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Detailed information for vg0506936871:

Variant ID: vg0506936871 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 6936871
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.81, A: 0.19, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTTAAAATGAATATCGCTAATATGTCCACAGCCAAACAGTTCAACGTTAGAGGGAAATCTAATCTCAGCATTCCCCTTTATTGTGTACCGTAGAAAAC[G/A]
TCCAGAGATAATTTAGTAGATAAAGAGTTTTGATATGATTTATATTGCATATAACATCCTAGGAAATACAGACAAGCGGACATGTAAAACAATACAAGAT

Reverse complement sequence

ATCTTGTATTGTTTTACATGTCCGCTTGTCTGTATTTCCTAGGATGTTATATGCAATATAAATCATATCAAAACTCTTTATCTACTAAATTATCTCTGGA[C/T]
GTTTTCTACGGTACACAATAAAGGGGAATGCTGAGATTAGATTTCCCTCTAACGTTGAACTGTTTGGCTGTGGACATATTAGCGATATTCATTTTAAAAA

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 58.00% 41.90% 0.04% 0.00% NA
All Indica  2759 88.40% 11.50% 0.07% 0.00% NA
All Japonica  1512 4.80% 95.20% 0.00% 0.00% NA
Aus  269 71.00% 29.00% 0.00% 0.00% NA
Indica I  595 95.80% 4.20% 0.00% 0.00% NA
Indica II  465 80.00% 20.00% 0.00% 0.00% NA
Indica III  913 89.00% 10.70% 0.22% 0.00% NA
Indica Intermediate  786 87.00% 13.00% 0.00% 0.00% NA
Temperate Japonica  767 1.60% 98.40% 0.00% 0.00% NA
Tropical Japonica  504 5.60% 94.40% 0.00% 0.00% NA
Japonica Intermediate  241 13.30% 86.70% 0.00% 0.00% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 44.40% 55.60% 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
vg0506936871 G -> A LOC_Os05g12140.1 3_prime_UTR_variant ; 423.0bp to feature; MODIFIER silent_mutation Average:61.421; most accessible tissue: Callus, score: 80.654 N N N N
vg0506936871 G -> A LOC_Os05g12140.2 3_prime_UTR_variant ; 423.0bp to feature; MODIFIER silent_mutation Average:61.421; most accessible tissue: Callus, score: 80.654 N N N N
vg0506936871 G -> A LOC_Os05g12130.1 downstream_gene_variant ; 280.0bp to feature; MODIFIER silent_mutation Average:61.421; most accessible tissue: Callus, score: 80.654 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0506936871 2.52E-11 9.22E-41 mr1039 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
vg0506936871 5.70E-08 5.13E-10 mr1039 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
vg0506936871 NA 2.55E-11 mr1514 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
vg0506936871 NA 2.72E-08 mr1593 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
vg0506936871 2.52E-09 1.66E-42 mr1632 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
vg0506936871 5.28E-07 5.72E-13 mr1632 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
vg0506936871 7.91E-10 3.76E-49 mr1873 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
vg0506936871 NA 3.75E-10 mr1873 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
vg0506936871 NA 1.66E-10 mr1904 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
vg0506936871 NA 4.28E-12 mr1940 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
vg0506936871 7.30E-13 3.90E-44 mr1039_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
vg0506936871 1.34E-09 3.81E-11 mr1039_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
vg0506936871 1.68E-09 1.36E-19 mr1514_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
vg0506936871 2.21E-06 2.00E-07 mr1514_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
vg0506936871 NA 1.14E-07 mr1593_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
vg0506936871 1.11E-16 9.89E-58 mr1632_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
vg0506936871 1.39E-12 1.19E-16 mr1632_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
vg0506936871 1.76E-08 1.85E-40 mr1873_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
vg0506936871 2.62E-06 1.76E-08 mr1873_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