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Detailed information for vg0205319588:

Variant ID: vg0205319588 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 5319588
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.94, T: 0.06, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:


CAATTATTGATTTAATGAAACTAAATTGATATTATATATATTACTATATTTATGCATAAACTTAGTTAAATTTGAAGTAGTTTGACTTTGACCAAAATCA[A/T]
AACGTCTTACAACCAGATCTGTTTAATATACTAGAGCGACAGAAGTAGCAGTATATTAGCTAGCTAGTATACTAGGTTAATATACTGCATCTGTTTCAGA

Reverse complement sequence

TCTGAAACAGATGCAGTATATTAACCTAGTATACTAGCTAGCTAATATACTGCTACTTCTGTCGCTCTAGTATATTAAACAGATCTGGTTGTAAGACGTT[T/A]
TGATTTTGGTCAAAGTCAAACTACTTCAAATTTAACTAAGTTTATGCATAAATATAGTAATATATATAATATCAATTTAGTTTCATTAAATCAATAATTG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.40% 43.50% 0.08% 0.00% NA
All Indica  2759 81.30% 18.50% 0.14% 0.00% NA
All Japonica  1512 1.80% 98.20% 0.00% 0.00% NA
Aus  269 96.70% 3.30% 0.00% 0.00% NA
Indica I  595 91.30% 8.70% 0.00% 0.00% NA
Indica II  465 84.30% 15.70% 0.00% 0.00% NA
Indica III  913 73.10% 26.90% 0.00% 0.00% NA
Indica Intermediate  786 81.70% 17.80% 0.51% 0.00% NA
Temperate Japonica  767 1.80% 98.20% 0.00% 0.00% NA
Tropical Japonica  504 0.80% 99.20% 0.00% 0.00% NA
Japonica Intermediate  241 3.70% 96.30% 0.00% 0.00% NA
VI/Aromatic  96 90.60% 9.40% 0.00% 0.00% NA
Intermediate  90 53.30% 46.70% 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
vg0205319588 A -> T LOC_Os02g10150.1 upstream_gene_variant ; 2194.0bp to feature; MODIFIER silent_mutation Average:36.497; most accessible tissue: Minghui63 root, score: 85.252 N N N N
vg0205319588 A -> T LOC_Os02g10140.1 downstream_gene_variant ; 1567.0bp to feature; MODIFIER silent_mutation Average:36.497; most accessible tissue: Minghui63 root, score: 85.252 N N N N
vg0205319588 A -> T LOC_Os02g10160.1 downstream_gene_variant ; 4944.0bp to feature; MODIFIER silent_mutation Average:36.497; most accessible tissue: Minghui63 root, score: 85.252 N N N N
vg0205319588 A -> T LOC_Os02g10140-LOC_Os02g10150 intergenic_region ; MODIFIER silent_mutation Average:36.497; most accessible tissue: Minghui63 root, score: 85.252 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0205319588 NA 6.05E-07 mr1003 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
vg0205319588 NA 1.43E-06 mr1006 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
vg0205319588 NA 4.24E-06 mr1007 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
vg0205319588 NA 5.73E-09 mr1051 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
vg0205319588 NA 1.75E-06 mr1052 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
vg0205319588 NA 5.49E-07 mr1536 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
vg0205319588 NA 1.30E-10 mr1683 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
vg0205319588 NA 7.08E-15 mr1909 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
vg0205319588 NA 7.29E-11 mr1921 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
vg0205319588 NA 1.80E-06 mr1006_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
vg0205319588 NA 3.88E-09 mr1051_2 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
vg0205319588 NA 6.60E-08 mr1536_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
vg0205319588 NA 7.53E-11 mr1705_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
vg0205319588 NA 2.69E-06 mr1915_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