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Detailed information for vg0131651142:

Variant ID: vg0131651142 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 31651142
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


GTTTTATGGTTCAAGTTGTAGAAAACCACACACATTTTAACACTTGGCACTTAAGTATATATATTTTGGTAGTTTAGTTTCACAAAACCACACTATCCAT[G/T]
AATGGATTTACCCGCGAGATGACGTGGTTGTTCCATCTAGGATGGGGACGTGGCATCCTGTTAATTTTGTCTGATGGCTGGTAATATGATGCCATGTCCT

Reverse complement sequence

AGGACATGGCATCATATTACCAGCCATCAGACAAAATTAACAGGATGCCACGTCCCCATCCTAGATGGAACAACCACGTCATCTCGCGGGTAAATCCATT[C/A]
ATGGATAGTGTGGTTTTGTGAAACTAAACTACCAAAATATATATACTTAAGTGCCAAGTGTTAAAATGTGTGTGGTTTTCTACAACTTGAACCATAAAAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.70% 10.60% 0.70% 0.00% NA
All Indica  2759 80.60% 18.20% 1.20% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.10% 3.00% 0.84% 0.00% NA
Indica II  465 96.30% 3.70% 0.00% 0.00% NA
Indica III  913 62.80% 36.70% 0.55% 0.00% NA
Indica Intermediate  786 80.30% 16.80% 2.93% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0131651142 G -> T LOC_Os01g55040.1 upstream_gene_variant ; 2386.0bp to feature; MODIFIER silent_mutation Average:79.97; most accessible tissue: Zhenshan97 root, score: 91.517 N N N N
vg0131651142 G -> T LOC_Os01g55050.1 downstream_gene_variant ; 474.0bp to feature; MODIFIER silent_mutation Average:79.97; most accessible tissue: Zhenshan97 root, score: 91.517 N N N N
vg0131651142 G -> T LOC_Os01g55050.2 downstream_gene_variant ; 474.0bp to feature; MODIFIER silent_mutation Average:79.97; most accessible tissue: Zhenshan97 root, score: 91.517 N N N N
vg0131651142 G -> T LOC_Os01g55040-LOC_Os01g55050 intergenic_region ; MODIFIER silent_mutation Average:79.97; most accessible tissue: Zhenshan97 root, score: 91.517 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0131651142 5.00E-06 NA mr1973 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
vg0131651142 2.03E-06 1.19E-06 mr1973 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
vg0131651142 6.97E-06 NA mr1970_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
vg0131651142 6.75E-08 NA mr1973_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
vg0131651142 2.97E-09 7.78E-08 mr1973_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