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Detailed information for vg0329036475:

Variant ID: vg0329036475 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 29036475
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, C: 0.02, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


GATACGAAAACGAATACGGATAGCTCGAATGCGGAAACAAATACGGATTATCTCGAATACGAATAAGAATCGAATATGATCGGACACGAATACGGAAACA[A/C]
ATTTTTCTCGGAACACGAAAACCAACTCAACTTCTAATGGAAACAAATATCAACATATATAATTAGCTCATTTTATATAAAATGAGGTATAATTTATAAA

Reverse complement sequence

TTTATAAATTATACCTCATTTTATATAAAATGAGCTAATTATATATGTTGATATTTGTTTCCATTAGAAGTTGAGTTGGTTTTCGTGTTCCGAGAAAAAT[T/G]
TGTTTCCGTATTCGTGTCCGATCATATTCGATTCTTATTCGTATTCGAGATAATCCGTATTTGTTTCCGCATTCGAGCTATCCGTATTCGTTTTCGTATC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 81.40% 18.50% 0.11% 0.00% NA
All Indica  2759 69.30% 30.50% 0.18% 0.00% NA
All Japonica  1512 99.20% 0.80% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.00% 1.00% 0.00% 0.00% NA
Indica II  465 49.50% 50.10% 0.43% 0.00% NA
Indica III  913 55.10% 44.80% 0.11% 0.00% NA
Indica Intermediate  786 75.20% 24.60% 0.25% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 98.40% 1.60% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 80.00% 20.00% 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
vg0329036475 A -> C LOC_Os03g50830.1 downstream_gene_variant ; 4226.0bp to feature; MODIFIER silent_mutation Average:27.518; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N
vg0329036475 A -> C LOC_Os03g50850.1 downstream_gene_variant ; 2819.0bp to feature; MODIFIER silent_mutation Average:27.518; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N
vg0329036475 A -> C LOC_Os03g50850.2 downstream_gene_variant ; 2819.0bp to feature; MODIFIER silent_mutation Average:27.518; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N
vg0329036475 A -> C LOC_Os03g50830-LOC_Os03g50850 intergenic_region ; MODIFIER silent_mutation Average:27.518; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0329036475 NA 9.76E-06 mr1010 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
vg0329036475 NA 2.10E-06 mr1030 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
vg0329036475 NA 6.66E-06 mr1051 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
vg0329036475 NA 2.45E-09 mr1663 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
vg0329036475 3.77E-06 3.76E-06 mr1663 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
vg0329036475 NA 1.52E-06 mr1958 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