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Detailed information for vg0208023522:

Variant ID: vg0208023522 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 8023522
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.88, A: 0.12, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:


TGGTATGCACTGTATGGATGTCGTACCATTTCACAGTAAGGAGGATATTTATTTATAATACATTCATATACAAATGCAAGAGTCATAATAACTTACTACT[A/G]
TAAGATTGTTAGAAATTCTTTGTATTGCTTGTGACTGTAATCGAGAGGGTCCAAGACTACCACGGTTCCGTCTTTAGGGTGGATAAGTAAACAGATATAA

Reverse complement sequence

TTATATCTGTTTACTTATCCACCCTAAAGACGGAACCGTGGTAGTCTTGGACCCTCTCGATTACAGTCACAAGCAATACAAAGAATTTCTAACAATCTTA[T/C]
AGTAGTAAGTTATTATGACTCTTGCATTTGTATATGAATGTATTATAAATAAATATCCTCCTTACTGTGAAATGGTACGACATCCATACAGTGCATACCA

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 55.50% 24.40% 20.04% 0.00% NA
All Indica  2759 36.60% 34.20% 29.18% 0.00% NA
All Japonica  1512 98.00% 1.70% 0.26% 0.00% NA
Aus  269 14.90% 42.80% 42.38% 0.00% NA
Indica I  595 35.80% 36.60% 27.56% 0.00% NA
Indica II  465 21.70% 47.30% 30.97% 0.00% NA
Indica III  913 47.40% 24.30% 28.26% 0.00% NA
Indica Intermediate  786 33.60% 36.00% 30.41% 0.00% NA
Temperate Japonica  767 98.30% 1.60% 0.13% 0.00% NA
Tropical Japonica  504 98.00% 1.60% 0.40% 0.00% NA
Japonica Intermediate  241 97.10% 2.50% 0.41% 0.00% NA
VI/Aromatic  96 43.80% 47.90% 8.33% 0.00% NA
Intermediate  90 54.40% 27.80% 17.78% 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
vg0208023522 A -> G LOC_Os02g14540.1 upstream_gene_variant ; 4167.0bp to feature; MODIFIER silent_mutation Average:27.026; most accessible tissue: Zhenshan97 root, score: 58.674 N N N N
vg0208023522 A -> G LOC_Os02g14560.1 downstream_gene_variant ; 4331.0bp to feature; MODIFIER silent_mutation Average:27.026; most accessible tissue: Zhenshan97 root, score: 58.674 N N N N
vg0208023522 A -> G LOC_Os02g14550.1 intron_variant ; MODIFIER silent_mutation Average:27.026; most accessible tissue: Zhenshan97 root, score: 58.674 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0208023522 NA 1.75E-07 mr1028 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
vg0208023522 NA 7.14E-11 mr1232 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
vg0208023522 NA 3.11E-07 mr1245 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
vg0208023522 NA 1.36E-06 mr1392 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
vg0208023522 NA 8.55E-07 mr1445 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
vg0208023522 NA 1.79E-08 mr1453 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
vg0208023522 NA 6.03E-06 mr1508 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
vg0208023522 NA 4.84E-18 mr1557 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
vg0208023522 NA 2.08E-06 mr1652 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
vg0208023522 NA 1.32E-06 mr1886 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
vg0208023522 4.85E-06 NA mr1944 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
vg0208023522 NA 5.21E-06 mr1944 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