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Detailed information for vg1217394893:

Variant ID: vg1217394893 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 17394893
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTATTAGTGGTCTCTCTATTATCATGCAAGTAAAGTAAATTTGATAGTATAGAAGAAAGAGAAAGGAGGAAAGAGAAATATGGTTGTTATGCAGGTCTAC[G/A]
GTTCAGAGTCGACTCTTAGCATTTATTAATGGTAGAGACCATATTGTCTTCAACTGTTGTATGACGTTAGTCTCTCTAGATAGCGTAGAGCTCATACCCG

Reverse complement sequence

CGGGTATGAGCTCTACGCTATCTAGAGAGACTAACGTCATACAACAGTTGAAGACAATATGGTCTCTACCATTAATAAATGCTAAGAGTCGACTCTGAAC[C/T]
GTAGACCTGCATAACAACCATATTTCTCTTTCCTCCTTTCTCTTTCTTCTATACTATCAAATTTACTTTACTTGCATGATAATAGAGAGACCACTAATAA

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 80.80% 19.00% 0.19% 0.00% NA
All Indica  2759 73.90% 25.80% 0.29% 0.00% NA
All Japonica  1512 88.90% 11.10% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 87.10% 12.90% 0.00% 0.00% NA
Indica II  465 96.60% 3.40% 0.00% 0.00% NA
Indica III  913 50.20% 49.50% 0.33% 0.00% NA
Indica Intermediate  786 78.10% 21.20% 0.64% 0.00% NA
Temperate Japonica  767 95.60% 4.40% 0.00% 0.00% NA
Tropical Japonica  504 85.50% 14.50% 0.00% 0.00% NA
Japonica Intermediate  241 74.70% 25.30% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 2.10% 1.04% 0.00% NA
Intermediate  90 84.40% 15.60% 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
vg1217394893 G -> A LOC_Os12g29330.1 downstream_gene_variant ; 2161.0bp to feature; MODIFIER silent_mutation Average:65.413; most accessible tissue: Minghui63 root, score: 77.832 N N N N
vg1217394893 G -> A LOC_Os12g29330-LOC_Os12g29340 intergenic_region ; MODIFIER silent_mutation Average:65.413; most accessible tissue: Minghui63 root, score: 77.832 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1217394893 NA 3.82E-06 mr1015 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
vg1217394893 NA 1.43E-08 mr1092_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
vg1217394893 NA 5.31E-07 mr1152_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
vg1217394893 NA 1.01E-06 mr1154_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
vg1217394893 NA 9.06E-06 mr1539_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
vg1217394893 NA 8.74E-06 mr1968_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