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Detailed information for vg1117476840:

Variant ID: vg1117476840 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 17476840
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: 0.01, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


TGAAATATTTGGGTGATCTCATCCATATATATGGATAGAGTAACAACCAACTCAGGGACACGACGGTTGGTCGTGCCCCACACCTCTTCTCGCCTCACGG[C/T]
GATTCTAGCAACGGACGCGATGGTTCCCAAACCATCGCGCCTCCAGTTGCCGCCTCTCTCCCCCCTGTATATTGTAACTGTTATCAATAAAGAATCCGCT

Reverse complement sequence

AGCGGATTCTTTATTGATAACAGTTACAATATACAGGGGGGAGAGAGGCGGCAACTGGAGGCGCGATGGTTTGGGAACCATCGCGTCCGTTGCTAGAATC[G/A]
CCGTGAGGCGAGAAGAGGTGTGGGGCACGACCAACCGTCGTGTCCCTGAGTTGGTTGTTACTCTATCCATATATATGGATGAGATCACCCAAATATTTCA

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 88.80% 9.00% 1.21% 1.04% NA
All Indica  2759 81.20% 15.20% 1.88% 1.70% NA
All Japonica  1512 99.50% 0.30% 0.13% 0.07% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 92.90% 4.00% 1.85% 1.18% NA
Indica II  465 81.50% 8.60% 4.95% 4.95% NA
Indica III  913 75.00% 23.90% 0.33% 0.77% NA
Indica Intermediate  786 79.30% 17.60% 1.91% 1.27% NA
Temperate Japonica  767 99.30% 0.40% 0.26% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.00% 0.41% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 0.00% 3.33% 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
vg1117476840 C -> T LOC_Os11g30040.1 downstream_gene_variant ; 3606.0bp to feature; MODIFIER silent_mutation Average:33.057; most accessible tissue: Zhenshan97 flag leaf, score: 55.285 N N N N
vg1117476840 C -> T LOC_Os11g30050.1 downstream_gene_variant ; 2604.0bp to feature; MODIFIER silent_mutation Average:33.057; most accessible tissue: Zhenshan97 flag leaf, score: 55.285 N N N N
vg1117476840 C -> T LOC_Os11g30040-LOC_Os11g30050 intergenic_region ; MODIFIER silent_mutation Average:33.057; most accessible tissue: Zhenshan97 flag leaf, score: 55.285 N N N N
vg1117476840 C -> DEL N N silent_mutation Average:33.057; 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
vg1117476840 NA 1.12E-06 mr1107 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
vg1117476840 NA 2.48E-06 mr1973 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
vg1117476840 4.72E-07 1.16E-07 mr1265_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
vg1117476840 NA 9.21E-06 mr1265_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
vg1117476840 2.62E-06 3.50E-07 mr1528_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
vg1117476840 NA 1.25E-06 mr1528_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
vg1117476840 NA 5.97E-08 mr1676_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
vg1117476840 NA 9.27E-06 mr1782_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
vg1117476840 NA 9.21E-06 mr1817_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
vg1117476840 NA 6.03E-07 mr1973_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