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Detailed information for vg0105134457:

Variant ID: vg0105134457 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 5134457
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.06, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


GACTGCAAGTTCCCTGTTCCTATTGACTTGCAGAGTCCAGACTCTAAAGATCAGTAGATAGCCATCTACTATCTTCAAATTATCTATAGTTAATGTAATA[A/G]
TCAATTCATACAATAGTTGCTTACTATACTATTAATACCTGGTCTCATCTGTCATACACACATTATGTCTTAGAGTCTGTGCTGCAGCTGGCTACATATC

Reverse complement sequence

GATATGTAGCCAGCTGCAGCACAGACTCTAAGACATAATGTGTGTATGACAGATGAGACCAGGTATTAATAGTATAGTAAGCAACTATTGTATGAATTGA[T/C]
TATTACATTAACTATAGATAATTTGAAGATAGTAGATGGCTATCTACTGATCTTTAGAGTCTGGACTCTGCAAGTCAATAGGAACAGGGAACTTGCAGTC

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 73.90% 25.80% 0.32% 0.00% NA
All Indica  2759 75.40% 24.10% 0.47% 0.00% NA
All Japonica  1512 77.20% 22.80% 0.00% 0.00% NA
Aus  269 33.80% 65.80% 0.37% 0.00% NA
Indica I  595 28.20% 71.30% 0.50% 0.00% NA
Indica II  465 97.00% 2.60% 0.43% 0.00% NA
Indica III  913 97.50% 2.30% 0.22% 0.00% NA
Indica Intermediate  786 72.60% 26.60% 0.76% 0.00% NA
Temperate Japonica  767 85.00% 15.00% 0.00% 0.00% NA
Tropical Japonica  504 63.10% 36.90% 0.00% 0.00% NA
Japonica Intermediate  241 81.70% 18.30% 0.00% 0.00% NA
VI/Aromatic  96 81.20% 18.80% 0.00% 0.00% NA
Intermediate  90 85.60% 13.30% 1.11% 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
vg0105134457 A -> G LOC_Os01g09880.1 upstream_gene_variant ; 1539.0bp to feature; MODIFIER silent_mutation Average:67.978; most accessible tissue: Callus, score: 97.824 N N N N
vg0105134457 A -> G LOC_Os01g09890.1 downstream_gene_variant ; 4006.0bp to feature; MODIFIER silent_mutation Average:67.978; most accessible tissue: Callus, score: 97.824 N N N N
vg0105134457 A -> G LOC_Os01g09880-LOC_Os01g09890 intergenic_region ; MODIFIER silent_mutation Average:67.978; most accessible tissue: Callus, score: 97.824 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0105134457 4.98E-16 8.65E-22 mr1057 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
vg0105134457 1.37E-14 2.01E-20 mr1057 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
vg0105134457 NA 5.85E-07 mr1272 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
vg0105134457 NA 4.56E-07 mr1574 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
vg0105134457 NA 9.73E-09 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
vg0105134457 NA 7.58E-10 mr1677 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
vg0105134457 NA 2.47E-06 mr1677 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
vg0105134457 NA 1.49E-07 mr1745 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
vg0105134457 NA 9.72E-07 mr1951 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
vg0105134457 3.88E-11 4.86E-16 mr1057_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
vg0105134457 9.02E-18 3.77E-23 mr1057_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
vg0105134457 NA 3.45E-07 mr1120_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
vg0105134457 NA 9.78E-06 mr1137_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
vg0105134457 NA 1.17E-06 mr1295_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
vg0105134457 NA 3.22E-07 mr1659_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
vg0105134457 NA 1.56E-07 mr1805_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