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Detailed information for vg0612532192:

Variant ID: vg0612532192 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 12532192
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGGGGGAAAACTTAGCATGTCGCAACAAAAGCATCGATTCGAGGCGTCAGCAAAACACCGCCGTCTGTTCCTAAAACAAAACCCCTTAGCGCCCCGGGGC[G/A]
GGAGTGGGGGACGGCCCTATGCAGACAGCAACAGCACCGGCTCTACGAAGTCCGAATTGAATCTTTTGGTTCCCTTGAATAAGAATTGTTGGGCGCGGCG

Reverse complement sequence

CGCCGCGCCCAACAATTCTTATTCAAGGGAACCAAAAGATTCAATTCGGACTTCGTAGAGCCGGTGCTGTTGCTGTCTGCATAGGGCCGTCCCCCACTCC[C/T]
GCCCCGGGGCGCTAAGGGGTTTTGTTTTAGGAACAGACGGCGGTGTTTTGCTGACGCCTCGAATCGATGCTTTTGTTGCGACATGCTAAGTTTTCCCCCC

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 62.00% 37.80% 0.11% 0.04% NA
All Indica  2759 95.40% 4.50% 0.04% 0.07% NA
All Japonica  1512 2.80% 97.20% 0.07% 0.00% NA
Aus  269 63.20% 36.80% 0.00% 0.00% NA
Indica I  595 93.90% 5.90% 0.00% 0.17% NA
Indica II  465 96.60% 3.20% 0.00% 0.22% NA
Indica III  913 98.90% 1.10% 0.00% 0.00% NA
Indica Intermediate  786 91.70% 8.10% 0.13% 0.00% NA
Temperate Japonica  767 3.00% 97.00% 0.00% 0.00% NA
Tropical Japonica  504 2.00% 98.00% 0.00% 0.00% NA
Japonica Intermediate  241 3.70% 95.90% 0.41% 0.00% NA
VI/Aromatic  96 42.70% 57.30% 0.00% 0.00% NA
Intermediate  90 51.10% 45.60% 3.33% 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
vg0612532192 G -> A LOC_Os06g21690.1 upstream_gene_variant ; 4966.0bp to feature; MODIFIER silent_mutation Average:48.239; most accessible tissue: Zhenshan97 flag leaf, score: 68.703 N N N N
vg0612532192 G -> A LOC_Os06g21680-LOC_Os06g21690 intergenic_region ; MODIFIER silent_mutation Average:48.239; most accessible tissue: Zhenshan97 flag leaf, score: 68.703 N N N N
vg0612532192 G -> DEL N N silent_mutation Average:48.239; most accessible tissue: Zhenshan97 flag leaf, score: 68.703 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0612532192 NA 2.66E-43 mr1067 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
vg0612532192 NA 1.29E-22 mr1888 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
vg0612532192 NA 1.00E-07 mr1946 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
vg0612532192 NA 1.09E-57 mr1067_2 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
vg0612532192 NA 2.23E-17 mr1199_2 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
vg0612532192 NA 2.01E-57 mr1526_2 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
vg0612532192 NA 5.03E-07 mr1819_2 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
vg0612532192 1.62E-06 NA mr1929_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