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Detailed information for vg0232811799:

Variant ID: vg0232811799 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 32811799
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, C: 0.03, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:


TCTTCCAGGAGCAAGTCGGCTATGATGAGTTTTAGGGTTTCGATCTAGTTCCCAAGTCGCGCCTGTGATGAATGGTCCAAGTCTTGGCTTCCGCTTTCCT[A/C]
TTTTGTAATGCAGTTGTGAGCTCGGGGTCTGTCTGCAGCCCATCATGACTGTAATCCTACTCTATAATAAAGAGACCTCTGTTGCTGTGGTATTCAGTTT

Reverse complement sequence

AAACTGAATACCACAGCAACAGAGGTCTCTTTATTATAGAGTAGGATTACAGTCATGATGGGCTGCAGACAGACCCCGAGCTCACAACTGCATTACAAAA[T/G]
AGGAAAGCGGAAGCCAAGACTTGGACCATTCATCACAGGCGCGACTTGGGAACTAGATCGAAACCCTAAAACTCATCATAGCCGACTTGCTCCTGGAAGA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.40% 7.60% 0.00% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 77.20% 22.80% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 0.00% 0.00% NA
Temperate Japonica  767 57.40% 42.60% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 92.90% 7.10% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0232811799 A -> C LOC_Os02g53640.1 upstream_gene_variant ; 1603.0bp to feature; MODIFIER silent_mutation Average:48.402; most accessible tissue: Minghui63 young leaf, score: 61.887 N N N N
vg0232811799 A -> C LOC_Os02g53650.1 upstream_gene_variant ; 382.0bp to feature; MODIFIER silent_mutation Average:48.402; most accessible tissue: Minghui63 young leaf, score: 61.887 N N N N
vg0232811799 A -> C LOC_Os02g53630.1 downstream_gene_variant ; 4072.0bp to feature; MODIFIER silent_mutation Average:48.402; most accessible tissue: Minghui63 young leaf, score: 61.887 N N N N
vg0232811799 A -> C LOC_Os02g53640-LOC_Os02g53650 intergenic_region ; MODIFIER silent_mutation Average:48.402; most accessible tissue: Minghui63 young leaf, score: 61.887 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0232811799 6.09E-09 NA mr1062_2 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
vg0232811799 6.84E-06 1.13E-08 mr1062_2 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
vg0232811799 NA 2.02E-06 mr1693_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