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Detailed information for vg1119581692:

Variant ID: vg1119581692 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 19581692
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


TGTGATATAAACATGTGATTGTCACACGTAACTTTAATTAGAATAAACCTTTGTGGTGAGGAGGCCTCTAATTTGGCAGCCCAACATCTGAGAGCTCTCC[C/T]
GATCAACATACCTTTAGCGATGATGCTGGTTACATACTGTCACAATTATATTGTTGCCATGCTATGTATAAATGATGGATCAATGCTTATTGTTTATAAT

Reverse complement sequence

ATTATAAACAATAAGCATTGATCCATCATTTATACATAGCATGGCAACAATATAATTGTGACAGTATGTAACCAGCATCATCGCTAAAGGTATGTTGATC[G/A]
GGAGAGCTCTCAGATGTTGGGCTGCCAAATTAGAGGCCTCCTCACCACAAAGGTTTATTCTAATTAAAGTTACGTGTGACAATCACATGTTTATATCACA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.90% 1.80% 0.25% 0.00% NA
All Indica  2759 99.70% 0.20% 0.04% 0.00% NA
All Japonica  1512 94.00% 5.20% 0.73% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 97.30% 1.80% 0.91% 0.00% NA
Tropical Japonica  504 93.10% 6.70% 0.20% 0.00% NA
Japonica Intermediate  241 85.90% 12.90% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg1119581692 C -> T LOC_Os11g33110.1 upstream_gene_variant ; 3975.0bp to feature; MODIFIER silent_mutation Average:64.181; most accessible tissue: Callus, score: 82.87 N N N N
vg1119581692 C -> T LOC_Os11g33100.1 intron_variant ; MODIFIER silent_mutation Average:64.181; most accessible tissue: Callus, score: 82.87 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1119581692 NA 3.43E-06 mr1117 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
vg1119581692 2.03E-07 NA mr1679 Jap_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
vg1119581692 NA 1.06E-06 mr1720 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
vg1119581692 8.93E-06 NA mr1079_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
vg1119581692 4.49E-07 1.35E-08 mr1113_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
vg1119581692 NA 8.42E-07 mr1117_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
vg1119581692 NA 5.01E-06 mr1119_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
vg1119581692 NA 9.14E-06 mr1240_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
vg1119581692 NA 8.91E-07 mr1496_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
vg1119581692 NA 2.16E-08 mr1750_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