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Detailed information for vg1126331556:

Variant ID: vg1126331556 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 26331556
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


CTTTGGGACGTAGTATTTGAAAAACACAAAAATGGGATAAATGCACGAATATGATGTCATGCATTATTGCATCCCAAAGGAAAAAAGTCCAGAGGCATTT[G/A]
CAAAACATTTTTTTAACCCGATAGGAAAAAACATAGGAATTCTAGAGACAACTAGGGGAAACCATGAGTTAAGACCTAATGTTAGTTTTCCTCCAAAACA

Reverse complement sequence

TGTTTTGGAGGAAAACTAACATTAGGTCTTAACTCATGGTTTCCCCTAGTTGTCTCTAGAATTCCTATGTTTTTTCCTATCGGGTTAAAAAAATGTTTTG[C/T]
AAATGCCTCTGGACTTTTTTCCTTTGGGATGCAATAATGCATGACATCATATTCGTGCATTTATCCCATTTTTGTGTTTTTCAAATACTACGTCCCAAAG

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 80.20% 19.70% 0.04% 0.00% NA
All Indica  2759 72.10% 27.80% 0.07% 0.00% NA
All Japonica  1512 98.30% 1.70% 0.00% 0.00% NA
Aus  269 53.50% 46.50% 0.00% 0.00% NA
Indica I  595 38.50% 61.50% 0.00% 0.00% NA
Indica II  465 83.20% 16.80% 0.00% 0.00% NA
Indica III  913 76.80% 23.10% 0.11% 0.00% NA
Indica Intermediate  786 85.60% 14.20% 0.13% 0.00% NA
Temperate Japonica  767 99.10% 0.90% 0.00% 0.00% NA
Tropical Japonica  504 98.60% 1.40% 0.00% 0.00% NA
Japonica Intermediate  241 95.00% 5.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 84.40% 15.60% 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
vg1126331556 G -> A LOC_Os11g43650.1 downstream_gene_variant ; 1099.0bp to feature; MODIFIER silent_mutation Average:29.868; most accessible tissue: Callus, score: 61.627 N N N N
vg1126331556 G -> A LOC_Os11g43650-LOC_Os11g43660 intergenic_region ; MODIFIER silent_mutation Average:29.868; most accessible tissue: Callus, score: 61.627 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1126331556 7.89E-09 7.94E-15 mr1191 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
vg1126331556 9.30E-10 7.42E-11 mr1191 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
vg1126331556 4.79E-09 1.23E-15 mr1644 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
vg1126331556 4.92E-09 3.24E-11 mr1644 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
vg1126331556 NA 4.77E-12 mr1662 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
vg1126331556 NA 3.27E-10 mr1662 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
vg1126331556 2.45E-08 4.35E-22 mr1191_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
vg1126331556 5.58E-08 2.74E-14 mr1191_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
vg1126331556 5.23E-06 9.47E-10 mr1530_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
vg1126331556 NA 5.60E-11 mr1662_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
vg1126331556 5.18E-06 1.24E-12 mr1662_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
vg1126331556 NA 1.05E-10 mr1745_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