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Detailed information for vg0502444924:

Variant ID: vg0502444924 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 2444924
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.95, T: 0.05, others allele: 0.00, population size: 128. )

Flanking Sequence (100 bp) in Reference Genome:


TTATAATCCACTAACTCCTAAATCTTAACATGCAAAGATGACACATCATCGTTCACTAACAAGTTGACACATCATCATCCACGAACAACCAATACATTTA[A/T]
CATCATGCAAACATGCTATATTATCTATAATTTAAAATTTATTATATTTTAGAGCTTTTAAAATGAAAGCATGTTAAATCATCATCCCCCATAATTCACA

Reverse complement sequence

TGTGAATTATGGGGGATGATGATTTAACATGCTTTCATTTTAAAAGCTCTAAAATATAATAAATTTTAAATTATAGATAATATAGCATGTTTGCATGATG[T/A]
TAAATGTATTGGTTGTTCGTGGATGATGATGTGTCAACTTGTTAGTGAACGATGATGTGTCATCTTTGCATGTTAAGATTTAGGAGTTAGTGGATTATAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.30% 5.70% 0.00% 0.00% NA
All Indica  2759 94.90% 5.10% 0.00% 0.00% NA
All Japonica  1512 97.70% 2.30% 0.00% 0.00% NA
Aus  269 97.00% 3.00% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 95.70% 4.30% 0.00% 0.00% NA
Indica III  913 94.50% 5.50% 0.00% 0.00% NA
Indica Intermediate  786 91.50% 8.50% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 98.80% 1.20% 0.00% 0.00% NA
Japonica Intermediate  241 88.40% 11.60% 0.00% 0.00% NA
VI/Aromatic  96 16.70% 83.30% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0502444924 A -> T LOC_Os05g05030.1 downstream_gene_variant ; 4307.0bp to feature; MODIFIER silent_mutation Average:32.615; most accessible tissue: Zhenshan97 flower, score: 56.847 N N N N
vg0502444924 A -> T LOC_Os05g05020-LOC_Os05g05030 intergenic_region ; MODIFIER silent_mutation Average:32.615; most accessible tissue: Zhenshan97 flower, score: 56.847 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0502444924 NA 7.20E-06 mr1229 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
vg0502444924 2.83E-06 NA mr1730 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