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Detailed information for vg0122345272:

Variant ID: vg0122345272 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 22345272
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.78, T: 0.22, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:


TGGTGGGTCCTGCCGAGATTTAGGCAACTACTATTAGGTATGTGGTATCCATAACCCTGACAGATACTATTTATATTTAAACTACGATTGCTCTTTTTTT[A/T]
AAATAAAAAATAAAATCCTTAAAAGGATATGTTGCATCCTAAACATAATCATTAAGATTTAGTATATTGATCATACCTTAATCATTTAAAAATTATTAAT

Reverse complement sequence

ATTAATAATTTTTAAATGATTAAGGTATGATCAATATACTAAATCTTAATGATTATGTTTAGGATGCAACATATCCTTTTAAGGATTTTATTTTTTATTT[T/A]
AAAAAAAGAGCAATCGTAGTTTAAATATAAATAGTATCTGTCAGGGTTATGGATACCACATACCTAATAGTAGTTGCCTAAATCTCGGCAGGACCCACCA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.40% 45.40% 0.13% 0.00% NA
All Indica  2759 81.60% 18.20% 0.18% 0.00% NA
All Japonica  1512 0.50% 99.50% 0.00% 0.00% NA
Aus  269 66.20% 33.80% 0.00% 0.00% NA
Indica I  595 96.50% 3.50% 0.00% 0.00% NA
Indica II  465 94.80% 5.20% 0.00% 0.00% NA
Indica III  913 69.70% 30.20% 0.11% 0.00% NA
Indica Intermediate  786 76.30% 23.20% 0.51% 0.00% NA
Temperate Japonica  767 0.00% 100.00% 0.00% 0.00% NA
Tropical Japonica  504 0.40% 99.60% 0.00% 0.00% NA
Japonica Intermediate  241 2.10% 97.90% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 50.00% 48.90% 1.11% 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
vg0122345272 A -> T LOC_Os01g39600.1 upstream_gene_variant ; 3794.0bp to feature; MODIFIER silent_mutation Average:40.269; most accessible tissue: Zhenshan97 panicle, score: 61.671 N N N N
vg0122345272 A -> T LOC_Os01g39600.2 upstream_gene_variant ; 3727.0bp to feature; MODIFIER silent_mutation Average:40.269; most accessible tissue: Zhenshan97 panicle, score: 61.671 N N N N
vg0122345272 A -> T LOC_Os01g39600-LOC_Os01g39630 intergenic_region ; MODIFIER silent_mutation Average:40.269; most accessible tissue: Zhenshan97 panicle, score: 61.671 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0122345272 NA 1.14E-34 mr1110 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
vg0122345272 NA 8.96E-09 mr1260 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
vg0122345272 NA 2.58E-10 mr1819 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
vg0122345272 3.36E-06 2.61E-06 mr1509_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