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Detailed information for vg0611438806:

Variant ID: vg0611438806 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 11438806
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.77, G: 0.23, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:


TGACGACTTGCAAGTTACAAAGAACGATGTCGAGACAATTATCAATTGGGAAAAGACATCTCCAAAGCTGGCTGAGATACCATTCAAGCCAGCAAGATGT[G/A]
TCCTAATGGTCTTGAATTGACACATCACACAAAGTATTAGTATTGTTTTATATAAATGTCTTTTGCTTATAATCGGATTTACTCACTAGGACAACACTGG

Reverse complement sequence

CCAGTGTTGTCCTAGTGAGTAAATCCGATTATAAGCAAAAGACATTTATATAAAACAATACTAATACTTTGTGTGATGTGTCAATTCAAGACCATTAGGA[C/T]
ACATCTTGCTGGCTTGAATGGTATCTCAGCCAGCTTTGGAGATGTCTTTTCCCAATTGATAATTGTCTCGACATCGTTCTTTGTAACTTGCAAGTCGTCA

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 37.90% 16.10% 1.23% 44.84% NA
All Indica  2759 4.30% 21.80% 1.78% 72.09% NA
All Japonica  1512 88.50% 8.80% 0.33% 2.38% NA
Aus  269 75.50% 0.40% 1.49% 22.68% NA
Indica I  595 7.40% 2.00% 2.52% 88.07% NA
Indica II  465 2.80% 6.70% 1.29% 89.25% NA
Indica III  913 1.20% 44.10% 1.53% 53.12% NA
Indica Intermediate  786 6.60% 19.70% 1.78% 71.88% NA
Temperate Japonica  767 95.80% 0.50% 0.39% 3.26% NA
Tropical Japonica  504 74.80% 24.20% 0.20% 0.79% NA
Japonica Intermediate  241 93.80% 2.90% 0.41% 2.90% NA
VI/Aromatic  96 85.40% 7.30% 0.00% 7.29% NA
Intermediate  90 52.20% 18.90% 0.00% 28.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0611438806 G -> A LOC_Os06g19960.1 upstream_gene_variant ; 346.0bp to feature; MODIFIER silent_mutation Average:11.97; most accessible tissue: Callus, score: 86.999 N N N N
vg0611438806 G -> A LOC_Os06g19950-LOC_Os06g19960 intergenic_region ; MODIFIER silent_mutation Average:11.97; most accessible tissue: Callus, score: 86.999 N N N N
vg0611438806 G -> DEL N N silent_mutation Average:11.97; most accessible tissue: Callus, score: 86.999 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0611438806 NA 4.61E-09 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
vg0611438806 NA 3.47E-07 mr1078 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
vg0611438806 NA 1.44E-06 mr1094 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
vg0611438806 NA 1.43E-07 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
vg0611438806 NA 2.23E-06 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
vg0611438806 NA 2.47E-08 mr1144 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
vg0611438806 NA 3.24E-09 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
vg0611438806 NA 3.26E-06 mr1094_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
vg0611438806 NA 2.93E-07 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
vg0611438806 NA 3.15E-07 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
vg0611438806 NA 2.30E-06 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
vg0611438806 NA 6.32E-08 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
vg0611438806 1.92E-07 NA mr1165_2 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
vg0611438806 NA 1.51E-08 mr1526_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
vg0611438806 5.28E-06 NA mr1971_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