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Detailed information for vg0804188825:

Variant ID: vg0804188825 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 4188825
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGTTGACTCCTTCACCCTCCCCCTTCCCACCTCTGCCCCAGCCCCAAATCCCAATGGCCTAATTCGATATGCTTGCTAGAGCTGGGATCATCATTGGCAC[C/A]
ACACCACCGCCAGTGAGTACGGGTATTATGCTAGTATGAGAAAATATTGCAAGAGTTTATTGTAGGAAATAAAATAATTCTGGGAATGGGGAGGTTGGAC

Reverse complement sequence

GTCCAACCTCCCCATTCCCAGAATTATTTTATTTCCTACAATAAACTCTTGCAATATTTTCTCATACTAGCATAATACCCGTACTCACTGGCGGTGGTGT[G/T]
GTGCCAATGATGATCCCAGCTCTAGCAAGCATATCGAATTAGGCCATTGGGATTTGGGGCTGGGGCAGAGGTGGGAAGGGGGAGGGTGAAGGAGTCAACT

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 83.30% 16.40% 0.06% 0.21% NA
All Indica  2759 71.90% 27.60% 0.07% 0.36% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 44.50% 54.80% 0.17% 0.50% NA
Indica II  465 91.60% 8.40% 0.00% 0.00% NA
Indica III  913 72.00% 27.60% 0.00% 0.44% NA
Indica Intermediate  786 81.00% 18.40% 0.13% 0.38% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg0804188825 C -> A LOC_Os08g07460.1 upstream_gene_variant ; 1774.0bp to feature; MODIFIER silent_mutation Average:55.502; most accessible tissue: Callus, score: 75.954 N N N N
vg0804188825 C -> A LOC_Os08g07470.1 downstream_gene_variant ; 679.0bp to feature; MODIFIER silent_mutation Average:55.502; most accessible tissue: Callus, score: 75.954 N N N N
vg0804188825 C -> A LOC_Os08g07480.1 downstream_gene_variant ; 2780.0bp to feature; MODIFIER silent_mutation Average:55.502; most accessible tissue: Callus, score: 75.954 N N N N
vg0804188825 C -> A LOC_Os08g07460-LOC_Os08g07470 intergenic_region ; MODIFIER silent_mutation Average:55.502; most accessible tissue: Callus, score: 75.954 N N N N
vg0804188825 C -> DEL N N silent_mutation Average:55.502; most accessible tissue: Callus, score: 75.954 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0804188825 NA 2.68E-06 mr1181 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
vg0804188825 5.51E-06 4.98E-08 mr1347 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