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Detailed information for vg0333694886:

Variant ID: vg0333694886 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 33694886
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.90, G: 0.09, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


ATTCCCGGCCATTCTTCTTGTAAATGAGACTACAATGGTACGATACTGGGGCCCAAAAGATCTCAGCTCTCTGGTGGACTTCTATAAAGAAACTACAGGT[A/G]
CAAGCATTGCTCTTCTTTTCCTGCATACAAGAATCGTAACAACTTTCAAATATATTAAACCCAGAAATGAGAACATAGCCTTTGGGTGCTATTTAGTTTG

Reverse complement sequence

CAAACTAAATAGCACCCAAAGGCTATGTTCTCATTTCTGGGTTTAATATATTTGAAAGTTGTTACGATTCTTGTATGCAGGAAAAGAAGAGCAATGCTTG[T/C]
ACCTGTAGTTTCTTTATAGAAGTCCACCAGAGAGCTGAGATCTTTTGGGCCCCAGTATCGTACCATTGTAGTCTCATTTACAAGAAGAATGGCCGGGAAT

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 77.60% 22.30% 0.02% 0.00% NA
All Indica  2759 71.90% 28.00% 0.04% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 1.50% 98.50% 0.00% 0.00% NA
Indica I  595 70.40% 29.40% 0.17% 0.00% NA
Indica II  465 85.80% 14.20% 0.00% 0.00% NA
Indica III  913 65.20% 34.80% 0.00% 0.00% NA
Indica Intermediate  786 72.80% 27.20% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 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 82.20% 17.80% 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
vg0333694886 A -> G LOC_Os03g59170.1 splice_region_variant&intron_variant ; LOW silent_mutation Average:63.604; most accessible tissue: Minghui63 flag leaf, score: 75.341 N N N N
vg0333694886 A -> G LOC_Os03g59160.1 upstream_gene_variant ; 2638.0bp to feature; MODIFIER silent_mutation Average:63.604; most accessible tissue: Minghui63 flag leaf, score: 75.341 N N N N
vg0333694886 A -> G LOC_Os03g59180.1 upstream_gene_variant ; 2219.0bp to feature; MODIFIER silent_mutation Average:63.604; most accessible tissue: Minghui63 flag leaf, score: 75.341 N N N N
vg0333694886 A -> G LOC_Os03g59180.2 upstream_gene_variant ; 2177.0bp to feature; MODIFIER silent_mutation Average:63.604; most accessible tissue: Minghui63 flag leaf, score: 75.341 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0333694886 NA 4.44E-07 mr1834_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
vg0333694886 8.15E-08 1.61E-08 mr1860_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