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Detailed information for vg0136607426:

Variant ID: vg0136607426 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 36607426
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 354. )

Flanking Sequence (100 bp) in Reference Genome:


AGCCGCCCACTTGTTTCCATGGATTGCATGAGCAGCCATTATAATGCGGTCTTCCTCCTCTGCAGAAACAGCAATAATAATTTAACAAGCAAGTTTTACA[G/A]
AGATGCAACGAAACTACACAACAGACTGAACGCGCAATGTTCATGCCCATAATGCTACAACCAAACTAGCATTGCCTCATAGACAAGACAAATACTCTTT

Reverse complement sequence

AAAGAGTATTTGTCTTGTCTATGAGGCAATGCTAGTTTGGTTGTAGCATTATGGGCATGAACATTGCGCGTTCAGTCTGTTGTGTAGTTTCGTTGCATCT[C/T]
TGTAAAACTTGCTTGTTAAATTATTATTGCTGTTTCTGCAGAGGAGGAAGACCGCATTATAATGGCTGCTCATGCAATCCATGGAAACAAGTGGGCGGCT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.70% 7.20% 0.06% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 84.40% 15.50% 0.13% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 98.30% 1.40% 0.26% 0.00% NA
Tropical Japonica  504 72.40% 27.60% 0.00% 0.00% NA
Japonica Intermediate  241 65.10% 34.90% 0.00% 0.00% NA
VI/Aromatic  96 10.40% 88.50% 1.04% 0.00% NA
Intermediate  90 84.40% 15.60% 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
vg0136607426 G -> A LOC_Os01g63170.1 upstream_gene_variant ; 3351.0bp to feature; MODIFIER silent_mutation Average:77.616; most accessible tissue: Zhenshan97 flower, score: 85.228 N N N N
vg0136607426 G -> A LOC_Os01g63160.1 intron_variant ; MODIFIER silent_mutation Average:77.616; most accessible tissue: Zhenshan97 flower, score: 85.228 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0136607426 NA 1.46E-07 mr1057 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
vg0136607426 NA 3.66E-08 mr1570 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
vg0136607426 NA 1.22E-10 mr1057_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
vg0136607426 NA 1.77E-06 mr1438_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
vg0136607426 2.83E-07 2.09E-10 mr1947_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