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Detailed information for vg0626616281:

Variant ID: vg0626616281 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 26616281
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


GCTTAAGCTTATCTCACACGCACGTAAAACGATGCGACTCATTAGTATATGATTAATAGAGTATTAAGTATTTTTTAAAAATGGATTAATATGATTTTTT[A/T]
AGTAATTTTTTTATAAAAAAATACACCGTTTAATAGTTTGGGAAGCGAGCGCGTAAAAAATGAGTAAGATAAGTTAGGAAAGAAGAGGAAAGAACACAAC

Reverse complement sequence

GTTGTGTTCTTTCCTCTTCTTTCCTAACTTATCTTACTCATTTTTTACGCGCTCGCTTCCCAAACTATTAAACGGTGTATTTTTTTATAAAAAAATTACT[T/A]
AAAAAATCATATTAATCCATTTTTAAAAAATACTTAATACTCTATTAATCATATACTAATGAGTCGCATCGTTTTACGTGCGTGTGAGATAAGCTTAAGC

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 91.20% 8.30% 0.49% 0.02% NA
All Indica  2759 85.20% 13.90% 0.83% 0.04% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 89.70% 8.20% 2.02% 0.00% NA
Indica II  465 49.20% 50.10% 0.65% 0.00% NA
Indica III  913 97.30% 2.50% 0.22% 0.00% NA
Indica Intermediate  786 89.10% 10.10% 0.76% 0.13% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0626616281 A -> T LOC_Os06g44130-LOC_Os06g44140 intergenic_region ; MODIFIER silent_mutation Average:40.559; most accessible tissue: Callus, score: 75.352 N N N N
vg0626616281 A -> DEL N N silent_mutation Average:40.559; most accessible tissue: Callus, score: 75.352 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0626616281 NA 8.86E-06 mr1536 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
vg0626616281 NA 5.91E-06 mr1472_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
vg0626616281 NA 8.51E-08 mr1498_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
vg0626616281 4.91E-06 4.90E-06 mr1630_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
vg0626616281 NA 8.01E-06 mr1887_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
vg0626616281 NA 3.31E-06 mr1888_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