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Detailed information for vg0320912059:

Variant ID: vg0320912059 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 20912059
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:


CATGTAACTACAGTGTAACTTATATGTAAGTTTCACATAATTTTGAATCGTTAGATCTATTACAAGATTTGTTTTGGTGAGGAAGAAAACAAATCATAGC[A/G]
CACACATATATGAAAGAATTTGTTCCCACGACCTCCATTTTACCGAAATAACATGTTACGGAGAGATTTTTGAAAGTTAGTTACACTATAGTTACAACAG

Reverse complement sequence

CTGTTGTAACTATAGTGTAACTAACTTTCAAAAATCTCTCCGTAACATGTTATTTCGGTAAAATGGAGGTCGTGGGAACAAATTCTTTCATATATGTGTG[T/C]
GCTATGATTTGTTTTCTTCCTCACCAAAACAAATCTTGTAATAGATCTAACGATTCAAAATTATGTGAAACTTACATATAAGTTACACTGTAGTTACATG

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 93.10% 6.90% 0.00% 0.00% NA
All Indica  2759 88.30% 11.70% 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 60.70% 39.30% 0.00% 0.00% NA
Indica II  465 96.30% 3.70% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 90.80% 9.20% 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 95.60% 4.40% 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
vg0320912059 A -> G LOC_Os03g37710.1 upstream_gene_variant ; 1024.0bp to feature; MODIFIER silent_mutation Average:34.419; most accessible tissue: Callus, score: 76.809 N N N N
vg0320912059 A -> G LOC_Os03g37700.1 downstream_gene_variant ; 3531.0bp to feature; MODIFIER silent_mutation Average:34.419; most accessible tissue: Callus, score: 76.809 N N N N
vg0320912059 A -> G LOC_Os03g37720.1 downstream_gene_variant ; 1551.0bp to feature; MODIFIER silent_mutation Average:34.419; most accessible tissue: Callus, score: 76.809 N N N N
vg0320912059 A -> G LOC_Os03g37710-LOC_Os03g37720 intergenic_region ; MODIFIER silent_mutation Average:34.419; most accessible tissue: Callus, score: 76.809 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0320912059 NA 4.69E-06 mr1217 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
vg0320912059 NA 8.60E-06 mr1434 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
vg0320912059 NA 4.37E-06 mr1434 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
vg0320912059 7.34E-07 7.33E-07 mr1845 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