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Detailed information for vg1125421780:

Variant ID: vg1125421780 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25421780
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, T: 0.11, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


CATTTCCTTATCTCCCGTGTGATAATTTTTATCATTTGTTTAGTGCTGGTCAATTGCTAGTGCCTGGTCTTTGCATCCGTCTGCCACTCTGTTGAATAGT[G/T]
CCATGCAATGCATGTTTTTTTTCCCAAAACCAAACCATACAACTTTCAGTTATAAAGGGAAACCAGAATGGTAGACCATGCAATTCATTTATTTTTCTGA

Reverse complement sequence

TCAGAAAAATAAATGAATTGCATGGTCTACCATTCTGGTTTCCCTTTATAACTGAAAGTTGTATGGTTTGGTTTTGGGAAAAAAAACATGCATTGCATGG[C/A]
ACTATTCAACAGAGTGGCAGACGGATGCAAAGACCAGGCACTAGCAATTGACCAGCACTAAACAAATGATAAAAATTATCACACGGGAGATAAGGAAATG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.50% 13.50% 0.00% 0.00% NA
All Indica  2759 93.50% 6.50% 0.00% 0.00% NA
All Japonica  1512 78.40% 21.60% 0.00% 0.00% NA
Aus  269 71.70% 28.30% 0.00% 0.00% NA
Indica I  595 98.50% 1.50% 0.00% 0.00% NA
Indica II  465 84.10% 15.90% 0.00% 0.00% NA
Indica III  913 96.90% 3.10% 0.00% 0.00% NA
Indica Intermediate  786 91.20% 8.80% 0.00% 0.00% NA
Temperate Japonica  767 95.60% 4.40% 0.00% 0.00% NA
Tropical Japonica  504 49.40% 50.60% 0.00% 0.00% NA
Japonica Intermediate  241 84.60% 15.40% 0.00% 0.00% NA
VI/Aromatic  96 52.10% 47.90% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg1125421780 G -> T LOC_Os11g42200.1 upstream_gene_variant ; 1921.0bp to feature; MODIFIER silent_mutation Average:44.962; most accessible tissue: Zhenshan97 root, score: 79.452 N N N N
vg1125421780 G -> T LOC_Os11g42210.1 downstream_gene_variant ; 4616.0bp to feature; MODIFIER silent_mutation Average:44.962; most accessible tissue: Zhenshan97 root, score: 79.452 N N N N
vg1125421780 G -> T LOC_Os11g42190-LOC_Os11g42200 intergenic_region ; MODIFIER silent_mutation Average:44.962; most accessible tissue: Zhenshan97 root, score: 79.452 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125421780 4.65E-08 NA mr1238 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
vg1125421780 2.26E-13 1.98E-14 mr1238 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
vg1125421780 8.15E-10 1.17E-10 mr1309 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
vg1125421780 NA 9.70E-06 mr1328 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
vg1125421780 1.18E-06 NA mr1484 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
vg1125421780 NA 3.84E-06 mr1484 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
vg1125421780 1.35E-13 1.88E-13 mr1662 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
vg1125421780 9.30E-07 1.72E-08 mr1662 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
vg1125421780 NA 2.78E-07 mr1723 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
vg1125421780 1.21E-07 3.58E-08 mr1841 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
vg1125421780 1.77E-08 NA mr1238_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
vg1125421780 3.04E-11 2.09E-12 mr1238_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
vg1125421780 3.41E-08 NA mr1484_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
vg1125421780 6.46E-11 2.56E-12 mr1484_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
vg1125421780 1.10E-16 1.12E-17 mr1662_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
vg1125421780 2.12E-06 NA 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
vg1125421780 2.85E-07 1.33E-09 mr1662_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
vg1125421780 1.94E-08 NA mr1841_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
vg1125421780 1.65E-13 4.65E-14 mr1841_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
vg1125421780 2.48E-07 2.31E-08 mr1900_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
vg1125421780 7.90E-06 2.59E-07 mr1925_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
vg1125421780 7.33E-07 NA mr1945_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
vg1125421780 1.50E-08 1.50E-08 mr1945_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