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Detailed information for vg0432657154:

Variant ID: vg0432657154 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 32657154
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, T: 0.03, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


GGATTATTTAGAACTCTTAATATCATGTGGGGGTACATATATGTCCAAATCAATGGAAATATGATGTGGGACTCAAATTAAATCTTCGTCTATGAACTCC[A/T]
AATTTAAGTAATTCAGAAAAGGTCCAAATTCAGCTAAAATAAAAACACAGGATACAACAGCACGTCCAAGAGAGAGCTGCAATTATAATGCATGCGTGGC

Reverse complement sequence

GCCACGCATGCATTATAATTGCAGCTCTCTCTTGGACGTGCTGTTGTATCCTGTGTTTTTATTTTAGCTGAATTTGGACCTTTTCTGAATTACTTAAATT[T/A]
GGAGTTCATAGACGAAGATTTAATTTGAGTCCCACATCATATTTCCATTGATTTGGACATATATGTACCCCCACATGATATTAAGAGTTCTAAATAATCC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.00% 43.60% 0.36% 0.00% NA
All Indica  2759 34.80% 64.60% 0.62% 0.00% NA
All Japonica  1512 84.30% 15.70% 0.00% 0.00% NA
Aus  269 98.10% 1.90% 0.00% 0.00% NA
Indica I  595 20.30% 79.50% 0.17% 0.00% NA
Indica II  465 42.80% 56.80% 0.43% 0.00% NA
Indica III  913 41.90% 57.20% 0.88% 0.00% NA
Indica Intermediate  786 32.70% 66.50% 0.76% 0.00% NA
Temperate Japonica  767 98.00% 2.00% 0.00% 0.00% NA
Tropical Japonica  504 58.30% 41.70% 0.00% 0.00% NA
Japonica Intermediate  241 95.00% 5.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 61.10% 38.90% 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
vg0432657154 A -> T LOC_Os04g54890.1 upstream_gene_variant ; 4426.0bp to feature; MODIFIER silent_mutation Average:45.28; most accessible tissue: Callus, score: 57.497 N N N N
vg0432657154 A -> T LOC_Os04g54900.1 downstream_gene_variant ; 599.0bp to feature; MODIFIER silent_mutation Average:45.28; most accessible tissue: Callus, score: 57.497 N N N N
vg0432657154 A -> T LOC_Os04g54890-LOC_Os04g54900 intergenic_region ; MODIFIER silent_mutation Average:45.28; most accessible tissue: Callus, score: 57.497 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0432657154 NA 2.64E-06 mr1156 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
vg0432657154 NA 1.17E-10 mr1403 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
vg0432657154 NA 3.72E-10 mr1720 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
vg0432657154 NA 2.40E-08 mr1763 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
vg0432657154 1.59E-10 NA mr1800_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
vg0432657154 1.40E-07 1.64E-06 mr1800_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
vg0432657154 3.68E-06 NA mr1873_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