference Genome:
AAGTGCTCTTGAGGAAGCTATTAATATTTTGAGAGCAAAAAATATGAAGTGTGAGAAGATGTATAGAAAACAGGAGTTTATCATTGAATCTCTTAATTCT[A/G]
AAATTGCTAGATTAAAATCTCTTATTCCCAATGATGATGATTGCAAAAATTGTAAGGTTTTAATGAATGAGATTTCAAAAATTAGAGATGTCAATGTTGC
Reverse complement sequence
GCAACATTGACATCTCTAATTTTTGAAATCTCATTCATTAAAACCTTACAATTTTTGCAATCATCATCATTGGGAATAAGAGATTTTAATCTAGCAATTT[T/C]
AGAATTAAGAGATTCAATGATAAACTCCTGTTTTCTATACATCTTCTCACACTTCATATTTTTTGCTCTCAAAATATTAATAGCTTCCTCAAGAGCACTT
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 | 20.80% | 10.00% | 3.98% | 65.28% | NA |
| All Indica | 2759 | 6.50% | 7.70% | 3.91% | 81.91% | NA |
| All Japonica | 1512 | 43.90% | 13.20% | 0.99% | 41.93% | NA |
| Aus | 269 | 5.20% | 18.20% | 23.05% | 53.53% | NA |
| Indica I | 595 | 9.70% | 6.90% | 1.51% | 81.85% | NA |
| Indica II | 465 | 6.70% | 3.20% | 2.58% | 87.53% | NA |
| Indica III | 913 | 4.90% | 9.90% | 6.13% | 79.08% | NA |
| Indica Intermediate | 786 | 5.60% | 8.50% | 3.94% | 81.93% | NA |
| Temperate Japonica | 767 | 74.30% | 21.90% | 0.13% | 3.65% | NA |
| Tropical Japonica | 504 | 3.20% | 5.00% | 2.38% | 89.48% | NA |
| Japonica Intermediate | 241 | 32.40% | 2.50% | 0.83% | 64.32% | NA |
| VI/Aromatic | 96 | 92.70% | 1.00% | 1.04% | 5.21% | NA |
| Intermediate | 90 | 40.00% | 11.10% | 2.22% | 46.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0816115289 | A -> G | LOC_Os08g26450.1 | missense_variant ; p.Lys405Glu; MODERATE | nonsynonymous_codon ; K405E | Average:7.666; most accessible tissue: Callus, score: 23.031 | benign  |
-1.285 |
TOLERATED | 1.00 |
| vg0816115289 | A -> DEL | LOC_Os08g26450.1 | N | frameshift_variant | Average:7.666; most accessible tissue: Callus, score: 23.031 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0816115289 | 7.45E-06 | 5.66E-06 | mr1440_2 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0816115289 | 1.44E-07 | 1.44E-07 | mr1440_2 | Jap_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |