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Detailed information for vg0309690725:

Variant ID: vg0309690725 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 9690725
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


TTTCCCCCATATTCCCAACTTTCCATCACATCATATCACATCAAAAACTTTTCTACACACATAAACTTCTAACTTTTTTTCTAAACTTCCAACTTTCTTC[A/G]
AACTTTTAACTTTTTAAGGGTTTGTAGGATTGGTGAAGATGTCATGTCAACATTCTTATGGTAGGTCTCATTAAATTTTGGACTAGGGCTGGCACATTTA

Reverse complement sequence

TAAATGTGCCAGCCCTAGTCCAAAATTTAATGAGACCTACCATAAGAATGTTGACATGACATCTTCACCAATCCTACAAACCCTTAAAAAGTTAAAAGTT[T/C]
GAAGAAAGTTGGAAGTTTAGAAAAAAAGTTAGAAGTTTATGTGTGTAGAAAAGTTTTTGATGTGATATGATGTGATGGAAAGTTGGGAATATGGGGGAAA

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 95.60% 3.70% 0.68% 0.00% NA
All Indica  2759 99.90% 0.00% 0.07% 0.00% NA
All Japonica  1512 86.80% 11.40% 1.85% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.00% 0.13% 0.00% NA
Temperate Japonica  767 74.40% 22.00% 3.52% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.20% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 2.20% 2.22% 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
vg0309690725 A -> G LOC_Os03g17410.1 upstream_gene_variant ; 4860.0bp to feature; MODIFIER silent_mutation Average:57.276; most accessible tissue: Callus, score: 80.974 N N N N
vg0309690725 A -> G LOC_Os03g17420.1 upstream_gene_variant ; 557.0bp to feature; MODIFIER silent_mutation Average:57.276; most accessible tissue: Callus, score: 80.974 N N N N
vg0309690725 A -> G LOC_Os03g17426.1 upstream_gene_variant ; 4317.0bp to feature; MODIFIER silent_mutation Average:57.276; most accessible tissue: Callus, score: 80.974 N N N N
vg0309690725 A -> G LOC_Os03g17410-LOC_Os03g17420 intergenic_region ; MODIFIER silent_mutation Average:57.276; most accessible tissue: Callus, score: 80.974 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0309690725 7.92E-07 7.92E-07 mr1360_2 Jap_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
vg0309690725 1.62E-06 1.62E-06 mr1452_2 Jap_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