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Detailed information for vg0406719900:

Variant ID: vg0406719900 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 6719900
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.66, G: 0.34, others allele: 0.00, population size: 35. )

Flanking Sequence (100 bp) in Reference Genome:


GTCAAAAAAGTGCCTATATTTAGTTTGCTGTCAAACTTTAGTAAATATATAAAAAATCCTGCCAAAAATTTTGGGAATATTGTCAATTTATCAAAATTTT[T/G]
GTATCACCAAAATTTGGTAAGGTTTATTTTAGCTACAATCTCAACAACCCCTAAATTAATTCCTACTTACTTGATGATGGAGCGTGCTTGTGATGGCTGG

Reverse complement sequence

CCAGCCATCACAAGCACGCTCCATCATCAAGTAAGTAGGAATTAATTTAGGGGTTGTTGAGATTGTAGCTAAAATAAACCTTACCAAATTTTGGTGATAC[A/C]
AAAATTTTGATAAATTGACAATATTCCCAAAATTTTTGGCAGGATTTTTTATATATTTACTAAAGTTTGACAGCAAACTAAATATAGGCACTTTTTTGAC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 35.00% 31.00% 0.53% 33.47% NA
All Indica  2759 5.20% 49.90% 0.72% 44.11% NA
All Japonica  1512 94.50% 1.90% 0.07% 3.51% NA
Aus  269 6.70% 1.10% 0.37% 91.82% NA
Indica I  595 7.90% 74.50% 0.17% 17.48% NA
Indica II  465 4.90% 25.80% 1.51% 67.74% NA
Indica III  913 1.60% 50.50% 0.55% 47.32% NA
Indica Intermediate  786 7.50% 45.00% 0.89% 46.56% NA
Temperate Japonica  767 96.20% 0.30% 0.13% 3.39% NA
Tropical Japonica  504 94.00% 4.00% 0.00% 1.98% NA
Japonica Intermediate  241 90.00% 2.90% 0.00% 7.05% NA
VI/Aromatic  96 22.90% 37.50% 0.00% 39.58% NA
Intermediate  90 46.70% 20.00% 3.33% 30.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0406719900 T -> DEL N N silent_mutation Average:10.075; most accessible tissue: Callus, score: 49.176 N N N N
vg0406719900 T -> G LOC_Os04g12190.1 downstream_gene_variant ; 3513.0bp to feature; MODIFIER silent_mutation Average:10.075; most accessible tissue: Callus, score: 49.176 N N N N
vg0406719900 T -> G LOC_Os04g12200.1 intron_variant ; MODIFIER silent_mutation Average:10.075; most accessible tissue: Callus, score: 49.176 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0406719900 NA 2.33E-22 mr1020 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
vg0406719900 NA 1.47E-20 mr1021 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
vg0406719900 NA 1.14E-13 mr1032 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
vg0406719900 NA 7.80E-17 mr1059 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
vg0406719900 NA 8.76E-17 mr1143 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
vg0406719900 NA 1.61E-16 mr1167 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
vg0406719900 1.18E-06 1.18E-06 mr1367 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
vg0406719900 NA 2.89E-20 mr1477 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
vg0406719900 NA 1.17E-14 mr1535 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
vg0406719900 NA 6.94E-11 mr1553 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
vg0406719900 NA 5.86E-16 mr1675 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
vg0406719900 NA 1.80E-06 mr1677 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
vg0406719900 NA 2.26E-14 mr1726 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
vg0406719900 NA 6.19E-18 mr1950 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
vg0406719900 NA 5.34E-15 mr1969 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
vg0406719900 NA 1.20E-20 mr1971 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
vg0406719900 NA 9.11E-17 mr1995 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
vg0406719900 NA 7.71E-14 mr1950_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