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Detailed information for vg0326661478:

Variant ID: vg0326661478 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 26661478
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.68, A: 0.32, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:


CCCAAACCTGTCTAAACCATTGTTTTTTTAGCCCTTGATGATCCATGAGATGCCAATCACCTCGTTTCCACACACCCGCTCCCTGGCCGAATCCCAAAAG[A/G]
GTGCCACTTCTCCATGCTAGAGGAGTTTGAGCTCCGACACCACTCATTAGCATTTCTTTTCTTTGTTTCTCCTCATACGAGTCGTATTTTGAACTAAAAT

Reverse complement sequence

ATTTTAGTTCAAAATACGACTCGTATGAGGAGAAACAAAGAAAAGAAATGCTAATGAGTGGTGTCGGAGCTCAAACTCCTCTAGCATGGAGAAGTGGCAC[T/C]
CTTTTGGGATTCGGCCAGGGAGCGGGTGTGTGGAAACGAGGTGATTGGCATCTCATGGATCATCAAGGGCTAAAAAAACAATGGTTTAGACAGGTTTGGG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 75.10% 24.40% 0.44% 0.00% NA
All Indica  2759 58.70% 40.50% 0.76% 0.00% NA
All Japonica  1512 99.10% 0.90% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 61.50% 37.80% 0.67% 0.00% NA
Indica II  465 48.00% 49.00% 3.01% 0.00% NA
Indica III  913 63.20% 36.80% 0.00% 0.00% NA
Indica Intermediate  786 57.80% 41.90% 0.38% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 98.40% 1.60% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 81.10% 18.90% 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
vg0326661478 A -> G LOC_Os03g47120.1 downstream_gene_variant ; 3631.0bp to feature; MODIFIER silent_mutation Average:35.033; most accessible tissue: Callus, score: 49.177 N N N N
vg0326661478 A -> G LOC_Os03g47120-LOC_Os03g47130 intergenic_region ; MODIFIER silent_mutation Average:35.033; most accessible tissue: Callus, score: 49.177 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0326661478 NA 8.24E-10 mr1193_2 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