Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0825239616:

Variant ID: vg0825239616 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 25239616
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACGCCGGCGGCCGCTCTCCATGGCCTCTAGCCTTGAGCTCCGCCGCCCATTCCCCTTCTGCCCTCTCTCACTCTCTCGTATAATCAGAATAGGTGCCTGA[C/T]
AGGTAGGGCCCACCATTTTTATTATTGTTATTTCCATGTTGGACTGCCACATCAATCAAACCAGTGTCATGTGTGCGCCACGTCAAACCAAAACCACCCC

Reverse complement sequence

GGGGTGGTTTTGGTTTGACGTGGCGCACACATGACACTGGTTTGATTGATGTGGCAGTCCAACATGGAAATAACAATAATAAAAATGGTGGGCCCTACCT[G/A]
TCAGGCACCTATTCTGATTATACGAGAGAGTGAGAGAGGGCAGAAGGGGAATGGGCGGCGGAGCTCAAGGCTAGAGGCCATGGAGAGCGGCCGCCGGCGT

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 93.80% 6.20% 0.00% 0.00% NA
All Indica  2759 91.50% 8.50% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 79.60% 20.40% 0.00% 0.00% NA
Indica I  595 97.60% 2.40% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 85.40% 14.60% 0.00% 0.00% NA
Indica Intermediate  786 88.90% 11.10% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0825239616 C -> T LOC_Os08g39850.1 upstream_gene_variant ; 1290.0bp to feature; MODIFIER silent_mutation Average:55.203; most accessible tissue: Minghui63 root, score: 65.927 N N N N
vg0825239616 C -> T LOC_Os08g39850.3 upstream_gene_variant ; 1290.0bp to feature; MODIFIER silent_mutation Average:55.203; most accessible tissue: Minghui63 root, score: 65.927 N N N N
vg0825239616 C -> T LOC_Os08g39850.4 upstream_gene_variant ; 4798.0bp to feature; MODIFIER silent_mutation Average:55.203; most accessible tissue: Minghui63 root, score: 65.927 N N N N
vg0825239616 C -> T LOC_Os08g39850.2 upstream_gene_variant ; 4798.0bp to feature; MODIFIER silent_mutation Average:55.203; most accessible tissue: Minghui63 root, score: 65.927 N N N N
vg0825239616 C -> T LOC_Os08g39840-LOC_Os08g39850 intergenic_region ; MODIFIER silent_mutation Average:55.203; most accessible tissue: Minghui63 root, score: 65.927 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0825239616 NA 6.76E-08 mr1112 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
vg0825239616 1.36E-06 NA mr1874 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
vg0825239616 NA 2.95E-06 mr1533_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
vg0825239616 NA 8.18E-06 mr1699_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
vg0825239616 NA 1.04E-06 mr1874_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