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Detailed information for vg0413358188:

Variant ID: vg0413358188 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 13358188
Reference Allele: GAlternative Allele: A,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


GTAGGGGCGGCTTTTAATACGTTTAACATCTTTTCGGGTAGACCTCTTAAGTGGTTTACCTACAAAAATAGATTTTTGGTGGACAACGATCTCGCCCCAC[G/A,T]
GTTGTCATTTTCATAGGCGGCTATTTAGCATCGAAAGGCCTACTTGCCTTTAAAAAATGTTATCGTTTGAAAAATGGTTTTTATGTTTGTAATAACGGTT

Reverse complement sequence

AACCGTTATTACAAACATAAAAACCATTTTTCAAACGATAACATTTTTTAAAGGCAAGTAGGCCTTTCGATGCTAAATAGCCGCCTATGAAAATGACAAC[C/T,A]
GTGGGGCGAGATCGTTGTCCACCAAAAATCTATTTTTGTAGGTAAACCACTTAAGAGGTCTACCCGAAAAGATGTTAAACGTATTAAAAGCCGCCCCTAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.00% 1.60% 4.53% 1.82% T: 0.04%
All Indica  2759 94.10% 2.70% 3.23% 0.00% NA
All Japonica  1512 86.40% 0.00% 8.00% 5.62% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 75.00% 11.40% 13.61% 0.00% NA
Indica II  465 98.70% 0.40% 0.86% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 98.90% 0.60% 0.51% 0.00% NA
Temperate Japonica  767 99.20% 0.00% 0.52% 0.26% NA
Tropical Japonica  504 65.50% 0.00% 20.44% 14.09% NA
Japonica Intermediate  241 89.20% 0.00% 5.81% 4.98% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 92.20% 1.10% 3.33% 1.11% T: 2.22%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0413358188 G -> DEL N N silent_mutation Average:51.219; most accessible tissue: Zhenshan97 young leaf, score: 78.938 N N N N
vg0413358188 G -> A LOC_Os04g23370.1 upstream_gene_variant ; 2690.0bp to feature; MODIFIER silent_mutation Average:51.219; most accessible tissue: Zhenshan97 young leaf, score: 78.938 N N N N
vg0413358188 G -> A LOC_Os04g23360-LOC_Os04g23370 intergenic_region ; MODIFIER silent_mutation Average:51.219; most accessible tissue: Zhenshan97 young leaf, score: 78.938 N N N N
vg0413358188 G -> T LOC_Os04g23370.1 upstream_gene_variant ; 2690.0bp to feature; MODIFIER silent_mutation Average:51.219; most accessible tissue: Zhenshan97 young leaf, score: 78.938 N N N N
vg0413358188 G -> T LOC_Os04g23360-LOC_Os04g23370 intergenic_region ; MODIFIER silent_mutation Average:51.219; most accessible tissue: Zhenshan97 young leaf, score: 78.938 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0413358188 NA 1.13E-06 mr1201 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
vg0413358188 NA 3.00E-06 mr1219 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
vg0413358188 NA 3.60E-07 mr1274 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
vg0413358188 2.49E-06 2.49E-06 mr1370 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
vg0413358188 NA 3.32E-06 mr1496 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