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Detailed information for vg0334688295:

Variant ID: vg0334688295 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 34688295
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


TACGGAAACCCACAACTGCACTTAAAATGGGACGGAGGGAGTAATTGGCAGTGATCAGCTTGCTATGATTGTGATTGAACTCAACCTGAGATCATTGAAC[A/G]
TAGGTACATAACATGATAGATGCAAGCCTTCCAAGAACTGAGAATTTTCAAGTTAACTTTACAAATTACAAATGTTCTTACATAATATAATCAACCTATA

Reverse complement sequence

TATAGGTTGATTATATTATGTAAGAACATTTGTAATTTGTAAAGTTAACTTGAAAATTCTCAGTTCTTGGAAGGCTTGCATCTATCATGTTATGTACCTA[T/C]
GTTCAATGATCTCAGGTTGAGTTCAATCACAATCATAGCAAGCTGATCACTGCCAATTACTCCCTCCGTCCCATTTTAAGTGCAGTTGTGGGTTTCCGTA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 59.90% 40.10% 0.06% 0.00% NA
All Indica  2759 34.90% 65.00% 0.11% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 78.80% 21.20% 0.00% 0.00% NA
Indica I  595 8.20% 91.80% 0.00% 0.00% NA
Indica II  465 24.50% 75.30% 0.22% 0.00% NA
Indica III  913 53.70% 46.20% 0.11% 0.00% NA
Indica Intermediate  786 39.30% 60.60% 0.13% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 62.20% 37.80% 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
vg0334688295 A -> G LOC_Os03g61060.1 3_prime_UTR_variant ; 278.0bp to feature; MODIFIER silent_mutation Average:71.841; most accessible tissue: Callus, score: 91.007 N N N N
vg0334688295 A -> G LOC_Os03g61060.2 3_prime_UTR_variant ; 278.0bp to feature; MODIFIER silent_mutation Average:71.841; most accessible tissue: Callus, score: 91.007 N N N N
vg0334688295 A -> G LOC_Os03g61050.1 downstream_gene_variant ; 214.0bp to feature; MODIFIER silent_mutation Average:71.841; most accessible tissue: Callus, score: 91.007 N N N N
vg0334688295 A -> G LOC_Os03g61070.1 downstream_gene_variant ; 4613.0bp to feature; MODIFIER silent_mutation Average:71.841; most accessible tissue: Callus, score: 91.007 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0334688295 NA 1.64E-06 mr1850 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
vg0334688295 NA 8.42E-08 mr1212_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
vg0334688295 NA 4.67E-10 mr1649_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
vg0334688295 2.47E-07 NA mr1671_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
vg0334688295 2.30E-07 NA mr1671_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
vg0334688295 NA 1.19E-08 mr1798_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