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Detailed information for vg0135235698:

Variant ID: vg0135235698 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 35235698
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATATTGGAAGACGAGTCTAGAATCCATATAGGAATACAATTTAGAAATAACTAAAATTTGATATTAAAAATAATTAATAACTATCACGTATATACAATAC[G/A]
GTATGAATATTACACAATGGTAGTTTGGTAAAGTTAGTAAAAAATTTAAAATTATGTCATCATTTTAATATATTTTAATAATAAATTGAGAAAACATATA

Reverse complement sequence

TATATGTTTTCTCAATTTATTATTAAAATATATTAAAATGATGACATAATTTTAAATTTTTTACTAACTTTACCAAACTACCATTGTGTAATATTCATAC[C/T]
GTATTGTATATACGTGATAGTTATTAATTATTTTTAATATCAAATTTTAGTTATTTCTAAATTGTATTCCTATATGGATTCTAGACTCGTCTTCCAATAT

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 94.80% 4.40% 0.74% 0.00% NA
All Indica  2759 99.90% 0.00% 0.04% 0.00% NA
All Japonica  1512 84.30% 13.60% 2.12% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.10% 0.13% 0.00% NA
Temperate Japonica  767 77.40% 19.20% 3.39% 0.00% NA
Tropical Japonica  504 97.60% 2.40% 0.00% 0.00% NA
Japonica Intermediate  241 78.00% 19.50% 2.49% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 1.10% 2.22% 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
vg0135235698 G -> A LOC_Os01g60920.1 upstream_gene_variant ; 2366.0bp to feature; MODIFIER silent_mutation Average:42.125; most accessible tissue: Callus, score: 58.219 N N N N
vg0135235698 G -> A LOC_Os01g60910.1 downstream_gene_variant ; 3965.0bp to feature; MODIFIER silent_mutation Average:42.125; most accessible tissue: Callus, score: 58.219 N N N N
vg0135235698 G -> A LOC_Os01g60910.2 downstream_gene_variant ; 1325.0bp to feature; MODIFIER silent_mutation Average:42.125; most accessible tissue: Callus, score: 58.219 N N N N
vg0135235698 G -> A LOC_Os01g60910-LOC_Os01g60920 intergenic_region ; MODIFIER silent_mutation Average:42.125; most accessible tissue: Callus, score: 58.219 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0135235698 NA 4.95E-06 mr1070 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
vg0135235698 4.46E-06 2.25E-07 mr1097 Jap_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
vg0135235698 NA 4.93E-06 mr1154 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