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Detailed information for vg1115413712:

Variant ID: vg1115413712 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 15413712
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGAGGAAGAGTGGAAGAGAAGTATGACAGGTGGGTCCCAGATTTTTTTATAAATAAAATCCTGACTGGACTGCCACGCGTACGCCACGTAAGACAAAACT[G/A]
TTCTGGATTGGGTCGAGGGGGGTAATTTATCTGGTATCGAAAGTTCAGGGTGAACGATGTCTGATTTTCGGGTTTAGAGAGGTAATTCGGTCGTCCGTAA

Reverse complement sequence

TTACGGACGACCGAATTACCTCTCTAAACCCGAAAATCAGACATCGTTCACCCTGAACTTTCGATACCAGATAAATTACCCCCCTCGACCCAATCCAGAA[C/T]
AGTTTTGTCTTACGTGGCGTACGCGTGGCAGTCCAGTCAGGATTTTATTTATAAAAAAATCTGGGACCCACCTGTCATACTTCTCTTCCACTCTTCCTCT

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 90.90% 9.10% 0.00% 0.00% NA
All Indica  2759 93.00% 7.00% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 17.80% 82.20% 0.00% 0.00% NA
Indica I  595 81.50% 18.50% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 97.00% 3.00% 0.00% 0.00% NA
Indica Intermediate  786 93.30% 6.70% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg1115413712 G -> A LOC_Os11g26830.1 upstream_gene_variant ; 4442.0bp to feature; MODIFIER silent_mutation Average:52.247; most accessible tissue: Callus, score: 69.541 N N N N
vg1115413712 G -> A LOC_Os11g26840.1 upstream_gene_variant ; 4919.0bp to feature; MODIFIER silent_mutation Average:52.247; most accessible tissue: Callus, score: 69.541 N N N N
vg1115413712 G -> A LOC_Os11g26830-LOC_Os11g26840 intergenic_region ; MODIFIER silent_mutation Average:52.247; most accessible tissue: Callus, score: 69.541 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1115413712 2.92E-07 NA mr1154 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
vg1115413712 3.53E-07 1.33E-06 mr1154 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
vg1115413712 NA 1.22E-07 mr1343 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
vg1115413712 1.17E-07 NA 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
vg1115413712 1.03E-09 9.99E-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
vg1115413712 4.59E-07 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
vg1115413712 1.22E-10 2.81E-10 mr1154_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
vg1115413712 NA 3.72E-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