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Detailed information for vg0405058837:

Variant ID: vg0405058837 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 5058837
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.75, A: 0.25, others allele: 0.00, population size: 177. )

Flanking Sequence (100 bp) in Reference Genome:


TTTGAAATAAGTGGTTTCCCGTTGTCCAAGAGCAGATACCAACGCATGCATGACAAGAAGTGCCTATGTCGCTTAAAATTATTTTTTGATCTGTTTATTG[T/A]
TATTATTTTCAACAAGTCATTGCAAAAACTTAAATAACACAGATTAACATCTTTCTGAGTTTAAAATTTTGAGACTCCTTATTTATTTTAAAAGTTTTGA

Reverse complement sequence

TCAAAACTTTTAAAATAAATAAGGAGTCTCAAAATTTTAAACTCAGAAAGATGTTAATCTGTGTTATTTAAGTTTTTGCAATGACTTGTTGAAAATAATA[A/T]
CAATAAACAGATCAAAAAATAATTTTAAGCGACATAGGCACTTCTTGTCATGCATGCGTTGGTATCTGCTCTTGGACAACGGGAAACCACTTATTTCAAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 64.30% 33.40% 0.06% 2.24% NA
All Indica  2759 91.90% 6.30% 0.11% 1.67% NA
All Japonica  1512 6.90% 89.40% 0.00% 3.77% NA
Aus  269 94.80% 4.80% 0.00% 0.37% NA
Indica I  595 96.10% 3.20% 0.17% 0.50% NA
Indica II  465 84.50% 9.90% 0.00% 5.59% NA
Indica III  913 94.50% 5.40% 0.00% 0.11% NA
Indica Intermediate  786 89.90% 7.80% 0.25% 2.04% NA
Temperate Japonica  767 1.20% 98.70% 0.00% 0.13% NA
Tropical Japonica  504 15.70% 73.20% 0.00% 11.11% NA
Japonica Intermediate  241 6.60% 93.40% 0.00% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 63.30% 34.40% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0405058837 T -> DEL N N silent_mutation Average:33.39; most accessible tissue: Zhenshan97 flower, score: 77.366 N N N N
vg0405058837 T -> A LOC_Os04g09450.1 downstream_gene_variant ; 862.0bp to feature; MODIFIER silent_mutation Average:33.39; most accessible tissue: Zhenshan97 flower, score: 77.366 N N N N
vg0405058837 T -> A LOC_Os04g09430-LOC_Os04g09450 intergenic_region ; MODIFIER silent_mutation Average:33.39; most accessible tissue: Zhenshan97 flower, score: 77.366 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0405058837 5.95E-07 6.71E-18 mr1035 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
vg0405058837 2.04E-06 2.18E-07 mr1035 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
vg0405058837 NA 8.98E-14 mr1626 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
vg0405058837 NA 1.04E-28 mr1631 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
vg0405058837 1.73E-06 7.12E-17 mr1035_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
vg0405058837 8.91E-08 NA mr1178_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
vg0405058837 NA 3.72E-63 mr1402_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
vg0405058837 NA 1.02E-23 mr1403_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
vg0405058837 NA 6.89E-06 mr1613_2 Jap_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
vg0405058837 NA 5.07E-33 mr1631_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
vg0405058837 NA 3.44E-08 mr1837_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
vg0405058837 NA 1.24E-18 mr1945_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
vg0405058837 NA 2.27E-06 mr1962_2 Jap_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