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Detailed information for vg0921976011:

Variant ID: vg0921976011 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 21976011
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 112. )

Flanking Sequence (100 bp) in Reference Genome:


AAATGAGTAGTATTACAAGATAGAAATTTATCCCCATACGTTTTAAGTTTACTTAATCAACAACTAGCTGGGTGGCCCGCGCAATTGCGCGGCTAGCACC[C/T]
AAACAAAATCATATATTTTTTAGTATAATTTTACTTAAAATTTATTAAATAGCTATCTTATTGTCTTAAGACTTTGAAAGACCAAACCTTATCATCCTCG

Reverse complement sequence

CGAGGATGATAAGGTTTGGTCTTTCAAAGTCTTAAGACAATAAGATAGCTATTTAATAAATTTTAAGTAAAATTATACTAAAAAATATATGATTTTGTTT[G/A]
GGTGCTAGCCGCGCAATTGCGCGGGCCACCCAGCTAGTTGTTGATTAAGTAAACTTAAAACGTATGGGGATAAATTTCTATCTTGTAATACTACTCATTT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 53.70% 46.00% 0.23% 0.04% NA
All Indica  2759 86.70% 12.90% 0.33% 0.07% NA
All Japonica  1512 0.50% 99.50% 0.07% 0.00% NA
Aus  269 35.30% 64.70% 0.00% 0.00% NA
Indica I  595 89.40% 10.40% 0.00% 0.17% NA
Indica II  465 88.00% 11.20% 0.86% 0.00% NA
Indica III  913 84.10% 15.60% 0.22% 0.11% NA
Indica Intermediate  786 86.90% 12.70% 0.38% 0.00% NA
Temperate Japonica  767 0.10% 99.90% 0.00% 0.00% NA
Tropical Japonica  504 0.80% 99.00% 0.20% 0.00% NA
Japonica Intermediate  241 0.80% 99.20% 0.00% 0.00% NA
VI/Aromatic  96 16.70% 83.30% 0.00% 0.00% NA
Intermediate  90 32.20% 66.70% 1.11% 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
vg0921976011 C -> DEL N N silent_mutation Average:42.285; most accessible tissue: Callus, score: 54.4 N N N N
vg0921976011 C -> T LOC_Os09g38150.1 upstream_gene_variant ; 1766.0bp to feature; MODIFIER silent_mutation Average:42.285; most accessible tissue: Callus, score: 54.4 N N N N
vg0921976011 C -> T LOC_Os09g38150-LOC_Os09g38170 intergenic_region ; MODIFIER silent_mutation Average:42.285; most accessible tissue: Callus, score: 54.4 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0921976011 NA 2.74E-10 mr1195 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
vg0921976011 NA 2.23E-29 mr1208 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
vg0921976011 NA 2.70E-11 mr1379 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
vg0921976011 NA 1.01E-07 mr1559 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
vg0921976011 NA 6.33E-10 mr1581 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
vg0921976011 2.90E-08 NA mr1865 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
vg0921976011 7.26E-06 9.45E-06 mr1865 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
vg0921976011 NA 3.69E-07 mr1302_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
vg0921976011 NA 2.08E-08 mr1418_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
vg0921976011 NA 7.54E-06 mr1419_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
vg0921976011 NA 4.32E-06 mr1420_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
vg0921976011 NA 4.01E-08 mr1488_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
vg0921976011 NA 5.96E-13 mr1506_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
vg0921976011 5.55E-06 5.55E-06 mr1506_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
vg0921976011 NA 8.17E-08 mr1604_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
vg0921976011 NA 8.85E-08 mr1824_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
vg0921976011 NA 8.32E-09 mr1835_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
vg0921976011 NA 7.04E-16 mr1836_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
vg0921976011 NA 7.04E-07 mr1992_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