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Detailed information for vg1115487596:

Variant ID: vg1115487596 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 15487596
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:


AGGTGAAACATCTTTTTGGAAAAAGGAGAGGGACAAGTGGGTGGGTCCAACAGATGAGCACGTGGGGGAGGGGGAGGGACCGATTTTCCCACCTCCCCCG[G/A]
TCAACCGATGCTGGGCATTCTCCTATATTAAGGGCACGGCTAAATCAATAATTAGCACACATTTAATGGGCCGGGTCAATGTTTGCTTGGCAAATCCAAT

Reverse complement sequence

ATTGGATTTGCCAAGCAAACATTGACCCGGCCCATTAAATGTGTGCTAATTATTGATTTAGCCGTGCCCTTAATATAGGAGAATGCCCAGCATCGGTTGA[C/T]
CGGGGGAGGTGGGAAAATCGGTCCCTCCCCCTCCCCCACGTGCTCATCTGTTGGACCCACCCACTTGTCCCTCTCCTTTTTCCAAAAAGATGTTTCACCT

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 69.30% 30.40% 0.28% 0.08% NA
All Indica  2759 52.60% 46.80% 0.47% 0.14% NA
All Japonica  1512 99.30% 0.70% 0.00% 0.00% NA
Aus  269 60.20% 39.80% 0.00% 0.00% NA
Indica I  595 23.00% 76.60% 0.34% 0.00% NA
Indica II  465 63.00% 36.30% 0.65% 0.00% NA
Indica III  913 61.00% 38.20% 0.55% 0.22% NA
Indica Intermediate  786 58.90% 40.50% 0.38% 0.25% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 98.60% 1.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 72.20% 27.80% 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
vg1115487596 G -> A LOC_Os11g26930.1 downstream_gene_variant ; 368.0bp to feature; MODIFIER silent_mutation Average:68.112; most accessible tissue: Zhenshan97 root, score: 78.04 N N N N
vg1115487596 G -> A LOC_Os11g26940.1 downstream_gene_variant ; 4092.0bp to feature; MODIFIER silent_mutation Average:68.112; most accessible tissue: Zhenshan97 root, score: 78.04 N N N N
vg1115487596 G -> A LOC_Os11g26930-LOC_Os11g26940 intergenic_region ; MODIFIER silent_mutation Average:68.112; most accessible tissue: Zhenshan97 root, score: 78.04 N N N N
vg1115487596 G -> DEL N N silent_mutation Average:68.112; most accessible tissue: Zhenshan97 root, score: 78.04 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1115487596 NA 6.63E-06 mr1077 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
vg1115487596 8.76E-06 2.77E-12 mr1097 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
vg1115487596 NA 1.08E-07 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
vg1115487596 NA 4.09E-06 mr1149 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
vg1115487596 NA 4.13E-07 mr1154 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
vg1115487596 NA 1.25E-07 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
vg1115487596 2.14E-08 6.41E-17 mr1097_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
vg1115487596 1.40E-07 1.32E-11 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
vg1115487596 3.34E-08 NA mr1102_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
vg1115487596 2.14E-06 9.47E-08 mr1102_2 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
vg1115487596 NA 1.87E-07 mr1152_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
vg1115487596 6.19E-09 NA mr1154_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
vg1115487596 3.65E-09 1.13E-14 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
vg1115487596 1.21E-07 NA mr1223_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
vg1115487596 6.99E-06 1.06E-06 mr1223_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