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Detailed information for vg1124808771:

Variant ID: vg1124808771 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 24808771
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


TTGGCCATAAAAAAGCCATGTGTAAGAGCAAGTTTAATAGTATAGCCCACTACTAACTCCAATTCATTTATAGTCAATCTAATAGCTAATTCATACAATA[G/A]
TTGCTTACTATACTATTAATATATATGGTCCCACCTGTCATACACACATTGCGTCTTGAAGTCCGTGCTGCAGCTGACTACAAATATGTAGCCCGCTGCT

Reverse complement sequence

AGCAGCGGGCTACATATTTGTAGTCAGCTGCAGCACGGACTTCAAGACGCAATGTGTGTATGACAGGTGGGACCATATATATTAATAGTATAGTAAGCAA[C/T]
TATTGTATGAATTAGCTATTAGATTGACTATAAATGAATTGGAGTTAGTAGTGGGCTATACTATTAAACTTGCTCTTACACATGGCTTTTTTATGGCCAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.70% 5.90% 0.04% 0.36% NA
All Indica  2759 97.70% 2.30% 0.00% 0.00% NA
All Japonica  1512 94.90% 5.10% 0.00% 0.00% NA
Aus  269 46.10% 46.80% 0.74% 6.32% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 95.70% 4.30% 0.00% 0.00% NA
Indica Intermediate  786 97.10% 2.90% 0.00% 0.00% NA
Temperate Japonica  767 98.30% 1.70% 0.00% 0.00% NA
Tropical Japonica  504 95.00% 5.00% 0.00% 0.00% NA
Japonica Intermediate  241 83.80% 16.20% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1124808771 G -> A LOC_Os11g41360.1 upstream_gene_variant ; 4080.0bp to feature; MODIFIER silent_mutation Average:51.241; most accessible tissue: Callus, score: 68.078 N N N N
vg1124808771 G -> A LOC_Os11g41350.1 downstream_gene_variant ; 869.0bp to feature; MODIFIER silent_mutation Average:51.241; most accessible tissue: Callus, score: 68.078 N N N N
vg1124808771 G -> A LOC_Os11g41330-LOC_Os11g41350 intergenic_region ; MODIFIER silent_mutation Average:51.241; most accessible tissue: Callus, score: 68.078 N N N N
vg1124808771 G -> DEL N N silent_mutation Average:51.241; most accessible tissue: Callus, score: 68.078 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1124808771 5.95E-07 NA mr1134_2 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
vg1124808771 6.86E-06 NA mr1134_2 Jap_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
vg1124808771 NA 8.71E-06 mr1855_2 Jap_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