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Detailed information for vg1125239418:

Variant ID: vg1125239418 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25239418
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:


GGTGCAGCAGCAGGAACGGTGCCCAGAGTGCCAACAGCTCATGCTCTGGTGACCTGCTGGTAACAGAGAGGTGGCCAAGCACGTAGATCGCTGTCCCGTC[G/A]
GCCAGCATGTATGCGGACCATATAAAGGCCCTTAGCACGCCAGAGTCAATGTACCGGCGGAATTCTGCCAAGATGAGGAGTGTGACTTGGACCATGAGGC

Reverse complement sequence

GCCTCATGGTCCAAGTCACACTCCTCATCTTGGCAGAATTCCGCCGGTACATTGACTCTGGCGTGCTAAGGGCCTTTATATGGTCCGCATACATGCTGGC[C/T]
GACGGGACAGCGATCTACGTGCTTGGCCACCTCTCTGTTACCAGCAGGTCACCAGAGCATGAGCTGTTGGCACTCTGGGCACCGTTCCTGCTGCTGCACC

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 61.90% 7.40% 2.31% 28.37% NA
All Indica  2759 55.40% 1.20% 3.37% 40.09% NA
All Japonica  1512 68.70% 19.20% 0.60% 11.51% NA
Aus  269 74.70% 7.10% 1.49% 16.73% NA
Indica I  595 40.00% 1.30% 4.87% 53.78% NA
Indica II  465 94.40% 0.20% 0.43% 4.95% NA
Indica III  913 45.70% 1.50% 3.94% 48.85% NA
Indica Intermediate  786 55.20% 1.10% 3.31% 40.33% NA
Temperate Japonica  767 93.60% 4.00% 0.13% 2.22% NA
Tropical Japonica  504 26.80% 46.00% 1.39% 25.79% NA
Japonica Intermediate  241 76.80% 11.60% 0.41% 11.20% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 74.40% 4.40% 3.33% 17.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1125239418 G -> A LOC_Os11g41970.1 upstream_gene_variant ; 4227.0bp to feature; MODIFIER silent_mutation Average:15.283; most accessible tissue: Callus, score: 72.039 N N N N
vg1125239418 G -> A LOC_Os11g41970-LOC_Os11g41990 intergenic_region ; MODIFIER silent_mutation Average:15.283; most accessible tissue: Callus, score: 72.039 N N N N
vg1125239418 G -> DEL N N silent_mutation Average:15.283; most accessible tissue: Callus, score: 72.039 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125239418 2.69E-07 NA mr1238 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
vg1125239418 NA 4.49E-08 mr1248 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
vg1125239418 NA 3.63E-09 mr1249 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
vg1125239418 NA 4.46E-06 mr1328 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
vg1125239418 1.31E-06 NA mr1484 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
vg1125239418 2.09E-07 NA 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
vg1125239418 NA 1.38E-07 mr1662 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
vg1125239418 3.25E-06 NA mr1238_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
vg1125239418 5.53E-06 NA mr1484_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
vg1125239418 1.00E-07 NA mr1662_2 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
vg1125239418 4.48E-07 3.17E-09 mr1662_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