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Detailed information for vg0820759056:

Variant ID: vg0820759056 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 20759056
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGACTATTAATAAAACTCATCCATAATCTTGGACTAATTCGCGAGACGAATCTATTGAGCCTAATTAATCTATGATTAGCCTATGTTATGCTACAGTAAA[T/C]
ATTCTCTAATTATAGATTAATTAGGCTTAAAAATTTTGTCTCGCAAATTAGCTTTCATTTATGTAATTAGTTTTGTAAGTAGTCTATATTTAAAATTAGT

Reverse complement sequence

ACTAATTTTAAATATAGACTACTTACAAAACTAATTACATAAATGAAAGCTAATTTGCGAGACAAAATTTTTAAGCCTAATTAATCTATAATTAGAGAAT[A/G]
TTTACTGTAGCATAACATAGGCTAATCATAGATTAATTAGGCTCAATAGATTCGTCTCGCGAATTAGTCCAAGATTATGGATGAGTTTTATTAATAGTCT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.20% 37.70% 0.13% 0.00% NA
All Indica  2759 94.50% 5.40% 0.11% 0.00% NA
All Japonica  1512 3.50% 96.40% 0.07% 0.00% NA
Aus  269 74.70% 25.30% 0.00% 0.00% NA
Indica I  595 98.30% 1.70% 0.00% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 91.10% 8.90% 0.00% 0.00% NA
Indica Intermediate  786 92.90% 6.70% 0.38% 0.00% NA
Temperate Japonica  767 2.00% 98.00% 0.00% 0.00% NA
Tropical Japonica  504 4.40% 95.60% 0.00% 0.00% NA
Japonica Intermediate  241 6.60% 92.90% 0.41% 0.00% NA
VI/Aromatic  96 37.50% 62.50% 0.00% 0.00% NA
Intermediate  90 47.80% 50.00% 2.22% 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
vg0820759056 T -> C LOC_Os08g33300.1 downstream_gene_variant ; 2478.0bp to feature; MODIFIER silent_mutation Average:52.885; most accessible tissue: Callus, score: 92.504 N N N N
vg0820759056 T -> C LOC_Os08g33290-LOC_Os08g33300 intergenic_region ; MODIFIER silent_mutation Average:52.885; most accessible tissue: Callus, score: 92.504 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0820759056 NA 4.89E-15 mr1228 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
vg0820759056 NA 8.59E-29 mr1638 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
vg0820759056 1.43E-06 7.57E-06 mr1791 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
vg0820759056 NA 1.64E-20 mr1838 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
vg0820759056 NA 2.59E-17 mr1968 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
vg0820759056 NA 2.87E-25 mr1350_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