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Detailed information for vg1125147337:

Variant ID: vg1125147337 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25147337
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


TCGAGCAATTTTTGCGGCGGCTGGGAGGAGGGGAAGGAAAAGTGGTTAGGGTTTGTTGGGGTTTGCACGAATCTCAAATCAATCCAATGGTCAAAAATTT[G/A]
CAAGATATTAGGAGGGTTTTCTACCAAATGATGAGTAGACAGTCCCTTTTTTTTTTCTTTTGCAGAACGTGAACCTGCTGAACTTGTACACACCCATGTA

Reverse complement sequence

TACATGGGTGTGTACAAGTTCAGCAGGTTCACGTTCTGCAAAAGAAAAAAAAAAGGGACTGTCTACTCATCATTTGGTAGAAAACCCTCCTAATATCTTG[C/T]
AAATTTTTGACCATTGGATTGATTTGAGATTCGTGCAAACCCCAACAAACCCTAACCACTTTTCCTTCCCCTCCTCCCAGCCGCCGCAAAAATTGCTCGA

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 79.80% 20.20% 0.02% 0.00% NA
All Indica  2759 72.10% 27.80% 0.04% 0.00% NA
All Japonica  1512 94.80% 5.20% 0.00% 0.00% NA
Aus  269 63.20% 36.80% 0.00% 0.00% NA
Indica I  595 93.80% 6.20% 0.00% 0.00% NA
Indica II  465 82.80% 17.20% 0.00% 0.00% NA
Indica III  913 52.10% 47.90% 0.00% 0.00% NA
Indica Intermediate  786 72.60% 27.20% 0.13% 0.00% NA
Temperate Japonica  767 98.40% 1.60% 0.00% 0.00% NA
Tropical Japonica  504 89.70% 10.30% 0.00% 0.00% NA
Japonica Intermediate  241 94.20% 5.80% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg1125147337 G -> A LOC_Os11g41820.1 downstream_gene_variant ; 1366.0bp to feature; MODIFIER silent_mutation Average:76.71; most accessible tissue: Zhenshan97 panicle, score: 87.126 N N N N
vg1125147337 G -> A LOC_Os11g41820.2 downstream_gene_variant ; 1366.0bp to feature; MODIFIER silent_mutation Average:76.71; most accessible tissue: Zhenshan97 panicle, score: 87.126 N N N N
vg1125147337 G -> A LOC_Os11g41800-LOC_Os11g41820 intergenic_region ; MODIFIER silent_mutation Average:76.71; most accessible tissue: Zhenshan97 panicle, score: 87.126 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125147337 9.09E-07 NA mr1133 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
vg1125147337 2.73E-06 1.47E-09 mr1133 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
vg1125147337 3.16E-06 NA mr1133_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
vg1125147337 2.13E-06 4.39E-11 mr1133_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
vg1125147337 NA 5.06E-09 mr1667_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
vg1125147337 NA 2.94E-08 mr1842_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