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Detailed information for vg1115480914:

Variant ID: vg1115480914 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 15480914
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


CAATGGAGGAGCTCGTCGGCAAATATATTCCACACCTTGCCGAAGGTCGGCAAGCTGCTTAAACCCTTCTAGGTACCTGATAGATGCTCTAGAACCCCTC[C/T]
CCGAGCCATGTCTAACTCACATAACCCTGATCACCTTCACGGCTTAACTATGCCACCGCCGCCCTAGCCGCTAGCTCAACCACATACCAAATTAACCCCT

Reverse complement sequence

AGGGGTTAATTTGGTATGTGGTTGAGCTAGCGGCTAGGGCGGCGGTGGCATAGTTAAGCCGTGAAGGTGATCAGGGTTATGTGAGTTAGACATGGCTCGG[G/A]
GAGGGGTTCTAGAGCATCTATCAGGTACCTAGAAGGGTTTAAGCAGCTTGCCGACCTTCGGCAAGGTGTGGAATATATTTGCCGACGAGCTCCTCCATTG

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 68.00% 30.10% 0.28% 1.63% NA
All Indica  2759 50.30% 46.40% 0.47% 2.79% NA
All Japonica  1512 99.30% 0.70% 0.00% 0.00% NA
Aus  269 60.20% 39.80% 0.00% 0.00% NA
Indica I  595 23.50% 76.10% 0.17% 0.17% NA
Indica II  465 62.60% 36.10% 0.65% 0.65% NA
Indica III  913 56.30% 37.90% 0.55% 5.26% NA
Indica Intermediate  786 56.40% 39.90% 0.51% 3.18% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 98.60% 1.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 74.40% 25.60% 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
vg1115480914 C -> T LOC_Os11g26920.1 upstream_gene_variant ; 4663.0bp to feature; MODIFIER silent_mutation Average:48.204; most accessible tissue: Minghui63 young leaf, score: 68.07 N N N N
vg1115480914 C -> T LOC_Os11g26930.1 upstream_gene_variant ; 4853.0bp to feature; MODIFIER silent_mutation Average:48.204; most accessible tissue: Minghui63 young leaf, score: 68.07 N N N N
vg1115480914 C -> T LOC_Os11g26920-LOC_Os11g26930 intergenic_region ; MODIFIER silent_mutation Average:48.204; most accessible tissue: Minghui63 young leaf, score: 68.07 N N N N
vg1115480914 C -> DEL N N silent_mutation Average:48.204; most accessible tissue: Minghui63 young leaf, score: 68.07 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1115480914 NA 3.09E-06 mr1077 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
vg1115480914 NA 1.45E-10 mr1097 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
vg1115480914 NA 6.30E-06 mr1097 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
vg1115480914 NA 8.39E-06 mr1149 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
vg1115480914 NA 7.23E-06 mr1154 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
vg1115480914 NA 2.36E-06 mr1842 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
vg1115480914 7.59E-06 NA mr1092_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
vg1115480914 3.85E-06 2.32E-07 mr1092_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
vg1115480914 1.69E-09 3.26E-17 mr1097_2 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
vg1115480914 1.83E-09 7.17E-12 mr1097_2 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
vg1115480914 8.20E-08 NA mr1102_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
vg1115480914 3.66E-06 3.22E-07 mr1102_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
vg1115480914 5.72E-06 2.16E-07 mr1152_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
vg1115480914 2.01E-09 NA mr1154_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
vg1115480914 2.28E-10 3.40E-14 mr1154_2 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
vg1115480914 2.50E-08 NA mr1223_2 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
vg1115480914 8.02E-07 8.52E-07 mr1223_2 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