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Detailed information for vg0133242822:

Variant ID: vg0133242822 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 33242822
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.07, others allele: 0.00, population size: 54. )

Flanking Sequence (100 bp) in Reference Genome:


ATACACTAGAAAGGTCATCGGAACGTAGTGAGTACTCTCGTAGTTTGTTTATATGTATATAGCTACAAAACTGGGACTGCACAATGACTTTCGAGATGGT[C/T]
CAGTGGCTATATGTCTCCAGAGTATGCAATGGACGGTGTGTTTTCCATGAAATCCGACGTCTTCAGCTTTGGCGTCCTAGTACTGGAGATTGTCGCCGGC

Reverse complement sequence

GCCGGCGACAATCTCCAGTACTAGGACGCCAAAGCTGAAGACGTCGGATTTCATGGAAAACACACCGTCCATTGCATACTCTGGAGACATATAGCCACTG[G/A]
ACCATCTCGAAAGTCATTGTGCAGTCCCAGTTTTGTAGCTATATACATATAAACAAACTACGAGAGTACTCACTACGTTCCGATGACCTTTCTAGTGTAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 65.20% 34.70% 0.06% 0.00% NA
All Indica  2759 96.60% 3.30% 0.11% 0.00% NA
All Japonica  1512 7.90% 92.10% 0.00% 0.00% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 93.80% 6.20% 0.00% 0.00% NA
Indica II  465 98.30% 1.50% 0.22% 0.00% NA
Indica III  913 98.80% 1.20% 0.00% 0.00% NA
Indica Intermediate  786 95.00% 4.70% 0.25% 0.00% NA
Temperate Japonica  767 11.70% 88.30% 0.00% 0.00% NA
Tropical Japonica  504 2.40% 97.60% 0.00% 0.00% NA
Japonica Intermediate  241 7.50% 92.50% 0.00% 0.00% NA
VI/Aromatic  96 2.10% 97.90% 0.00% 0.00% NA
Intermediate  90 34.40% 65.60% 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
vg0133242822 C -> T LOC_Os01g57540.1 splice_region_variant&intron_variant ; LOW silent_mutation Average:56.337; most accessible tissue: Callus, score: 82.796 N N N N
vg0133242822 C -> T LOC_Os01g57550.1 upstream_gene_variant ; 1920.0bp to feature; MODIFIER silent_mutation Average:56.337; most accessible tissue: Callus, score: 82.796 N N N N
vg0133242822 C -> T LOC_Os01g57550.2 upstream_gene_variant ; 1882.0bp to feature; MODIFIER silent_mutation Average:56.337; most accessible tissue: Callus, score: 82.796 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0133242822 NA 4.16E-09 mr1005 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
vg0133242822 9.38E-13 1.72E-129 mr1008 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
vg0133242822 1.04E-08 2.48E-20 mr1008 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
vg0133242822 3.28E-13 1.63E-128 mr1009 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
vg0133242822 3.22E-10 1.86E-20 mr1009 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
vg0133242822 6.56E-07 9.51E-80 mr1014 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
vg0133242822 NA 6.17E-06 mr1014 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
vg0133242822 8.76E-07 4.28E-81 mr1015 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
vg0133242822 NA 2.70E-07 mr1015 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
vg0133242822 NA 1.46E-06 mr1527 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
vg0133242822 NA 1.25E-09 mr1004_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
vg0133242822 5.42E-15 6.15E-132 mr1008_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
vg0133242822 2.40E-10 2.12E-21 mr1008_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
vg0133242822 2.88E-09 9.31E-94 mr1015_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
vg0133242822 2.72E-06 5.30E-09 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
vg0133242822 NA 3.95E-26 mr1074_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
vg0133242822 NA 2.17E-16 mr1146_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
vg0133242822 NA 4.33E-15 mr1148_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
vg0133242822 NA 1.58E-18 mr1239_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
vg0133242822 3.53E-06 NA mr1257_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