Search for Variation information by Variation ID:
Detailed information for vg1125483609:
| Variant ID: vg1125483609 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 25483609 |
| Reference Allele: G | Alternative Allele: A,T |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CCGACTGAAGGAATCCGACTGCTTGAAGACTTCGTTCATCACGCCCTTTGGAGCATACTGCTATGTCACCATGCCATTCGGACTGAAAAATGCAGGAGCA[G/A,T]
CTTATCAACGTATGATCCAGAGATGCTTCTCAACGCAAATCGGTCGCAACGTTGAAGCCTATGTGGATGATGTAGTCGTCAAGACCAAGCAAAAGGATGA
Reverse complement sequence
TCATCCTTTTGCTTGGTCTTGACGACTACATCATCCACATAGGCTTCAACGTTGCGACCGATTTGCGTTGAGAAGCATCTCTGGATCATACGTTGATAAG[C/T,A]
TGCTCCTGCATTTTTCAGTCCGAATGGCATGGTGACATAGCAGTATGCTCCAAAGGGCGTGATGAACGAAGTCTTCAAGCAGTCGGATTCCTTCAGTCGG
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 | 43.20% | 11.00% | 41.07% | 4.74% | T: 0.02% |
| All Indica | 2759 | 43.40% | 0.90% | 49.91% | 5.76% | T: 0.04% |
| All Japonica | 1512 | 37.20% | 29.30% | 29.63% | 3.84% | NA |
| Aus | 269 | 64.30% | 13.00% | 22.30% | 0.37% | NA |
| Indica I | 595 | 81.20% | 0.30% | 14.96% | 3.53% | NA |
| Indica II | 465 | 68.60% | 0.40% | 21.72% | 9.03% | T: 0.22% |
| Indica III | 913 | 8.50% | 0.80% | 86.31% | 4.38% | NA |
| Indica Intermediate | 786 | 40.30% | 1.80% | 50.76% | 7.12% | NA |
| Temperate Japonica | 767 | 53.80% | 34.60% | 10.17% | 1.43% | NA |
| Tropical Japonica | 504 | 14.30% | 16.30% | 61.51% | 7.94% | NA |
| Japonica Intermediate | 241 | 32.40% | 39.80% | 24.90% | 2.90% | NA |
| VI/Aromatic | 96 | 78.10% | 1.00% | 20.83% | 0.00% | NA |
| Intermediate | 90 | 36.70% | 16.70% | 40.00% | 6.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1125483609 | G -> T | LOC_Os11g42320.1 | missense_variant ; p.Ala1117Ser; MODERATE | nonsynonymous_codon ; A1117S | Average:28.357; most accessible tissue: Zhenshan97 panicle, score: 52.263 | benign  |
-0.802 |
DELETERIOUS | 0.00 |
| vg1125483609 | G -> A | LOC_Os11g42320.1 | missense_variant ; p.Ala1117Thr; MODERATE | nonsynonymous_codon ; A1117T | Average:28.357; most accessible tissue: Zhenshan97 panicle, score: 52.263 | benign |
-1.49 |
TOLERATED | 1.00 |
| vg1125483609 | G -> DEL | LOC_Os11g42320.1 | N | frameshift_variant | Average:28.357; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1125483609 | 1.90E-06 | NA | mr1530_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 |
| vg1125483609 | 1.39E-06 | NA | mr1530_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 |