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Detailed information for vg1109007680:

Variant ID: vg1109007680 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 9007680
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAAAACACATTTTCCTTACTAGATATTAGTTAGGTATGCATCAACTAATACCTGCTTCTAGCATCCGAATATATTCCCAAAAGACATAAACAACAGGGAT[G/A]
TAAAATTTTGCTTGCAAGATCCATTTATTAACATATGTAATTTAGCGCTAAATGAAATGTTTTATCGCAAATAACTTTGCAGCTGGGCACTCGAAGACAG

Reverse complement sequence

CTGTCTTCGAGTGCCCAGCTGCAAAGTTATTTGCGATAAAACATTTCATTTAGCGCTAAATTACATATGTTAATAAATGGATCTTGCAAGCAAAATTTTA[C/T]
ATCCCTGTTGTTTATGTCTTTTGGGAATATATTCGGATGCTAGAAGCAGGTATTAGTTGATGCATACCTAACTAATATCTAGTAAGGAAAATGTGTTTTT

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 78.80% 21.20% 0.00% 0.00% NA
All Indica  2759 69.90% 30.10% 0.00% 0.00% NA
All Japonica  1512 93.10% 6.90% 0.00% 0.00% NA
Aus  269 86.20% 13.80% 0.00% 0.00% NA
Indica I  595 72.30% 27.70% 0.00% 0.00% NA
Indica II  465 82.20% 17.80% 0.00% 0.00% NA
Indica III  913 61.80% 38.20% 0.00% 0.00% NA
Indica Intermediate  786 70.40% 29.60% 0.00% 0.00% NA
Temperate Japonica  767 98.40% 1.60% 0.00% 0.00% NA
Tropical Japonica  504 84.90% 15.10% 0.00% 0.00% NA
Japonica Intermediate  241 93.40% 6.60% 0.00% 0.00% NA
VI/Aromatic  96 86.50% 13.50% 0.00% 0.00% NA
Intermediate  90 77.80% 22.20% 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
vg1109007680 G -> A LOC_Os11g16320.1 downstream_gene_variant ; 2686.0bp to feature; MODIFIER silent_mutation Average:52.906; most accessible tissue: Callus, score: 80.824 N N N N
vg1109007680 G -> A LOC_Os11g16330.3 downstream_gene_variant ; 1591.0bp to feature; MODIFIER silent_mutation Average:52.906; most accessible tissue: Callus, score: 80.824 N N N N
vg1109007680 G -> A LOC_Os11g16330.1 intron_variant ; MODIFIER silent_mutation Average:52.906; most accessible tissue: Callus, score: 80.824 N N N N
vg1109007680 G -> A LOC_Os11g16330.4 intron_variant ; MODIFIER silent_mutation Average:52.906; most accessible tissue: Callus, score: 80.824 N N N N
vg1109007680 G -> A LOC_Os11g16330.2 intron_variant ; MODIFIER silent_mutation Average:52.906; most accessible tissue: Callus, score: 80.824 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1109007680 NA 6.23E-08 mr1188 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
vg1109007680 NA 8.22E-06 mr1306 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
vg1109007680 3.53E-06 NA mr1804 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
vg1109007680 NA 1.03E-07 mr1188_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
vg1109007680 NA 3.77E-06 mr1217_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
vg1109007680 NA 7.30E-06 mr1850_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