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Detailed information for vg0400468558:

Variant ID: vg0400468558 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 468558
Reference Allele: GAlternative Allele: A,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, T: 0.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


ATTAAAATGGCGAGGCCCAAAATTTCCAAACAATAGCATTTCTCAACTTAAAATGTCATACGTGAAGCTAAAATTACATATGTAATTTGGGATTTACATG[G/A,T]
TAAATACACTAAAATTACATATATAATTTAGTGACTAACAATGTAAATATATGATGACTATTTTTTCATGAAAAATATGACGGCATAAATATGAGAAAAT

Reverse complement sequence

ATTTTCTCATATTTATGCCGTCATATTTTTCATGAAAAAATAGTCATCATATATTTACATTGTTAGTCACTAAATTATATATGTAATTTTAGTGTATTTA[C/T,A]
CATGTAAATCCCAAATTACATATGTAATTTTAGCTTCACGTATGACATTTTAAGTTGAGAAATGCTATTGTTTGGAAATTTTGGGCCTCGCCATTTTAAT

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 95.20% 4.50% 0.02% 0.00% T: 0.21%
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 86.10% 13.80% 0.07% 0.00% NA
Aus  269 96.30% 0.00% 0.00% 0.00% T: 3.72%
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 73.10% 26.70% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0400468558 G -> A LOC_Os04g01690.1 downstream_gene_variant ; 1274.0bp to feature; MODIFIER silent_mutation Average:71.21; most accessible tissue: Callus, score: 85.873 N N N N
vg0400468558 G -> A LOC_Os04g01710.1 downstream_gene_variant ; 2542.0bp to feature; MODIFIER silent_mutation Average:71.21; most accessible tissue: Callus, score: 85.873 N N N N
vg0400468558 G -> A LOC_Os04g01690.2 downstream_gene_variant ; 1274.0bp to feature; MODIFIER silent_mutation Average:71.21; most accessible tissue: Callus, score: 85.873 N N N N
vg0400468558 G -> A LOC_Os04g01690.3 downstream_gene_variant ; 1274.0bp to feature; MODIFIER silent_mutation Average:71.21; most accessible tissue: Callus, score: 85.873 N N N N
vg0400468558 G -> A LOC_Os04g01690-LOC_Os04g01710 intergenic_region ; MODIFIER silent_mutation Average:71.21; most accessible tissue: Callus, score: 85.873 N N N N
vg0400468558 G -> T LOC_Os04g01690.1 downstream_gene_variant ; 1274.0bp to feature; MODIFIER silent_mutation Average:71.21; most accessible tissue: Callus, score: 85.873 N N N N
vg0400468558 G -> T LOC_Os04g01710.1 downstream_gene_variant ; 2542.0bp to feature; MODIFIER silent_mutation Average:71.21; most accessible tissue: Callus, score: 85.873 N N N N
vg0400468558 G -> T LOC_Os04g01690.2 downstream_gene_variant ; 1274.0bp to feature; MODIFIER silent_mutation Average:71.21; most accessible tissue: Callus, score: 85.873 N N N N
vg0400468558 G -> T LOC_Os04g01690.3 downstream_gene_variant ; 1274.0bp to feature; MODIFIER silent_mutation Average:71.21; most accessible tissue: Callus, score: 85.873 N N N N
vg0400468558 G -> T LOC_Os04g01690-LOC_Os04g01710 intergenic_region ; MODIFIER silent_mutation Average:71.21; most accessible tissue: Callus, score: 85.873 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0400468558 7.61E-09 NA mr1210 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
vg0400468558 1.91E-07 1.68E-07 mr1210 Jap_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
vg0400468558 1.15E-08 NA mr1305 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
vg0400468558 1.40E-06 8.40E-07 mr1305 Jap_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
vg0400468558 3.16E-06 NA mr1585 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
vg0400468558 8.88E-10 NA mr1586 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
vg0400468558 5.90E-07 1.99E-07 mr1586 Jap_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
vg0400468558 2.35E-09 NA mr1670 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
vg0400468558 2.81E-07 2.81E-07 mr1670 Jap_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
vg0400468558 2.77E-10 NA mr1672 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
vg0400468558 1.27E-06 1.72E-06 mr1672 Jap_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
vg0400468558 5.74E-08 NA mr1305_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
vg0400468558 1.56E-06 1.15E-06 mr1305_2 Jap_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
vg0400468558 5.83E-10 2.09E-07 mr1585_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
vg0400468558 7.35E-08 1.82E-07 mr1585_2 Jap_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
vg0400468558 3.67E-22 NA mr1670_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
vg0400468558 5.59E-13 5.59E-13 mr1670_2 Jap_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
vg0400468558 2.11E-27 NA mr1672_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
vg0400468558 5.50E-19 1.58E-15 mr1672_2 Jap_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
vg0400468558 1.67E-06 NA mr1765_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
vg0400468558 8.73E-06 5.28E-06 mr1765_2 Jap_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