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Detailed information for vg0606129619:

Variant ID: vg0606129619 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 6129619
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCCAGGGGAGCTAAGGTAGCCATCCAACTCTTCCGTCGAGACTGTCCCAAGAGGTTGGAGTATAACGCCAACCTCTCTGGATCTAGATTGGATCGGGGCC[G/A]
AAGCCGGAGCTTGTCTAGATCTTCGAGTGGGAGATGTCTTGGCTGTGAAGACAGCGGCCAAATCATCAGGAAGTCTCATCAGGATTGAGGGATAGAACCC

Reverse complement sequence

GGGTTCTATCCCTCAATCCTGATGAGACTTCCTGATGATTTGGCCGCTGTCTTCACAGCCAAGACATCTCCCACTCGAAGATCTAGACAAGCTCCGGCTT[C/T]
GGCCCCGATCCAATCTAGATCCAGAGAGGTTGGCGTTATACTCCAACCTCTTGGGACAGTCTCGACGGAAGAGTTGGATGGCTACCTTAGCTCCCCTGGC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.10% 4.50% 8.29% 0.11% NA
All Indica  2759 82.60% 5.60% 11.67% 0.18% NA
All Japonica  1512 96.40% 1.30% 2.25% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 84.00% 3.90% 11.93% 0.17% NA
Indica II  465 83.20% 7.50% 9.03% 0.22% NA
Indica III  913 82.00% 5.60% 12.05% 0.33% NA
Indica Intermediate  786 81.70% 5.70% 12.60% 0.00% NA
Temperate Japonica  767 95.30% 2.00% 2.74% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 92.90% 2.10% 4.98% 0.00% NA
VI/Aromatic  96 24.00% 42.70% 33.33% 0.00% NA
Intermediate  90 95.60% 0.00% 4.44% 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
vg0606129619 G -> A LOC_Os06g11560.1 upstream_gene_variant ; 218.0bp to feature; MODIFIER silent_mutation Average:17.284; most accessible tissue: Zhenshan97 root, score: 32.766 N N N N
vg0606129619 G -> A LOC_Os06g11570.1 upstream_gene_variant ; 2284.0bp to feature; MODIFIER silent_mutation Average:17.284; most accessible tissue: Zhenshan97 root, score: 32.766 N N N N
vg0606129619 G -> A LOC_Os06g11560-LOC_Os06g11570 intergenic_region ; MODIFIER silent_mutation Average:17.284; most accessible tissue: Zhenshan97 root, score: 32.766 N N N N
vg0606129619 G -> DEL N N silent_mutation Average:17.284; most accessible tissue: Zhenshan97 root, score: 32.766 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0606129619 3.40E-06 NA mr1795 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
vg0606129619 NA 2.22E-06 mr1795_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
vg0606129619 NA 1.79E-06 mr1913_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