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Detailed information for vg0302609274:

Variant ID: vg0302609274 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 2609274
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


GCCTATAGAGCGTGGGCTAATGGTGGCCATGGAGGCTAGCTAAGCTACTTCTTCTTGGGGAGGAATGGCTATGCATGGCCTCCATAGTCGACGACTTTTA[C/T]
CTCTACTAAGGTAGGGCAACTTGTATCCTTTGGCAATTATTCGGTGGATGTCTGTTGGTGGTGGTGTTAGGGATTGGAGCCGGATGAATCTTGAGTTTGA

Reverse complement sequence

TCAAACTCAAGATTCATCCGGCTCCAATCCCTAACACCACCACCAACAGACATCCACCGAATAATTGCCAAAGGATACAAGTTGCCCTACCTTAGTAGAG[G/A]
TAAAAGTCGTCGACTATGGAGGCCATGCATAGCCATTCCTCCCCAAGAAGAAGTAGCTTAGCTAGCCTCCATGGCCACCATTAGCCCACGCTCTATAGGC

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 90.30% 8.40% 1.33% 0.00% NA
All Indica  2759 83.60% 14.10% 2.25% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 86.20% 9.40% 4.37% 0.00% NA
Indica II  465 98.30% 0.60% 1.08% 0.00% NA
Indica III  913 75.80% 23.90% 0.33% 0.00% NA
Indica Intermediate  786 82.10% 14.40% 3.56% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 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 93.30% 5.60% 1.11% 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
vg0302609274 C -> T LOC_Os03g05334.1 5_prime_UTR_variant ; 48.0bp to feature; MODIFIER silent_mutation Average:67.523; most accessible tissue: Callus, score: 89.682 N N N N
vg0302609274 C -> T LOC_Os03g05330.1 downstream_gene_variant ; 3772.0bp to feature; MODIFIER silent_mutation Average:67.523; most accessible tissue: Callus, score: 89.682 N N N N
vg0302609274 C -> T LOC_Os03g05340.1 downstream_gene_variant ; 766.0bp to feature; MODIFIER silent_mutation Average:67.523; most accessible tissue: Callus, score: 89.682 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0302609274 NA 5.67E-07 mr1155 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
vg0302609274 3.98E-07 3.98E-07 mr1449 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