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Detailed information for vg0419756923:

Variant ID: vg0419756923 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 19756923
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.82, T: 0.18, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:


ATCCCCTGAACTCCTGAAGCGGAGAGGCGGCCGGCTCGAGCACATCGAGGAGGCGCAAGGGGGCTTCCATCTCCCTCCGCCGGTGTTGCCTCACCATCCC[C/T]
CGTAGGTGGAGCAGTCCGTGTAGATCAAGCCGCTGCCACCCCTCCTCATCGCCCGAAGCAGGTGCCAACGATGTGGATCGAGGGTTCGACGCAAGGCGGC

Reverse complement sequence

GCCGCCTTGCGTCGAACCCTCGATCCACATCGTTGGCACCTGCTTCGGGCGATGAGGAGGGGTGGCAGCGGCTTGATCTACACGGACTGCTCCACCTACG[G/A]
GGGATGGTGAGGCAACACCGGCGGAGGGAGATGGAAGCCCCCTTGCGCCTCCTCGATGTGCTCGAGCCGGCCGCCTCTCCGCTTCAGGAGTTCAGGGGAT

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 60.00% 39.80% 0.15% 0.00% NA
All Indica  2759 94.20% 5.70% 0.14% 0.00% NA
All Japonica  1512 0.50% 99.50% 0.00% 0.00% NA
Aus  269 67.30% 32.30% 0.37% 0.00% NA
Indica I  595 91.60% 8.20% 0.17% 0.00% NA
Indica II  465 91.40% 8.60% 0.00% 0.00% NA
Indica III  913 97.60% 2.30% 0.11% 0.00% NA
Indica Intermediate  786 93.80% 6.00% 0.25% 0.00% NA
Temperate Japonica  767 0.40% 99.60% 0.00% 0.00% NA
Tropical Japonica  504 0.60% 99.40% 0.00% 0.00% NA
Japonica Intermediate  241 0.40% 99.60% 0.00% 0.00% NA
VI/Aromatic  96 34.40% 65.60% 0.00% 0.00% NA
Intermediate  90 18.90% 78.90% 2.22% 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
vg0419756923 C -> T LOC_Os04g32750.1 upstream_gene_variant ; 1695.0bp to feature; MODIFIER silent_mutation Average:61.172; most accessible tissue: Zhenshan97 panicle, score: 84.374 N N N N
vg0419756923 C -> T LOC_Os04g32760.1 upstream_gene_variant ; 3885.0bp to feature; MODIFIER silent_mutation Average:61.172; most accessible tissue: Zhenshan97 panicle, score: 84.374 N N N N
vg0419756923 C -> T LOC_Os04g32750-LOC_Os04g32760 intergenic_region ; MODIFIER silent_mutation Average:61.172; most accessible tissue: Zhenshan97 panicle, score: 84.374 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0419756923 NA 5.01E-06 mr1750 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
vg0419756923 NA 1.34E-15 mr1040_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
vg0419756923 NA 2.20E-10 mr1349_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
vg0419756923 NA 1.73E-06 mr1349_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
vg0419756923 NA 8.42E-20 mr1362_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
vg0419756923 NA 7.34E-08 mr1540_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
vg0419756923 NA 1.87E-07 mr1568_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
vg0419756923 NA 4.77E-20 mr1581_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
vg0419756923 NA 7.26E-17 mr1712_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
vg0419756923 NA 1.78E-12 mr1713_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
vg0419756923 NA 2.69E-13 mr1717_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
vg0419756923 NA 5.54E-07 mr1732_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
vg0419756923 NA 4.79E-17 mr1836_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