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Detailed information for vg0622495913:

Variant ID: vg0622495913 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 22495913
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


ACGGCGCCAAAGAGGCTGGCGCCGTCCTGTTGAACGACGGCGCCAGGCACTCTGGCGCCCCAAAAAGGACCATTTTTGGGATAAGTTTTTCTAGGGGTCT[A/G]
CTTACGAAATAAGTTTTTCAAAAGGACCAAAATGTGAAAAATCCAGTTGGTATTAGTACTAACTAGTTCGAGCAGTCCGATGAATCGTAGTGTACAGTAC

Reverse complement sequence

GTACTGTACACTACGATTCATCGGACTGCTCGAACTAGTTAGTACTAATACCAACTGGATTTTTCACATTTTGGTCCTTTTGAAAAACTTATTTCGTAAG[T/C]
AGACCCCTAGAAAAACTTATCCCAAAAATGGTCCTTTTTGGGGCGCCAGAGTGCCTGGCGCCGTCGTTCAACAGGACGGCGCCAGCCTCTTTGGCGCCGT

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 77.60% 22.00% 0.40% 0.00% NA
All Indica  2759 98.30% 1.70% 0.04% 0.00% NA
All Japonica  1512 39.60% 59.30% 1.06% 0.00% NA
Aus  269 89.20% 10.80% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 97.30% 2.60% 0.11% 0.00% NA
Indica Intermediate  786 97.80% 2.20% 0.00% 0.00% NA
Temperate Japonica  767 47.50% 52.30% 0.26% 0.00% NA
Tropical Japonica  504 38.90% 58.30% 2.78% 0.00% NA
Japonica Intermediate  241 16.20% 83.80% 0.00% 0.00% NA
VI/Aromatic  96 53.10% 45.80% 1.04% 0.00% NA
Intermediate  90 74.40% 24.40% 1.11% 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
vg0622495913 A -> G LOC_Os06g38040.1 upstream_gene_variant ; 3778.0bp to feature; MODIFIER silent_mutation Average:56.529; most accessible tissue: Zhenshan97 panicle, score: 72.468 N N N N
vg0622495913 A -> G LOC_Os06g38050.1 upstream_gene_variant ; 680.0bp to feature; MODIFIER silent_mutation Average:56.529; most accessible tissue: Zhenshan97 panicle, score: 72.468 N N N N
vg0622495913 A -> G LOC_Os06g38040-LOC_Os06g38050 intergenic_region ; MODIFIER silent_mutation Average:56.529; most accessible tissue: Zhenshan97 panicle, score: 72.468 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0622495913 1.54E-07 NA mr1136 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
vg0622495913 NA 6.31E-07 mr1136 Jap_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
vg0622495913 NA 2.17E-06 mr1691_2 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
vg0622495913 NA 9.88E-11 mr1851_2 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