\

Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1125822467:

Variant ID: vg1125822467 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25822467
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.82, T: 0.18, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:


AGCTATTTGCTATACTCTCTTCCTCCCATTTCCCATTTTAAAGTTTTCGTGTTAAATGTTTTATTTAAAAAATTAAAAAATATTAGTCATATATAAAGTA[C/T]
TATTTATTTTTTATTATCTAATAATAATAAAATATGACTAATCATAAAAATATTTTAAATAAGACAGATAATCAAAGTTGGATTCAGAAACTCATAACTG

Reverse complement sequence

CAGTTATGAGTTTCTGAATCCAACTTTGATTATCTGTCTTATTTAAAATATTTTTATGATTAGTCATATTTTATTATTATTAGATAATAAAAAATAAATA[G/A]
TACTTTATATATGACTAATATTTTTTAATTTTTTAAATAAAACATTTAACACGAAAACTTTAAAATGGGAAATGGGAGGAAGAGAGTATAGCAAATAGCT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 74.80% 24.00% 0.80% 0.40% NA
All Indica  2759 64.50% 33.90% 1.23% 0.40% NA
All Japonica  1512 93.40% 6.40% 0.13% 0.07% NA
Aus  269 67.30% 31.60% 0.37% 0.74% NA
Indica I  595 91.60% 7.60% 0.67% 0.17% NA
Indica II  465 82.20% 17.40% 0.43% 0.00% NA
Indica III  913 46.10% 51.70% 1.53% 0.66% NA
Indica Intermediate  786 54.80% 42.90% 1.78% 0.51% NA
Temperate Japonica  767 98.20% 1.80% 0.00% 0.00% NA
Tropical Japonica  504 85.50% 14.10% 0.20% 0.20% NA
Japonica Intermediate  241 94.60% 5.00% 0.41% 0.00% NA
VI/Aromatic  96 95.80% 0.00% 0.00% 4.17% NA
Intermediate  90 76.70% 21.10% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1125822467 C -> T LOC_Os11g42860.1 upstream_gene_variant ; 4449.0bp to feature; MODIFIER silent_mutation Average:38.249; most accessible tissue: Minghui63 panicle, score: 85.069 N N N N
vg1125822467 C -> T LOC_Os11g42870.1 downstream_gene_variant ; 328.0bp to feature; MODIFIER silent_mutation Average:38.249; most accessible tissue: Minghui63 panicle, score: 85.069 N N N N
vg1125822467 C -> T LOC_Os11g42860-LOC_Os11g42870 intergenic_region ; MODIFIER silent_mutation Average:38.249; most accessible tissue: Minghui63 panicle, score: 85.069 N N N N
vg1125822467 C -> DEL N N silent_mutation Average:38.249; most accessible tissue: Minghui63 panicle, score: 85.069 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125822467 NA 7.61E-07 mr1063 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
vg1125822467 7.30E-10 4.02E-28 mr1133 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
vg1125822467 2.61E-09 1.40E-18 mr1133 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
vg1125822467 NA 7.10E-09 mr1533 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
vg1125822467 NA 8.07E-08 mr1662 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
vg1125822467 9.92E-07 9.50E-16 mr1667 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
vg1125822467 2.14E-06 4.43E-11 mr1667 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
vg1125822467 NA 7.18E-11 mr1980 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
vg1125822467 1.15E-07 1.19E-22 mr1133_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
vg1125822467 1.92E-07 1.70E-17 mr1133_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
vg1125822467 NA 5.55E-07 mr1662_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
vg1125822467 8.82E-07 1.40E-14 mr1667_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
vg1125822467 8.73E-07 6.71E-12 mr1667_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