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Detailed information for vg1115483994:

Variant ID: vg1115483994 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 15483994
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:


TTTACTCCACATTCCATGGCCTTGGAACTCGTCGTAAACATGTGACATAACCCTTCACCCATCCTAGCCGTGAACAAAAGTACCGACCCAACCCTGCCTA[C/T]
GGCCAGTATCCTAGATAGGCAGGCCAGGATTGAGCCCCTAGCAACAGGATCTAGACCGGGTGCGCCACACACATAGGGGTGAGACCACCCGCGTACTAGT

Reverse complement sequence

ACTAGTACGCGGGTGGTCTCACCCCTATGTGTGTGGCGCACCCGGTCTAGATCCTGTTGCTAGGGGCTCAATCCTGGCCTGCCTATCTAGGATACTGGCC[G/A]
TAGGCAGGGTTGGGTCGGTACTTTTGTTCACGGCTAGGATGGGTGAAGGGTTATGTCACATGTTTACGACGAGTTCCAAGGCCATGGAATGTGGAGTAAA

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 67.80% 30.30% 0.30% 1.57% NA
All Indica  2759 50.10% 46.80% 0.51% 2.68% NA
All Japonica  1512 99.30% 0.70% 0.00% 0.00% NA
Aus  269 60.60% 39.40% 0.00% 0.00% NA
Indica I  595 23.00% 76.80% 0.00% 0.17% NA
Indica II  465 62.20% 36.30% 0.43% 1.08% NA
Indica III  913 56.20% 37.90% 0.88% 5.04% NA
Indica Intermediate  786 56.20% 40.50% 0.51% 2.80% 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 73.30% 26.70% 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
vg1115483994 C -> T LOC_Os11g26930.1 upstream_gene_variant ; 1773.0bp to feature; MODIFIER silent_mutation Average:41.626; most accessible tissue: Zhenshan97 flag leaf, score: 55.285 N N N N
vg1115483994 C -> T LOC_Os11g26920-LOC_Os11g26930 intergenic_region ; MODIFIER silent_mutation Average:41.626; most accessible tissue: Zhenshan97 flag leaf, score: 55.285 N N N N
vg1115483994 C -> DEL N N silent_mutation Average:41.626; most accessible tissue: Zhenshan97 flag leaf, score: 55.285 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1115483994 NA 3.00E-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
vg1115483994 4.95E-06 3.64E-12 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
vg1115483994 NA 1.01E-07 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
vg1115483994 NA 6.79E-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
vg1115483994 NA 2.00E-07 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
vg1115483994 NA 2.67E-08 mr1829 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
vg1115483994 NA 3.72E-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
vg1115483994 NA 5.67E-07 mr1861 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
vg1115483994 3.30E-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
vg1115483994 3.54E-06 7.39E-08 mr1092_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
vg1115483994 3.18E-09 1.83E-17 mr1097_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
vg1115483994 9.91E-09 7.16E-12 mr1097_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
vg1115483994 9.30E-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
vg1115483994 NA 8.13E-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
vg1115483994 NA 1.23E-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
vg1115483994 3.19E-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
vg1115483994 1.08E-09 1.13E-14 mr1154_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
vg1115483994 6.13E-08 NA mr1223_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
vg1115483994 5.10E-06 1.76E-06 mr1223_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
vg1115483994 NA 5.41E-09 mr1829_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