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Detailed information for vg0142903531:

Variant ID: vg0142903531 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 42903531
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAAAAGATAATAACTCTCTCATACTATATTTACTCTAGCAACAAACTCGATGCATGCACCATCCCCAATATTTCCTAGCCAATAGCAAATCAAGATATTG[C/T]
ATGTGGGTTATAAATACTTGTGTGCATGGATACATGCATCAATGTCTATTTACTCCAATACACAAATAACGAATAGACTTAATAAATGAACACAAATATG

Reverse complement sequence

CATATTTGTGTTCATTTATTAAGTCTATTCGTTATTTGTGTATTGGAGTAAATAGACATTGATGCATGTATCCATGCACACAAGTATTTATAACCCACAT[G/A]
CAATATCTTGATTTGCTATTGGCTAGGAAATATTGGGGATGGTGCATGCATCGAGTTTGTTGCTAGAGTAAATATAGTATGAGAGAGTTATTATCTTTTC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.90% 7.00% 0.04% 0.00% NA
All Indica  2759 88.00% 12.00% 0.07% 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 76.10% 23.90% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 87.20% 12.80% 0.00% 0.00% NA
Indica Intermediate  786 91.00% 8.80% 0.25% 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 96.70% 3.30% 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
vg0142903531 C -> T LOC_Os01g74090.1 upstream_gene_variant ; 1512.0bp to feature; MODIFIER silent_mutation Average:46.738; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N
vg0142903531 C -> T LOC_Os01g74100.1 upstream_gene_variant ; 854.0bp to feature; MODIFIER silent_mutation Average:46.738; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N
vg0142903531 C -> T LOC_Os01g74080.1 downstream_gene_variant ; 3608.0bp to feature; MODIFIER silent_mutation Average:46.738; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N
vg0142903531 C -> T LOC_Os01g74110.1 downstream_gene_variant ; 2035.0bp to feature; MODIFIER silent_mutation Average:46.738; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N
vg0142903531 C -> T LOC_Os01g74090-LOC_Os01g74100 intergenic_region ; MODIFIER silent_mutation Average:46.738; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0142903531 NA 1.39E-06 mr1641 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
vg0142903531 NA 4.43E-07 mr1839 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
vg0142903531 NA 8.20E-06 mr1959 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
vg0142903531 NA 3.99E-06 mr1013_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
vg0142903531 NA 2.27E-06 mr1015_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
vg0142903531 NA 7.04E-06 mr1031_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
vg0142903531 4.45E-06 4.45E-06 mr1049_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
vg0142903531 NA 6.36E-07 mr1543_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
vg0142903531 3.69E-06 8.70E-09 mr1904_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