Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0512269844:

Variant ID: vg0512269844 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 12269844
Reference Allele: GAlternative Allele: A,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


CGATCCAAAATTGTCCTTCCTTCTGACGGCGTTTTGTGCATGAACGATCCTCAAGCGGTTATGTCCAGATAGAATGCAGACTCCTTATCCAAACCCGTAT[G/A,T]
GAAATGTTGGAGTAGCACATACTCGGGTAAGGACAGGGTTGGTCCGGACTACACTAAATTAGTGAATTTGGACCAGGCTGCACCGATTGATTCATTTTTG

Reverse complement sequence

CAAAAATGAATCAATCGGTGCAGCCTGGTCCAAATTCACTAATTTAGTGTAGTCCGGACCAACCCTGTCCTTACCCGAGTATGTGCTACTCCAACATTTC[C/T,A]
ATACGGGTTTGGATAAGGAGTCTGCATTCTATCTGGACATAACCGCTTGAGGATCGTTCATGCACAAAACGCCGTCAGAAGGAAGGACAATTTTGGATCG

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 94.30% 3.30% 1.59% 0.83% NA
All Indica  2759 90.30% 5.60% 2.68% 1.41% NA
All Japonica  1512 99.90% 0.00% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 82.40% 10.80% 3.70% 3.19% NA
Indica II  465 94.20% 4.10% 1.29% 0.43% NA
Indica III  913 93.10% 3.30% 2.85% 0.77% NA
Indica Intermediate  786 90.80% 5.20% 2.54% 1.40% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0512269844 G -> T LOC_Os05g20880.1 upstream_gene_variant ; 3010.0bp to feature; MODIFIER N Average:53.748; most accessible tissue: Zhenshan97 flag leaf, score: 75.455 N N N N
vg0512269844 G -> T LOC_Os05g20890.1 upstream_gene_variant ; 159.0bp to feature; MODIFIER N Average:53.748; most accessible tissue: Zhenshan97 flag leaf, score: 75.455 N N N N
vg0512269844 G -> T LOC_Os05g20900.1 downstream_gene_variant ; 3083.0bp to feature; MODIFIER N Average:53.748; most accessible tissue: Zhenshan97 flag leaf, score: 75.455 N N N N
vg0512269844 G -> T LOC_Os05g20890-LOC_Os05g20900 intergenic_region ; MODIFIER N Average:53.748; most accessible tissue: Zhenshan97 flag leaf, score: 75.455 N N N N
vg0512269844 G -> DEL N N silent_mutation Average:53.748; most accessible tissue: Zhenshan97 flag leaf, score: 75.455 N N N N
vg0512269844 G -> A LOC_Os05g20880.1 upstream_gene_variant ; 3010.0bp to feature; MODIFIER silent_mutation Average:53.748; most accessible tissue: Zhenshan97 flag leaf, score: 75.455 N N N N
vg0512269844 G -> A LOC_Os05g20890.1 upstream_gene_variant ; 159.0bp to feature; MODIFIER silent_mutation Average:53.748; most accessible tissue: Zhenshan97 flag leaf, score: 75.455 N N N N
vg0512269844 G -> A LOC_Os05g20900.1 downstream_gene_variant ; 3083.0bp to feature; MODIFIER silent_mutation Average:53.748; most accessible tissue: Zhenshan97 flag leaf, score: 75.455 N N N N
vg0512269844 G -> A LOC_Os05g20890-LOC_Os05g20900 intergenic_region ; MODIFIER silent_mutation Average:53.748; most accessible tissue: Zhenshan97 flag leaf, score: 75.455 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0512269844 NA 6.09E-06 mr1125 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
vg0512269844 1.29E-06 1.29E-06 mr1160 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