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Detailed information for vg0526069160:

Variant ID: vg0526069160 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 26069160
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.05, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:


CTGCTCCCTTATATGCCACTAGTTCAAGTTTTTCCACCCTTTTATGCCACTCCCACCACTATAGTGTTAGTTGACTGTCAGTCAAAGGTTACTTTTTTTC[G/A]
TAAATGACCAATATGCCCTCTCAACTAAAAAATGTGTAAACTTCAAAAAATCATAACTAATTTATTTTAAATCCTTTTTGAGTGAACAAAATTTTGTCAG

Reverse complement sequence

CTGACAAAATTTTGTTCACTCAAAAAGGATTTAAAATAAATTAGTTATGATTTTTTGAAGTTTACACATTTTTTAGTTGAGAGGGCATATTGGTCATTTA[C/T]
GAAAAAAAGTAACCTTTGACTGACAGTCAACTAACACTATAGTGGTGGGAGTGGCATAAAAGGGTGGAAAAACTTGAACTAGTGGCATATAAGGGAGCAG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 61.50% 38.40% 0.13% 0.00% NA
All Indica  2759 93.80% 5.90% 0.22% 0.00% NA
All Japonica  1512 0.80% 99.20% 0.00% 0.00% NA
Aus  269 98.10% 1.90% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 78.70% 20.60% 0.65% 0.00% NA
Indica III  913 97.00% 2.70% 0.22% 0.00% NA
Indica Intermediate  786 94.50% 5.30% 0.13% 0.00% NA
Temperate Japonica  767 1.30% 98.70% 0.00% 0.00% NA
Tropical Japonica  504 0.40% 99.60% 0.00% 0.00% NA
Japonica Intermediate  241 0.00% 100.00% 0.00% 0.00% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 42.20% 57.80% 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
vg0526069160 G -> A LOC_Os05g44840.1 upstream_gene_variant ; 2861.0bp to feature; MODIFIER silent_mutation Average:20.327; most accessible tissue: Minghui63 panicle, score: 42.799 N N N N
vg0526069160 G -> A LOC_Os05g44850.1 upstream_gene_variant ; 376.0bp to feature; MODIFIER silent_mutation Average:20.327; most accessible tissue: Minghui63 panicle, score: 42.799 N N N N
vg0526069160 G -> A LOC_Os05g44860.1 downstream_gene_variant ; 1007.0bp to feature; MODIFIER silent_mutation Average:20.327; most accessible tissue: Minghui63 panicle, score: 42.799 N N N N
vg0526069160 G -> A LOC_Os05g44850-LOC_Os05g44860 intergenic_region ; MODIFIER silent_mutation Average:20.327; most accessible tissue: Minghui63 panicle, score: 42.799 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0526069160 1.46E-06 NA mr1106 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
vg0526069160 NA 6.80E-06 mr1106 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
vg0526069160 NA 1.11E-07 mr1162 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
vg0526069160 NA 5.16E-07 mr1785 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
vg0526069160 NA 2.64E-11 mr1902 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