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Detailed information for vg0502139452:

Variant ID: vg0502139452 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 2139452
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.60, T: 0.39, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:


GAGTAATAATTAAATCTAGCAACATCAATTTTATATGATTGATTTTTTTTGCTATTAATAGTTAAAATTTAAAATGTTTGACTTGTCACTATGCTAAAAA[C/T]
ACTTATATTTTGGAACAGATGTAGTAGTTATATTTTGGGACGAAGATAGCAGTTGGGAAAACTTTCAGATGCCTCCATATCAGGAGACCATGCCTGCATG

Reverse complement sequence

CATGCAGGCATGGTCTCCTGATATGGAGGCATCTGAAAGTTTTCCCAACTGCTATCTTCGTCCCAAAATATAACTACTACATCTGTTCCAAAATATAAGT[G/A]
TTTTTAGCATAGTGACAAGTCAAACATTTTAAATTTTAACTATTAATAGCAAAAAAAATCAATCATATAAAATTGATGTTGCTAGATTTAATTATTACTC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 57.50% 42.30% 0.15% 0.04% NA
All Indica  2759 78.10% 21.60% 0.14% 0.07% NA
All Japonica  1512 16.10% 83.80% 0.07% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.50% 0.30% 0.00% 0.17% NA
Indica II  465 83.00% 16.30% 0.43% 0.22% NA
Indica III  913 57.30% 42.60% 0.11% 0.00% NA
Indica Intermediate  786 83.30% 16.50% 0.13% 0.00% NA
Temperate Japonica  767 5.10% 94.80% 0.13% 0.00% NA
Tropical Japonica  504 29.40% 70.60% 0.00% 0.00% NA
Japonica Intermediate  241 23.70% 76.30% 0.00% 0.00% NA
VI/Aromatic  96 14.60% 85.40% 0.00% 0.00% NA
Intermediate  90 37.80% 60.00% 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
vg0502139452 C -> T LOC_Os05g04584.1 upstream_gene_variant ; 4337.0bp to feature; MODIFIER silent_mutation Average:28.384; most accessible tissue: Zhenshan97 young leaf, score: 54.618 N N N N
vg0502139452 C -> T LOC_Os05g04570-LOC_Os05g04584 intergenic_region ; MODIFIER silent_mutation Average:28.384; most accessible tissue: Zhenshan97 young leaf, score: 54.618 N N N N
vg0502139452 C -> DEL N N silent_mutation Average:28.384; most accessible tissue: Zhenshan97 young leaf, score: 54.618 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0502139452 NA 5.80E-07 mr1227 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
vg0502139452 NA 8.32E-08 mr1514 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
vg0502139452 NA 2.62E-13 mr1667 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
vg0502139452 NA 5.11E-06 mr1681 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
vg0502139452 NA 2.34E-08 mr1030_2 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
vg0502139452 NA 5.87E-06 mr1030_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
vg0502139452 NA 2.50E-26 mr1149_2 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
vg0502139452 1.28E-06 NA mr1218_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
vg0502139452 NA 2.63E-27 mr1441_2 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
vg0502139452 NA 3.87E-08 mr1748_2 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
vg0502139452 NA 8.84E-08 mr1837_2 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
vg0502139452 NA 7.88E-11 mr1844_2 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
vg0502139452 NA 2.16E-06 mr1957_2 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