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Detailed information for vg0130922613:

Variant ID: vg0130922613 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 30922613
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


CTACCAACATATAGTCAAAATGTGAAATTGTAGTAAAGTATGTTCTAGATGATGCCAAATCTAGATTAGGTATTACCAATGAATGGGCTTCAATCCAAAT[C/T]
AAACACAACTACTATTCAAATTACCAAAATATTGGTAGGGCATGTTTTTGGTAACAATCCAAATAGGCCCTTAATTTTTTTACCACCTAATCCGCAATGC

Reverse complement sequence

GCATTGCGGATTAGGTGGTAAAAAAATTAAGGGCCTATTTGGATTGTTACCAAAAACATGCCCTACCAATATTTTGGTAATTTGAATAGTAGTTGTGTTT[G/A]
ATTTGGATTGAAGCCCATTCATTGGTAATACCTAATCTAGATTTGGCATCATCTAGAACATACTTTACTACAATTTCACATTTTGACTATATGTTGGTAG

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 91.00% 9.00% 0.00% 0.00% NA
All Indica  2759 84.60% 15.40% 0.00% 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 96.00% 4.00% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 69.30% 30.70% 0.00% 0.00% NA
Indica Intermediate  786 85.20% 14.80% 0.00% 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 97.80% 2.20% 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
vg0130922613 C -> T LOC_Os01g53790.1 downstream_gene_variant ; 1272.0bp to feature; MODIFIER silent_mutation Average:54.523; most accessible tissue: Minghui63 panicle, score: 71.773 N N N N
vg0130922613 C -> T LOC_Os01g53800.1 downstream_gene_variant ; 156.0bp to feature; MODIFIER silent_mutation Average:54.523; most accessible tissue: Minghui63 panicle, score: 71.773 N N N N
vg0130922613 C -> T LOC_Os01g53790-LOC_Os01g53800 intergenic_region ; MODIFIER silent_mutation Average:54.523; most accessible tissue: Minghui63 panicle, score: 71.773 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0130922613 1.79E-06 NA mr1097 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
vg0130922613 6.21E-06 3.55E-06 mr1097 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
vg0130922613 NA 1.40E-06 mr1677 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
vg0130922613 NA 4.07E-06 mr1677 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
vg0130922613 NA 8.70E-06 mr1678 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
vg0130922613 NA 5.17E-07 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
vg0130922613 NA 3.64E-07 mr1973_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