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Detailed information for vg0628274142:

Variant ID: vg0628274142 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 28274142
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAAGTTGAGGCTAAGACAAAGAGTGTGTGAAGTTGAGGCTAAGATAAAAAATAGACTTATTCTATGGAGAAGCACGATGGGCTGTCGTGCCTTCGGGTTG[G/A]
CTCGGCATGGCCCGAGTCTTATTGGACCATGCCTTGGGCTATGTGTAGCCCGTGGGCTGGCACAGCACGGCCCGACGTGTAGGCGAGCCGTGCCGGCCCT

Reverse complement sequence

AGGGCCGGCACGGCTCGCCTACACGTCGGGCCGTGCTGTGCCAGCCCACGGGCTACACATAGCCCAAGGCATGGTCCAATAAGACTCGGGCCATGCCGAG[C/T]
CAACCCGAAGGCACGACAGCCCATCGTGCTTCTCCATAGAATAAGTCTATTTTTTATCTTAGCCTCAACTTCACACACTCTTTGTCTTAGCCTCAACTTC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 55.90% 43.70% 0.11% 0.28% NA
All Indica  2759 89.40% 10.00% 0.14% 0.40% NA
All Japonica  1512 3.00% 96.90% 0.07% 0.00% NA
Aus  269 29.00% 71.00% 0.00% 0.00% NA
Indica I  595 95.00% 3.90% 0.34% 0.84% NA
Indica II  465 80.00% 20.00% 0.00% 0.00% NA
Indica III  913 91.60% 8.10% 0.11% 0.22% NA
Indica Intermediate  786 88.30% 11.10% 0.13% 0.51% NA
Temperate Japonica  767 3.10% 96.70% 0.13% 0.00% NA
Tropical Japonica  504 3.60% 96.40% 0.00% 0.00% NA
Japonica Intermediate  241 1.70% 98.30% 0.00% 0.00% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 52.20% 45.60% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0628274142 G -> A LOC_Os06g46560.1 upstream_gene_variant ; 1209.0bp to feature; MODIFIER silent_mutation Average:74.661; most accessible tissue: Zhenshan97 panicle, score: 87.126 N N N N
vg0628274142 G -> A LOC_Os06g46570.1 upstream_gene_variant ; 1501.0bp to feature; MODIFIER silent_mutation Average:74.661; most accessible tissue: Zhenshan97 panicle, score: 87.126 N N N N
vg0628274142 G -> A LOC_Os06g46570.2 upstream_gene_variant ; 1501.0bp to feature; MODIFIER silent_mutation Average:74.661; most accessible tissue: Zhenshan97 panicle, score: 87.126 N N N N
vg0628274142 G -> A LOC_Os06g46560-LOC_Os06g46570 intergenic_region ; MODIFIER silent_mutation Average:74.661; most accessible tissue: Zhenshan97 panicle, score: 87.126 N N N N
vg0628274142 G -> DEL N N silent_mutation Average:74.661; most accessible tissue: Zhenshan97 panicle, score: 87.126 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0628274142 4.52E-06 4.52E-06 mr1392 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
vg0628274142 NA 2.44E-19 mr1598 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