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Detailed information for vg1125871704:

Variant ID: vg1125871704 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25871704
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.53, C: 0.47, others allele: 0.00, population size: 70. )

Flanking Sequence (100 bp) in Reference Genome:


TGATGACTTAGGGGCTTACCAAATTTTGGCATTAACACCCCCACCCCCACCGTGTCCCTTTTGTTATGGTTTTCTTCATTGCCAACCTTTACCGTCTATG[G/C]
ATGAGTCACATCGTGGGACACACCCTACCACTTTTCTCACCGTCGTTTGGTCGATGGAGCACCGACACCCATTTTCCCTCCTCTTTTATTTCTCGCATTG

Reverse complement sequence

CAATGCGAGAAATAAAAGAGGAGGGAAAATGGGTGTCGGTGCTCCATCGACCAAACGACGGTGAGAAAAGTGGTAGGGTGTGTCCCACGATGTGACTCAT[C/G]
CATAGACGGTAAAGGTTGGCAATGAAGAAAACCATAACAAAAGGGACACGGTGGGGGTGGGGGTGTTAATGCCAAAATTTGGTAAGCCCCTAAGTCATCA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 36.60% 26.80% 1.29% 35.29% NA
All Indica  2759 32.80% 38.30% 1.59% 27.29% NA
All Japonica  1512 44.60% 7.10% 0.66% 47.62% NA
Aus  269 25.30% 26.00% 1.86% 46.84% NA
Indica I  595 76.00% 20.30% 0.34% 3.36% NA
Indica II  465 23.70% 19.40% 3.01% 53.98% NA
Indica III  913 20.00% 48.70% 1.86% 29.35% NA
Indica Intermediate  786 20.20% 51.10% 1.40% 27.23% NA
Temperate Japonica  767 64.70% 4.60% 0.39% 30.38% NA
Tropical Japonica  504 14.90% 10.30% 0.99% 73.81% NA
Japonica Intermediate  241 43.20% 8.30% 0.83% 47.72% NA
VI/Aromatic  96 53.10% 3.10% 0.00% 43.75% NA
Intermediate  90 35.60% 32.20% 2.22% 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
vg1125871704 G -> DEL N N silent_mutation Average:40.266; most accessible tissue: Callus, score: 72.682 N N N N
vg1125871704 G -> C LOC_Os11g42920.1 downstream_gene_variant ; 2148.0bp to feature; MODIFIER silent_mutation Average:40.266; most accessible tissue: Callus, score: 72.682 N N N N
vg1125871704 G -> C LOC_Os11g42910-LOC_Os11g42920 intergenic_region ; MODIFIER silent_mutation Average:40.266; most accessible tissue: Callus, score: 72.682 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125871704 NA 2.78E-06 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
vg1125871704 NA 6.96E-14 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
vg1125871704 2.03E-10 2.03E-10 mr1191 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
vg1125871704 3.00E-12 2.99E-12 mr1644 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
vg1125871704 NA 2.48E-06 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
vg1125871704 NA 5.76E-07 mr1063_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
vg1125871704 NA 1.77E-17 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
vg1125871704 NA 1.92E-10 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
vg1125871704 6.74E-12 6.74E-12 mr1191_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
vg1125871704 NA 2.37E-12 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
vg1125871704 NA 2.93E-07 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