Search for Variation information by Variation ID:
Detailed information for vg1110437041:
| Variant ID: vg1110437041 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 10437041 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AAGAGTGTACCTCCCACCAGCTTGCCACACATTGTCGAAGGATGAGAAGATCGCAATGCTATCATGTCTGGCAGATATTAAAGTTCCTTCGGGCTATTGT[G/A]
CGAGAATAAGTAAGCACGTTAAATTAGAGGATCCAAAGCTGGTTGGAATGAAGTCTCACGATTGCCACGTGCTAATCACACAGATATTGCCAGTTGCTAT
Reverse complement sequence
ATAGCAACTGGCAATATCTGTGTGATTAGCACGTGGCAATCGTGAGACTTCATTCCAACCAGCTTTGGATCCTCTAATTTAACGTGCTTACTTATTCTCG[C/T]
ACAATAGCCCGAAGGAACTTTAATATCTGCCAGACATGATAGCATTGCGATCTTCTCATCCTTCGACAATGTGTGGCAAGCTGGTGGGAGGTACACTCTT
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 | 93.70% | 4.80% | 0.28% | 1.23% | NA |
| All Indica | 2759 | 93.00% | 6.40% | 0.22% | 0.36% | NA |
| All Japonica | 1512 | 99.60% | 0.00% | 0.13% | 0.26% | NA |
| Aus | 269 | 84.00% | 16.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 80.30% | 19.50% | 0.17% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 96.10% | 3.10% | 0.33% | 0.55% | NA |
| Indica Intermediate | 786 | 95.00% | 4.10% | 0.25% | 0.64% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 0.83% | 1.24% | NA |
| VI/Aromatic | 96 | 49.00% | 2.10% | 4.17% | 44.79% | NA |
| Intermediate | 90 | 91.10% | 6.70% | 1.11% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1110437041 | G -> A | LOC_Os11g18510.1 | missense_variant ; p.Ala484Thr; MODERATE | nonsynonymous_codon ; A484T | Average:30.719; most accessible tissue: Minghui63 young leaf, score: 51.901 | benign  |
0.567 |
TOLERATED | 0.47 |
| vg1110437041 | G -> DEL | LOC_Os11g18510.1 | N | frameshift_variant | Average:30.719; most accessible tissue: Minghui63 young leaf, score: 51.901 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1110437041 | 3.65E-07 | 3.23E-06 | mr1154 | Ind_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 |
| vg1110437041 | 1.55E-08 | 1.23E-09 | mr1097_2 | Ind_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 |
| vg1110437041 | 9.99E-08 | 1.75E-07 | mr1154_2 | Ind_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 |