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Detailed information for vg0134766241:

Variant ID: vg0134766241 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 34766241
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCATGATTTTCTAAAAATATATATATCCAAGCAAACTCCCACAGTGAATTTCATCTTAACTAAACCATATAACAATAATAAGATTAAAATAGACTTCACC[T/C]
ATTGCAACGCACGAGCATTTTTTCTAGTAGAAATAAAATTTCAGAGTTGTATATTAAATCTAAGGCTTGTTTGGCATGGGTCTAGTTTCAACTCCATCTC

Reverse complement sequence

GAGATGGAGTTGAAACTAGACCCATGCCAAACAAGCCTTAGATTTAATATACAACTCTGAAATTTTATTTCTACTAGAAAAAATGCTCGTGCGTTGCAAT[A/G]
GGTGAAGTCTATTTTAATCTTATTATTGTTATATGGTTTAGTTAAGATGAAATTCACTGTGGGAGTTTGCTTGGATATATATATTTTTAGAAAATCATGA

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 77.60% 22.40% 0.00% 0.00% NA
All Indica  2759 99.30% 0.70% 0.00% 0.00% NA
All Japonica  1512 39.70% 60.30% 0.00% 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 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 98.90% 1.10% 0.00% 0.00% NA
Indica Intermediate  786 98.90% 1.10% 0.00% 0.00% NA
Temperate Japonica  767 46.40% 53.60% 0.00% 0.00% NA
Tropical Japonica  504 41.30% 58.70% 0.00% 0.00% NA
Japonica Intermediate  241 14.90% 85.10% 0.00% 0.00% NA
VI/Aromatic  96 10.40% 89.60% 0.00% 0.00% NA
Intermediate  90 54.40% 45.60% 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
vg0134766241 T -> C LOC_Os01g60110.1 downstream_gene_variant ; 2876.0bp to feature; MODIFIER silent_mutation Average:33.612; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0134766241 T -> C LOC_Os01g60100-LOC_Os01g60110 intergenic_region ; MODIFIER silent_mutation Average:33.612; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0134766241 2.62E-06 NA mr1019_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
vg0134766241 NA 3.63E-08 mr1084_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
vg0134766241 NA 1.61E-07 mr1205_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
vg0134766241 4.91E-07 NA mr1261_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