\

Search for Variation information by Variation ID:

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

Detailed information for vg0709475005:

Variant ID: vg0709475005 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 9475005
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTGCTCGCTCGCTCGCACGATGGATGGGGATCGGCGCAGCGGCGGTGGCGGAGGATGTGCTCACCAGGATGCGGCGGATGCAGTAGGACGAACAACGAAG[C/T]
CCTACTTGCTCGCGGGATGGATGGGGATCGGCGGAAGCGGAGGCGGCAGAGCCGTAGAGGTGGCCAAGAGCAAAAAGGCGAGAAGGTAACTCACGCACGG

Reverse complement sequence

CCGTGCGTGAGTTACCTTCTCGCCTTTTTGCTCTTGGCCACCTCTACGGCTCTGCCGCCTCCGCTTCCGCCGATCCCCATCCATCCCGCGAGCAAGTAGG[G/A]
CTTCGTTGTTCGTCCTACTGCATCCGCCGCATCCTGGTGAGCACATCCTCCGCCACCGCCGCTGCGCCGATCCCCATCCATCGTGCGAGCGAGCGAGCAG

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 97.30% 2.10% 0.59% 0.00% NA
All Indica  2759 95.50% 3.60% 0.98% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 89.60% 6.70% 3.70% 0.00% NA
Indica II  465 95.90% 3.90% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 94.40% 5.10% 0.51% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 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% 1.10% 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
vg0709475005 C -> T LOC_Os07g16240.1 upstream_gene_variant ; 190.0bp to feature; MODIFIER silent_mutation Average:67.678; most accessible tissue: Zhenshan97 young leaf, score: 87.859 N N N N
vg0709475005 C -> T LOC_Os07g16224-LOC_Os07g16240 intergenic_region ; MODIFIER silent_mutation Average:67.678; most accessible tissue: Zhenshan97 young leaf, score: 87.859 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0709475005 NA 9.25E-08 mr1216 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
vg0709475005 NA 1.76E-06 mr1060_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
vg0709475005 NA 6.62E-06 mr1748_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
vg0709475005 NA 1.76E-06 mr1807_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