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Detailed information for vg0129784098:

Variant ID: vg0129784098 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 29784098
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.93, T: 0.07, others allele: 0.00, population size: 182. )

Flanking Sequence (100 bp) in Reference Genome:


AACTAGTGTTTTTTGTGTAATAGTTCTTCACTTAGCGTGTCACCCGCTTGGTACATCTCCAGTATTGGCAACAAATTTGAAGCAGCAGCCAAAAACACAC[A/T]
TTTGTCATTACGAACCTGTGGAATATTGAAATACAGCTTAGATAAAATTCAGTAAAAGAACTCAGAGATGCAGTTAGTTTCCCATATCCTAATAATACAA

Reverse complement sequence

TTGTATTATTAGGATATGGGAAACTAACTGCATCTCTGAGTTCTTTTACTGAATTTTATCTAAGCTGTATTTCAATATTCCACAGGTTCGTAATGACAAA[T/A]
GTGTGTTTTTGGCTGCTGCTTCAAATTTGTTGCCAATACTGGAGATGTACCAAGCGGGTGACACGCTAAGTGAAGAACTATTACACAAAAAACACTAGTT

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 88.00% 12.00% 0.02% 0.00% NA
All Indica  2759 98.70% 1.30% 0.00% 0.00% NA
All Japonica  1512 80.60% 19.40% 0.00% 0.00% NA
Aus  269 55.00% 45.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 96.10% 3.90% 0.00% 0.00% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 46.80% 53.20% 0.00% 0.00% NA
Japonica Intermediate  241 91.30% 8.70% 0.00% 0.00% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 72.20% 26.70% 1.11% 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
vg0129784098 A -> T LOC_Os01g51800.1 3_prime_UTR_variant ; 1068.0bp to feature; MODIFIER silent_mutation Average:39.301; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N
vg0129784098 A -> T LOC_Os01g51790.1 downstream_gene_variant ; 950.0bp to feature; MODIFIER silent_mutation Average:39.301; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N
vg0129784098 A -> T LOC_Os01g51810.1 downstream_gene_variant ; 2037.0bp to feature; MODIFIER silent_mutation Average:39.301; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0129784098 NA 7.52E-06 mr1072_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
vg0129784098 2.36E-06 NA mr1124_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
vg0129784098 4.14E-06 6.00E-07 mr1124_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
vg0129784098 NA 1.70E-06 mr1346_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
vg0129784098 NA 5.01E-06 mr1438_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
vg0129784098 NA 4.00E-08 mr1642_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
vg0129784098 NA 1.21E-07 mr1815_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