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Detailed information for vg0134320353:

Variant ID: vg0134320353 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 34320353
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.96, G: 0.04, others allele: 0.00, population size: 112. )

Flanking Sequence (100 bp) in Reference Genome:


TGGGCTGACCAAGATTGGCAAGGCAAGTCTGTTAGAGTGTGTTTTTTTCCAAAATTACTAAATTTTCACTTGGAGAGAGATAGATAGACTGTTTGAGATG[T/G]
TCTAAGTGAAAGCAAAAGGACTTGAATTTAAATTAATCTTAACATATTTTCAACATAATTCTCTTTTAACATTAGCTTTTTAAGTCGCTACAAATAAATA

Reverse complement sequence

TATTTATTTGTAGCGACTTAAAAAGCTAATGTTAAAAGAGAATTATGTTGAAAATATGTTAAGATTAATTTAAATTCAAGTCCTTTTGCTTTCACTTAGA[A/C]
CATCTCAAACAGTCTATCTATCTCTCTCCAAGTGAAAATTTAGTAATTTTGGAAAAAAACACACTCTAACAGACTTGCCTTGCCAATCTTGGTCAGCCCA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 80.50% 19.40% 0.08% 0.00% NA
All Indica  2759 76.70% 23.10% 0.14% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 3.30% 96.70% 0.00% 0.00% NA
Indica I  595 97.30% 2.70% 0.00% 0.00% NA
Indica II  465 77.20% 22.80% 0.00% 0.00% NA
Indica III  913 70.40% 29.40% 0.22% 0.00% NA
Indica Intermediate  786 68.20% 31.60% 0.25% 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 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 85.60% 14.40% 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
vg0134320353 T -> G LOC_Os01g59360.1 upstream_gene_variant ; 4957.0bp to feature; MODIFIER silent_mutation Average:69.906; most accessible tissue: Minghui63 panicle, score: 90.408 N N N N
vg0134320353 T -> G LOC_Os01g59350-LOC_Os01g59360 intergenic_region ; MODIFIER silent_mutation Average:69.906; most accessible tissue: Minghui63 panicle, score: 90.408 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0134320353 NA 6.93E-08 mr1193 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
vg0134320353 NA 2.69E-11 mr1587 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
vg0134320353 NA 4.54E-07 mr1587 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
vg0134320353 NA 6.22E-08 mr1803 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
vg0134320353 NA 4.76E-18 mr1587_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