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Detailed information for vg0208505848:

Variant ID: vg0208505848 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 8505848
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


GTGCTTTCTATTGTACTCATGGGTCATGGCAATTGAAGAATATGATATTATTGGAATAATTGTGCCAAAAAAAACTCATGTAAACATTTTCAAGCCAACT[C/T]
ACACATTTAAAAGTAAAAATGCAACAGCATACTGGCAGATTTTTTTTAGTAAATTTCATAAAACCTTACATATTATGATCCAAGTTGCATAAAATTTCAT

Reverse complement sequence

ATGAAATTTTATGCAACTTGGATCATAATATGTAAGGTTTTATGAAATTTACTAAAAAAAATCTGCCAGTATGCTGTTGCATTTTTACTTTTAAATGTGT[G/A]
AGTTGGCTTGAAAATGTTTACATGAGTTTTTTTTGGCACAATTATTCCAATAATATCATATTCTTCAATTGCCATGACCCATGAGTACAATAGAAAGCAC

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 84.60% 15.30% 0.11% 0.00% NA
All Indica  2759 83.90% 15.90% 0.14% 0.00% NA
All Japonica  1512 83.70% 16.30% 0.07% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 62.70% 37.00% 0.34% 0.00% NA
Indica II  465 94.80% 5.20% 0.00% 0.00% NA
Indica III  913 90.80% 9.10% 0.11% 0.00% NA
Indica Intermediate  786 85.50% 14.40% 0.13% 0.00% NA
Temperate Japonica  767 97.50% 2.30% 0.13% 0.00% NA
Tropical Japonica  504 58.10% 41.90% 0.00% 0.00% NA
Japonica Intermediate  241 92.90% 7.10% 0.00% 0.00% NA
VI/Aromatic  96 74.00% 26.00% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0208505848 C -> T LOC_Os02g15230.1 downstream_gene_variant ; 871.0bp to feature; MODIFIER silent_mutation Average:79.6; most accessible tissue: Zhenshan97 root, score: 88.238 N N N N
vg0208505848 C -> T LOC_Os02g15240.1 downstream_gene_variant ; 2656.0bp to feature; MODIFIER silent_mutation Average:79.6; most accessible tissue: Zhenshan97 root, score: 88.238 N N N N
vg0208505848 C -> T LOC_Os02g15230.2 downstream_gene_variant ; 872.0bp to feature; MODIFIER silent_mutation Average:79.6; most accessible tissue: Zhenshan97 root, score: 88.238 N N N N
vg0208505848 C -> T LOC_Os02g15230.3 downstream_gene_variant ; 872.0bp to feature; MODIFIER silent_mutation Average:79.6; most accessible tissue: Zhenshan97 root, score: 88.238 N N N N
vg0208505848 C -> T LOC_Os02g15230-LOC_Os02g15240 intergenic_region ; MODIFIER silent_mutation Average:79.6; most accessible tissue: Zhenshan97 root, score: 88.238 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0208505848 NA 2.92E-06 mr1336 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
vg0208505848 2.90E-07 1.70E-12 mr1410 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
vg0208505848 NA 8.25E-06 mr1174_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
vg0208505848 NA 9.39E-07 mr1347_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
vg0208505848 1.33E-09 1.43E-12 mr1410_2 Jap_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