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Detailed information for vg0800341569:

Variant ID: vg0800341569 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 341569
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.71, A: 0.31, others allele: 0.00, population size: 154. )

Flanking Sequence (100 bp) in Reference Genome:


TCTTACTCCAGGATTCCCGCGAACGGATCAAAGCACTGGACGTATCGACGAATGTATCGCAAGAACTGCAAGAGCAAGTAAAACTACCTTCATTTTTTTT[A/T]
AAATATATCATACCGTTAACTTTATACATCATTGTGTCTGGATGCTTATAGTACTTGCTCTAAACTAGTCACTCCATTCTAAATTGATCGTCTTACATGT

Reverse complement sequence

ACATGTAAGACGATCAATTTAGAATGGAGTGACTAGTTTAGAGCAAGTACTATAAGCATCCAGACACAATGATGTATAAAGTTAACGGTATGATATATTT[T/A]
AAAAAAAATGAAGGTAGTTTTACTTGCTCTTGCAGTTCTTGCGATACATTCGTCGATACGTCCAGTGCTTTGATCCGTTCGCGGGAATCCTGGAGTAAGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 61.50% 38.50% 0.00% 0.00% NA
All Indica  2759 96.10% 3.90% 0.00% 0.00% NA
All Japonica  1512 2.10% 97.90% 0.00% 0.00% NA
Aus  269 37.20% 62.80% 0.00% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 94.60% 5.40% 0.00% 0.00% NA
Indica III  913 98.00% 2.00% 0.00% 0.00% NA
Indica Intermediate  786 92.40% 7.60% 0.00% 0.00% NA
Temperate Japonica  767 1.60% 98.40% 0.00% 0.00% NA
Tropical Japonica  504 2.80% 97.20% 0.00% 0.00% NA
Japonica Intermediate  241 2.50% 97.50% 0.00% 0.00% NA
VI/Aromatic  96 83.30% 16.70% 0.00% 0.00% NA
Intermediate  90 45.60% 54.40% 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
vg0800341569 A -> T LOC_Os08g01570.1 upstream_gene_variant ; 3747.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0800341569 A -> T LOC_Os08g01580.1 upstream_gene_variant ; 646.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0800341569 A -> T LOC_Os08g01570-LOC_Os08g01580 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0800341569 2.14E-06 7.72E-17 mr1746 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
vg0800341569 NA 7.26E-19 mr1913 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
vg0800341569 NA 7.55E-21 mr1298_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
vg0800341569 NA 1.36E-19 mr1731_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
vg0800341569 3.03E-11 1.90E-30 mr1746_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
vg0800341569 NA 1.90E-34 mr1913_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