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Detailed information for vg0334658706:

Variant ID: vg0334658706 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 34658706
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAGCATATATGTTTTCTCATTATATTATTTAAATATATTACAATGACATCATAATTTTAAATTTTGCAATAACTTTACAAAACTACTAATGTGTAATATT[C/T]
ATATTGTATTTTATATACGTGTTAGTTATTAATTATTTTTAATATCAAATTTTAGTTATTTGTAAATTATATATATTCATATATGGACTCTAGACTCGTC

Reverse complement sequence

GACGAGTCTAGAGTCCATATATGAATATATATAATTTACAAATAACTAAAATTTGATATTAAAAATAATTAATAACTAACACGTATATAAAATACAATAT[G/A]
AATATTACACATTAGTAGTTTTGTAAAGTTATTGCAAAATTTAAAATTATGATGTCATTGTAATATATTTAAATAATATAATGAGAAAACATATATGCTA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.20% 7.70% 0.04% 0.00% NA
All Indica  2759 87.00% 12.90% 0.07% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.50% 1.50% 0.00% 0.00% NA
Indica II  465 85.80% 14.20% 0.00% 0.00% NA
Indica III  913 78.10% 21.70% 0.22% 0.00% NA
Indica Intermediate  786 89.40% 10.60% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 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 92.20% 7.80% 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
vg0334658706 C -> T LOC_Os03g61010.1 upstream_gene_variant ; 4637.0bp to feature; MODIFIER silent_mutation Average:24.47; most accessible tissue: Zhenshan97 panicle, score: 61.671 N N N N
vg0334658706 C -> T LOC_Os03g60992-LOC_Os03g61010 intergenic_region ; MODIFIER silent_mutation Average:24.47; most accessible tissue: Zhenshan97 panicle, score: 61.671 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0334658706 1.21E-06 1.21E-06 mr1655 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
vg0334658706 2.02E-06 NA mr1671 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
vg0334658706 9.69E-09 4.42E-07 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