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Detailed information for vg0406060650:

Variant ID: vg0406060650 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 6060650
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.82, G: 0.18, others allele: 0.00, population size: 112. )

Flanking Sequence (100 bp) in Reference Genome:


ACCAGGTTACAAACCACCAAGGGATGTAATGTGCCCGGTATTAATAGCTGGAGTGTGTTAAATACCCGGCTTTAAAGTTTGAGGGTGTATTTTATACAAA[A/G]
TGAATAATTAAGGGGGTTAAAATAGACTTATCCCTTTTTTTTAAGTCATAAGGATTTTTATCCAATTATTTTTCTTCTTTACATGTATTGTCCAATTCTT

Reverse complement sequence

AAGAATTGGACAATACATGTAAAGAAGAAAAATAATTGGATAAAAATCCTTATGACTTAAAAAAAAGGGATAAGTCTATTTTAACCCCCTTAATTATTCA[T/C]
TTTGTATAAAATACACCCTCAAACTTTAAAGCCGGGTATTTAACACACTCCAGCTATTAATACCGGGCACATTACATCCCTTGGTGGTTTGTAACCTGGT

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 77.70% 22.20% 0.06% 0.00% NA
All Indica  2759 78.90% 21.00% 0.07% 0.00% NA
All Japonica  1512 79.80% 20.20% 0.07% 0.00% NA
Aus  269 62.80% 37.20% 0.00% 0.00% NA
Indica I  595 79.20% 20.80% 0.00% 0.00% NA
Indica II  465 80.90% 19.10% 0.00% 0.00% NA
Indica III  913 81.90% 18.10% 0.00% 0.00% NA
Indica Intermediate  786 74.00% 25.70% 0.25% 0.00% NA
Temperate Japonica  767 95.20% 4.80% 0.00% 0.00% NA
Tropical Japonica  504 51.80% 48.00% 0.20% 0.00% NA
Japonica Intermediate  241 89.20% 10.80% 0.00% 0.00% NA
VI/Aromatic  96 55.20% 44.80% 0.00% 0.00% NA
Intermediate  90 75.60% 24.40% 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
vg0406060650 A -> G LOC_Os04g11140.1 upstream_gene_variant ; 744.0bp to feature; MODIFIER silent_mutation Average:41.022; most accessible tissue: Callus, score: 64.184 N N N N
vg0406060650 A -> G LOC_Os04g11150.1 upstream_gene_variant ; 1447.0bp to feature; MODIFIER silent_mutation Average:41.022; most accessible tissue: Callus, score: 64.184 N N N N
vg0406060650 A -> G LOC_Os04g11140-LOC_Os04g11150 intergenic_region ; MODIFIER silent_mutation Average:41.022; most accessible tissue: Callus, score: 64.184 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0406060650 NA 5.47E-06 mr1035 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
vg0406060650 NA 8.77E-06 mr1100 Jap_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
vg0406060650 NA 1.13E-07 mr1613 Jap_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
vg0406060650 NA 4.89E-06 mr1619 Jap_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
vg0406060650 4.86E-07 4.07E-08 mr1071_2 Jap_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
vg0406060650 1.34E-06 1.89E-08 mr1080_2 Jap_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
vg0406060650 4.34E-06 8.90E-10 mr1100_2 Jap_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
vg0406060650 8.04E-07 3.20E-08 mr1203_2 Jap_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
vg0406060650 NA 2.99E-07 mr1402_2 Jap_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
vg0406060650 1.81E-07 6.35E-10 mr1613_2 Jap_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
vg0406060650 NA 5.76E-07 mr1619_2 Jap_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
vg0406060650 1.93E-06 1.39E-09 mr1913_2 Jap_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
vg0406060650 1.06E-06 2.21E-10 mr1962_2 Jap_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