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Detailed information for vg0324931493:

Variant ID: vg0324931493 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 24931493
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, T: 0.03, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


GAGGCTCGGGAGCCGCCATCCTCCACCCCATCTACGCGGGAGGGCTCGGAAGCTGCTGTCGCCGCCATCATCGTCGTTGTCCTCATAGCAGACCCTGAAA[A/T]
TTTGACCAATAAAAACAAAACTCTAAAAATACGGACCTTCGAAAACTTTTAAATTAATTGCATCATGCCGATCTTATTCGCCTATTTTATTTGGATTTGA

Reverse complement sequence

TCAAATCCAAATAAAATAGGCGAATAAGATCGGCATGATGCAATTAATTTAAAAGTTTTCGAAGGTCCGTATTTTTAGAGTTTTGTTTTTATTGGTCAAA[T/A]
TTTCAGGGTCTGCTATGAGGACAACGACGATGATGGCGGCGACAGCAGCTTCCGAGCCCTCCCGCGTAGATGGGGTGGAGGATGGCGGCTCCCGAGCCTC

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 56.50% 43.30% 0.19% 0.00% NA
All Indica  2759 27.20% 72.50% 0.33% 0.00% NA
All Japonica  1512 99.10% 0.90% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 29.70% 69.70% 0.50% 0.00% NA
Indica II  465 6.50% 93.50% 0.00% 0.00% NA
Indica III  913 29.50% 70.30% 0.22% 0.00% NA
Indica Intermediate  786 34.90% 64.60% 0.51% 0.00% NA
Temperate Japonica  767 99.30% 0.70% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 65.60% 34.40% 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
vg0324931493 A -> T LOC_Os03g44340.1 splice_region_variant&intron_variant ; LOW silent_mutation Average:55.005; most accessible tissue: Zhenshan97 young leaf, score: 80.056 N N N N
vg0324931493 A -> T LOC_Os03g44330.1 upstream_gene_variant ; 3390.0bp to feature; MODIFIER silent_mutation Average:55.005; most accessible tissue: Zhenshan97 young leaf, score: 80.056 N N N N
vg0324931493 A -> T LOC_Os03g44350.1 upstream_gene_variant ; 4162.0bp to feature; MODIFIER silent_mutation Average:55.005; most accessible tissue: Zhenshan97 young leaf, score: 80.056 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0324931493 NA 9.26E-06 mr1030 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
vg0324931493 NA 3.06E-10 mr1316 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
vg0324931493 NA 7.40E-13 mr1329 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
vg0324931493 NA 7.80E-11 mr1524 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
vg0324931493 NA 8.42E-10 mr1578 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
vg0324931493 NA 7.06E-08 mr1671 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
vg0324931493 NA 2.12E-07 mr1716 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
vg0324931493 NA 9.83E-11 mr1819 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
vg0324931493 4.83E-07 NA mr1013_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
vg0324931493 5.18E-08 NA mr1031_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
vg0324931493 NA 3.17E-12 mr1330_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
vg0324931493 NA 4.14E-06 mr1582_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
vg0324931493 NA 5.46E-19 mr1870_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