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Detailed information for vg0306562863:

Variant ID: vg0306562863 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 6562863
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.00, T: 0.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


TGGAATGGATAATCCTATGCACATTTTGGAGGAAAGTTAGCAATAGGTCTATCCTCTTGGAACATTTCCTCTGAGTCTATCTCTCTCATCTGATTCCTGT[G/T]
TTTTTCCTGTGATCCAATCAAATGGCCATTCCTGTGTTTTGCAATCCTCTATTTTACAATTGTATTCCTGTCAGAATCCTGTGTTTTTCCTATTCCTCTG

Reverse complement sequence

CAGAGGAATAGGAAAAACACAGGATTCTGACAGGAATACAATTGTAAAATAGAGGATTGCAAAACACAGGAATGGCCATTTGATTGGATCACAGGAAAAA[C/A]
ACAGGAATCAGATGAGAGAGATAGACTCAGAGGAAATGTTCCAAGAGGATAGACCTATTGCTAACTTTCCTCCAAAATGTGCATAGGATTATCCATTCCA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.00% 4.20% 0.80% 0.00% NA
All Indica  2759 94.70% 4.00% 1.27% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.07% 0.00% NA
Aus  269 94.80% 5.20% 0.00% 0.00% NA
Indica I  595 99.30% 0.00% 0.67% 0.00% NA
Indica II  465 87.70% 9.90% 2.37% 0.00% NA
Indica III  913 96.70% 2.80% 0.44% 0.00% NA
Indica Intermediate  786 93.00% 5.00% 2.04% 0.00% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 36.50% 61.50% 2.08% 0.00% NA
Intermediate  90 86.70% 13.30% 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
vg0306562863 G -> T LOC_Os03g12414.1 upstream_gene_variant ; 838.0bp to feature; MODIFIER silent_mutation Average:54.884; most accessible tissue: Minghui63 flower, score: 81.973 N N N N
vg0306562863 G -> T LOC_Os03g12440.1 upstream_gene_variant ; 3286.0bp to feature; MODIFIER silent_mutation Average:54.884; most accessible tissue: Minghui63 flower, score: 81.973 N N N N
vg0306562863 G -> T LOC_Os03g12414.2 upstream_gene_variant ; 838.0bp to feature; MODIFIER silent_mutation Average:54.884; most accessible tissue: Minghui63 flower, score: 81.973 N N N N
vg0306562863 G -> T LOC_Os03g12430.1 downstream_gene_variant ; 491.0bp to feature; MODIFIER silent_mutation Average:54.884; most accessible tissue: Minghui63 flower, score: 81.973 N N N N
vg0306562863 G -> T LOC_Os03g12414-LOC_Os03g12430 intergenic_region ; MODIFIER silent_mutation Average:54.884; most accessible tissue: Minghui63 flower, score: 81.973 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0306562863 NA 1.84E-07 mr1090 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
vg0306562863 NA 1.83E-07 mr1211 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
vg0306562863 NA 2.33E-09 mr1498 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
vg0306562863 NA 9.59E-10 mr1769 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
vg0306562863 NA 3.82E-06 mr1925 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
vg0306562863 NA 1.81E-08 mr1951 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
vg0306562863 NA 8.24E-07 mr1090_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
vg0306562863 NA 9.32E-08 mr1211_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
vg0306562863 NA 4.68E-06 mr1310_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
vg0306562863 NA 4.65E-09 mr1498_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
vg0306562863 3.74E-06 4.03E-14 mr1769_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
vg0306562863 NA 8.47E-06 mr1916_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
vg0306562863 NA 1.34E-06 mr1951_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