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Detailed information for vg0401963741:

Variant ID: vg0401963741 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 1963741
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:


ACATTTAATGTGAATCCCCCATTGTATGCGAGTTCAACTAAGCATGGCTAAGCAATCCCTAACTCAACATCTAATCATGTTATATCCCCAAGCTAACAAA[G/T]
GAACAAGGTAACAAATAGTATGGCTGAGACAGTAGGTAATCATCTCATGGTAGCATTGTAAAATAATGCAGTATTTAAAGGAAAACAATAGGGCATTTGC

Reverse complement sequence

GCAAATGCCCTATTGTTTTCCTTTAAATACTGCATTATTTTACAATGCTACCATGAGATGATTACCTACTGTCTCAGCCATACTATTTGTTACCTTGTTC[C/A]
TTTGTTAGCTTGGGGATATAACATGATTAGATGTTGAGTTAGGGATTGCTTAGCCATGCTTAGTTGAACTCGCATACAATGGGGGATTCACATTAAATGT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.00% 7.30% 0.38% 0.40% NA
All Indica  2759 98.80% 1.20% 0.00% 0.00% NA
All Japonica  1512 78.10% 19.40% 1.19% 1.26% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 98.60% 1.40% 0.00% 0.00% NA
Indica Intermediate  786 97.70% 2.30% 0.00% 0.00% NA
Temperate Japonica  767 69.20% 28.40% 1.56% 0.78% NA
Tropical Japonica  504 85.90% 11.50% 0.79% 1.79% NA
Japonica Intermediate  241 90.00% 7.50% 0.83% 1.66% NA
VI/Aromatic  96 90.60% 9.40% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0401963741 G -> DEL N N silent_mutation Average:47.77; most accessible tissue: Zhenshan97 young leaf, score: 68.315 N N N N
vg0401963741 G -> T LOC_Os04g04200.1 downstream_gene_variant ; 4829.0bp to feature; MODIFIER silent_mutation Average:47.77; most accessible tissue: Zhenshan97 young leaf, score: 68.315 N N N N
vg0401963741 G -> T LOC_Os04g04210.1 downstream_gene_variant ; 2052.0bp to feature; MODIFIER silent_mutation Average:47.77; most accessible tissue: Zhenshan97 young leaf, score: 68.315 N N N N
vg0401963741 G -> T LOC_Os04g04220.1 downstream_gene_variant ; 3672.0bp to feature; MODIFIER silent_mutation Average:47.77; most accessible tissue: Zhenshan97 young leaf, score: 68.315 N N N N
vg0401963741 G -> T LOC_Os04g04210-LOC_Os04g04220 intergenic_region ; MODIFIER silent_mutation Average:47.77; most accessible tissue: Zhenshan97 young leaf, score: 68.315 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0401963741 9.61E-07 NA mr1751 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
vg0401963741 4.28E-06 1.46E-06 mr1751 Jap_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