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Detailed information for vg0612205203:

Variant ID: vg0612205203 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 12205203
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:


TCTCCCCCTTTTTAAAAGAAAGAAATTCCCAATTGAACATTCCCAATTGAACCAAAAACATGCTCTCCAAAAACTCTTCTTTTCTTCCCCTTTTGACAAT[G/T]
ATTTCATCAAACATAGGAATTATGTTCATTAAAGTATAAGAGCTTAGCATACATATAGCATATCATGTCATGTGTTGCAATAAAAAGAAAATGAACCCAT

Reverse complement sequence

ATGGGTTCATTTTCTTTTTATTGCAACACATGACATGATATGCTATATGTATGCTAAGCTCTTATACTTTAATGAACATAATTCCTATGTTTGATGAAAT[C/A]
ATTGTCAAAAGGGGAAGAAAAGAAGAGTTTTTGGAGAGCATGTTTTTGGTTCAATTGGGAATGTTCAATTGGGAATTTCTTTCTTTTAAAAAGGGGGAGA

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 95.50% 4.50% 0.00% 0.00% NA
All Indica  2759 92.80% 7.20% 0.00% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 91.20% 8.80% 0.00% 0.00% NA
Indica III  913 88.10% 11.90% 0.00% 0.00% NA
Indica Intermediate  786 93.60% 6.40% 0.00% 0.00% NA
Temperate Japonica  767 99.00% 1.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0612205203 G -> T LOC_Os06g21130.1 downstream_gene_variant ; 2262.0bp to feature; MODIFIER silent_mutation Average:19.206; most accessible tissue: Callus, score: 33.265 N N N N
vg0612205203 G -> T LOC_Os06g21120.1 downstream_gene_variant ; 4541.0bp to feature; MODIFIER silent_mutation Average:19.206; most accessible tissue: Callus, score: 33.265 N N N N
vg0612205203 G -> T LOC_Os06g21120-LOC_Os06g21130 intergenic_region ; MODIFIER silent_mutation Average:19.206; most accessible tissue: Callus, score: 33.265 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0612205203 6.92E-06 NA mr1068 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
vg0612205203 1.77E-07 4.02E-09 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
vg0612205203 2.82E-06 NA mr1111 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
vg0612205203 7.93E-07 4.19E-07 mr1121 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
vg0612205203 7.57E-08 2.21E-09 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
vg0612205203 3.71E-07 NA mr1068_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
vg0612205203 2.90E-09 4.44E-09 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
vg0612205203 2.90E-07 NA mr1094_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
vg0612205203 4.82E-06 NA mr1096_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
vg0612205203 9.38E-07 NA mr1111_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
vg0612205203 6.36E-08 1.51E-07 mr1121_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
vg0612205203 5.93E-07 NA mr1144_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
vg0612205203 1.51E-08 6.25E-10 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