Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0206177435:

Variant ID: vg0206177435 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 6177435
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.51, A: 0.50, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


TCACAGTTTCAAAAAGTCCTCGTCCGTTCAACAAAATGTCCGTGTCCGATTCCATACAAAATATGATCAATGAATTTAAAAAAACGGTTTAAACATGAAT[G/A]
ACGTATCAAAATTTTAGCAAAAACATCTTCAATTTTTATAATAGTAGAGATTAATATAATTTTTTAAAAAAATCTATGTTACACAATTAGGGTTAATATG

Reverse complement sequence

CATATTAACCCTAATTGTGTAACATAGATTTTTTTAAAAAATTATATTAATCTCTACTATTATAAAAATTGAAGATGTTTTTGCTAAAATTTTGATACGT[C/T]
ATTCATGTTTAAACCGTTTTTTTAAATTCATTGATCATATTTTGTATGGAATCGGACACGGACATTTTGTTGAACGGACGAGGACTTTTTGAAACTGTGA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 67.10% 32.70% 0.13% 0.00% NA
All Indica  2759 54.70% 45.20% 0.14% 0.00% NA
All Japonica  1512 98.10% 1.90% 0.00% 0.00% NA
Aus  269 27.90% 71.40% 0.74% 0.00% NA
Indica I  595 83.20% 16.60% 0.17% 0.00% NA
Indica II  465 60.40% 39.40% 0.22% 0.00% NA
Indica III  913 37.00% 62.90% 0.11% 0.00% NA
Indica Intermediate  786 50.30% 49.60% 0.13% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 96.20% 3.80% 0.00% 0.00% NA
Japonica Intermediate  241 96.70% 3.30% 0.00% 0.00% NA
VI/Aromatic  96 39.60% 60.40% 0.00% 0.00% NA
Intermediate  90 75.60% 24.40% 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
vg0206177435 G -> A LOC_Os02g11920.1 upstream_gene_variant ; 3647.0bp to feature; MODIFIER silent_mutation Average:53.915; most accessible tissue: Callus, score: 80.871 N N N N
vg0206177435 G -> A LOC_Os02g11920-LOC_Os02g11930 intergenic_region ; MODIFIER silent_mutation Average:53.915; most accessible tissue: Callus, score: 80.871 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0206177435 NA 1.71E-06 mr1004 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
vg0206177435 NA 4.54E-06 mr1006 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
vg0206177435 NA 3.32E-06 mr1007 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
vg0206177435 NA 4.51E-06 mr1052 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
vg0206177435 NA 4.71E-06 mr1097 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
vg0206177435 NA 9.56E-10 mr1004_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
vg0206177435 NA 2.69E-07 mr1006_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
vg0206177435 NA 3.89E-11 mr1065_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
vg0206177435 7.06E-06 NA mr1091_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
vg0206177435 4.60E-06 1.33E-11 mr1091_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
vg0206177435 NA 8.01E-06 mr1092_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
vg0206177435 NA 2.81E-06 mr1097_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
vg0206177435 NA 2.59E-08 mr1112_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
vg0206177435 NA 4.61E-06 mr1154_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
vg0206177435 2.44E-06 NA mr1877_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
vg0206177435 7.20E-06 3.40E-08 mr1877_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