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Detailed information for vg0919164093:

Variant ID: vg0919164093 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 19164093
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACTGTACTAGTGTAATGGTAGAAATCAAATTTAAACCGTGTTAGCCTGGCAATTTTAAATGCTAGTTAACTTGTATTTAACTATAATATAACTTGTATAT[A/G]
GCTTTTAAAAATCCAATGGTCGTAAAACGGAGGTCGTGGGACCGAATCCCCTCATCTATGCCCATGCTGTGATTTTTTTTCCTTCCTAGTTTGCGCGAAT

Reverse complement sequence

ATTCGCGCAAACTAGGAAGGAAAAAAAATCACAGCATGGGCATAGATGAGGGGATTCGGTCCCACGACCTCCGTTTTACGACCATTGGATTTTTAAAAGC[T/C]
ATATACAAGTTATATTATAGTTAAATACAAGTTAACTAGCATTTAAAATTGCCAGGCTAACACGGTTTAAATTTGATTTCTACCATTACACTAGTACAGT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 84.00% 15.90% 0.15% 0.00% NA
All Indica  2759 72.70% 27.00% 0.25% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 74.10% 25.90% 0.00% 0.00% NA
Indica II  465 83.40% 15.90% 0.65% 0.00% NA
Indica III  913 67.80% 31.90% 0.33% 0.00% NA
Indica Intermediate  786 71.10% 28.80% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0919164093 A -> G LOC_Os09g32095.1 upstream_gene_variant ; 4602.0bp to feature; MODIFIER silent_mutation Average:44.473; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N
vg0919164093 A -> G LOC_Os09g32100.1 upstream_gene_variant ; 2257.0bp to feature; MODIFIER silent_mutation Average:44.473; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N
vg0919164093 A -> G LOC_Os09g32095-LOC_Os09g32100 intergenic_region ; MODIFIER silent_mutation Average:44.473; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0919164093 NA 8.31E-06 mr1002 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
vg0919164093 NA 4.28E-06 mr1138 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
vg0919164093 NA 3.77E-06 mr1607 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
vg0919164093 NA 4.63E-13 mr1707 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
vg0919164093 NA 6.23E-08 mr1707 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
vg0919164093 NA 1.38E-13 mr1728 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
vg0919164093 NA 2.84E-08 mr1728 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
vg0919164093 NA 4.78E-10 mr1860 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
vg0919164093 NA 2.83E-06 mr1860 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
vg0919164093 NA 6.28E-10 mr1707_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
vg0919164093 NA 2.82E-11 mr1728_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
vg0919164093 NA 1.34E-08 mr1860_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