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Detailed information for vg0611636429:

Variant ID: vg0611636429 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 11636429
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.73, T: 0.27, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:


AGTAATTGAGCTCTGAAAATTCCGATAAAATTCCAGAGAGTATAATTAATTATGGAGAATTTAATAGAAATTAAATCTAGCCGTGCTTTTATATTTATAA[A/T]
ATTTTATTTCCCATATTTAACTTCACTTGTAAATTAATAAACATTTAATATAAATTCTAAAAATAATTTATTAAATAATTTATAAGTACTGAAACGAAAA

Reverse complement sequence

TTTTCGTTTCAGTACTTATAAATTATTTAATAAATTATTTTTAGAATTTATATTAAATGTTTATTAATTTACAAGTGAAGTTAAATATGGGAAATAAAAT[T/A]
TTATAAATATAAAAGCACGGCTAGATTTAATTTCTATTAAATTCTCCATAATTAATTATACTCTCTGGAATTTTATCGGAATTTTCAGAGCTCAATTACT

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 69.60% 21.00% 5.44% 4.04% NA
All Indica  2759 81.50% 9.10% 4.71% 4.71% NA
All Japonica  1512 52.10% 36.00% 8.20% 3.70% NA
Aus  269 69.50% 30.10% 0.00% 0.37% NA
Indica I  595 76.50% 7.70% 12.10% 3.70% NA
Indica II  465 75.70% 7.50% 6.24% 10.54% NA
Indica III  913 87.60% 9.60% 0.44% 2.30% NA
Indica Intermediate  786 81.70% 10.30% 3.18% 4.83% NA
Temperate Japonica  767 30.00% 49.70% 14.21% 6.13% NA
Tropical Japonica  504 81.00% 16.50% 1.59% 0.99% NA
Japonica Intermediate  241 61.80% 33.60% 2.90% 1.66% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 66.70% 25.60% 3.33% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0611636429 A -> T LOC_Os06g20280.1 downstream_gene_variant ; 861.0bp to feature; MODIFIER silent_mutation Average:52.272; most accessible tissue: Callus, score: 80.467 N N N N
vg0611636429 A -> T LOC_Os06g20270-LOC_Os06g20280 intergenic_region ; MODIFIER silent_mutation Average:52.272; most accessible tissue: Callus, score: 80.467 N N N N
vg0611636429 A -> DEL N N silent_mutation Average:52.272; most accessible tissue: Callus, score: 80.467 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0611636429 NA 4.89E-08 mr1695 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
vg0611636429 3.00E-08 NA mr1065_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
vg0611636429 1.40E-07 NA mr1067_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
vg0611636429 4.12E-08 NA mr1068_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
vg0611636429 4.31E-06 NA mr1078_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
vg0611636429 3.76E-07 NA mr1087_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
vg0611636429 7.12E-11 4.78E-10 mr1087_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
vg0611636429 4.09E-06 NA mr1090_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
vg0611636429 4.21E-06 NA mr1091_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
vg0611636429 2.71E-07 NA mr1091_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
vg0611636429 NA 2.06E-06 mr1096_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
vg0611636429 2.19E-07 NA mr1108_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
vg0611636429 6.33E-09 NA mr1108_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
vg0611636429 2.33E-06 NA mr1111_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
vg0611636429 4.50E-09 4.11E-07 mr1111_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
vg0611636429 1.28E-06 NA mr1112_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
vg0611636429 3.90E-09 NA mr1112_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
vg0611636429 5.37E-07 2.87E-06 mr1121_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
vg0611636429 8.30E-07 NA mr1144_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
vg0611636429 1.37E-06 NA mr1234_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
vg0611636429 2.67E-09 NA mr1234_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
vg0611636429 3.41E-09 5.09E-08 mr1526_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
vg0611636429 NA 4.21E-06 mr1695_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