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Detailed information for vg0828075962:

Variant ID: vg0828075962 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 28075962
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:


AATTTGGCTAACTATTGGCTAGATTGATTGGTACGCTAATGTACATGGTAAAACACAAATGTTCAGACAGAGAGATGGAAAAGTTGTTAATAGCAACTTG[C/A]
TGGGTGCATGTGGCTGGGCGAAGCTCTGAAGTGAAAAACTCAGAGTCATTAACAAGATATATAAACTTTTTACAGAAACCAGAGGAAGAAAGACATAAGA

Reverse complement sequence

TCTTATGTCTTTCTTCCTCTGGTTTCTGTAAAAAGTTTATATATCTTGTTAATGACTCTGAGTTTTTCACTTCAGAGCTTCGCCCAGCCACATGCACCCA[G/T]
CAAGTTGCTATTAACAACTTTTCCATCTCTCTGTCTGAACATTTGTGTTTTACCATGTACATTAGCGTACCAATCAATCTAGCCAATAGTTAGCCAAATT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.40% 4.00% 1.61% 0.00% NA
All Indica  2759 90.80% 6.70% 2.54% 0.00% NA
All Japonica  1512 99.70% 0.20% 0.13% 0.00% NA
Aus  269 98.90% 0.00% 1.12% 0.00% NA
Indica I  595 87.60% 8.40% 4.03% 0.00% NA
Indica II  465 97.80% 0.20% 1.94% 0.00% NA
Indica III  913 92.00% 7.60% 0.44% 0.00% NA
Indica Intermediate  786 87.70% 8.10% 4.20% 0.00% NA
Temperate Japonica  767 99.70% 0.00% 0.26% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 4.40% 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
vg0828075962 C -> A LOC_Os08g44660.1 upstream_gene_variant ; 1566.0bp to feature; MODIFIER silent_mutation Average:58.471; most accessible tissue: Callus, score: 84.359 N N N N
vg0828075962 C -> A LOC_Os08g44640.1 downstream_gene_variant ; 1324.0bp to feature; MODIFIER silent_mutation Average:58.471; most accessible tissue: Callus, score: 84.359 N N N N
vg0828075962 C -> A LOC_Os08g44640.3 downstream_gene_variant ; 1948.0bp to feature; MODIFIER silent_mutation Average:58.471; most accessible tissue: Callus, score: 84.359 N N N N
vg0828075962 C -> A LOC_Os08g44640.2 downstream_gene_variant ; 1324.0bp to feature; MODIFIER silent_mutation Average:58.471; most accessible tissue: Callus, score: 84.359 N N N N
vg0828075962 C -> A LOC_Os08g44650.1 intron_variant ; MODIFIER silent_mutation Average:58.471; most accessible tissue: Callus, score: 84.359 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0828075962 NA 8.83E-06 mr1291 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
vg0828075962 4.83E-06 4.83E-06 mr1966 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
vg0828075962 NA 5.37E-06 mr1975 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
vg0828075962 NA 7.70E-06 mr1291_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
vg0828075962 NA 1.25E-07 mr1543_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