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Detailed information for vg0136211264:

Variant ID: vg0136211264 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 36211264
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


CGATGTGTACGTTTGTACAAAGTGTGTTTTTTTACCGTTTTTGTTTTTAATTTTTCAAACTCCAAAACATTTTTAATGGGTTTGCCAATTTGTTCATTAA[G/A]
GGGGAGATTGTAATATCAACGTGTGTTTTGATTCTTATTCTGTGATGAACAATTGGCATATGTGATTATCGGTTTTGATATTTGGAGATTATCGTCGAAG

Reverse complement sequence

CTTCGACGATAATCTCCAAATATCAAAACCGATAATCACATATGCCAATTGTTCATCACAGAATAAGAATCAAAACACACGTTGATATTACAATCTCCCC[C/T]
TTAATGAACAAATTGGCAAACCCATTAAAAATGTTTTGGAGTTTGAAAAATTAAAAACAAAAACGGTAAAAAAACACACTTTGTACAAACGTACACATCG

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 98.00% 2.00% 0.00% 0.00% NA
All Indica  2759 96.70% 3.30% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 90.60% 9.40% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 98.80% 1.20% 0.00% 0.00% NA
Indica Intermediate  786 96.90% 3.10% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 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 96.70% 3.30% 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
vg0136211264 G -> A LOC_Os01g62540.1 upstream_gene_variant ; 3069.0bp to feature; MODIFIER silent_mutation Average:21.237; most accessible tissue: Callus, score: 29.06 N N N N
vg0136211264 G -> A LOC_Os01g62520.1 downstream_gene_variant ; 617.0bp to feature; MODIFIER silent_mutation Average:21.237; most accessible tissue: Callus, score: 29.06 N N N N
vg0136211264 G -> A LOC_Os01g62530.1 downstream_gene_variant ; 1026.0bp to feature; MODIFIER silent_mutation Average:21.237; most accessible tissue: Callus, score: 29.06 N N N N
vg0136211264 G -> A LOC_Os01g62520-LOC_Os01g62530 intergenic_region ; MODIFIER silent_mutation Average:21.237; most accessible tissue: Callus, score: 29.06 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0136211264 NA 7.75E-07 mr1060 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
vg0136211264 NA 1.36E-06 mr1621 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
vg0136211264 NA 5.94E-08 mr1458_2 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
vg0136211264 4.98E-06 NA mr1973_2 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