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Detailed information for vg0219348866:

Variant ID: vg0219348866 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 19348866
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


ATATGAGCAAAGCCATCGCAATGAATGATTATAGAACGATTTAGCCAAGAAAAAATAATACATAAATACTCCCTCCGTTTCACAATGTAAGTCATTCTAT[C/T]
ATTTCCCACATTCATATTGATGTTAATGAATCTAGACATATATATCTATCTAGATTCATTAACATCAATATGAATGTAGAAAATGGTGGAATAACTTAAA

Reverse complement sequence

TTTAAGTTATTCCACCATTTTCTACATTCATATTGATGTTAATGAATCTAGATAGATATATATGTCTAGATTCATTAACATCAATATGAATGTGGGAAAT[G/A]
ATAGAATGACTTACATTGTGAAACGGAGGGAGTATTTATGTATTATTTTTTCTTGGCTAAATCGTTCTATAATCATTCATTGCGATGGCTTTGCTCATAT

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 95.80% 3.30% 0.87% 0.00% NA
All Indica  2759 96.80% 2.10% 1.05% 0.00% NA
All Japonica  1512 99.80% 0.00% 0.20% 0.00% NA
Aus  269 59.90% 36.80% 3.35% 0.00% NA
Indica I  595 91.40% 5.00% 3.53% 0.00% NA
Indica II  465 97.60% 2.20% 0.22% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 97.20% 1.90% 0.89% 0.00% NA
Temperate Japonica  767 99.70% 0.00% 0.26% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0219348866 C -> T LOC_Os02g32630.1 downstream_gene_variant ; 2680.0bp to feature; MODIFIER silent_mutation Average:45.965; most accessible tissue: Minghui63 root, score: 81.681 N N N N
vg0219348866 C -> T LOC_Os02g32650.1 downstream_gene_variant ; 3710.0bp to feature; MODIFIER silent_mutation Average:45.965; most accessible tissue: Minghui63 root, score: 81.681 N N N N
vg0219348866 C -> T LOC_Os02g32650.2 downstream_gene_variant ; 3761.0bp to feature; MODIFIER silent_mutation Average:45.965; most accessible tissue: Minghui63 root, score: 81.681 N N N N
vg0219348866 C -> T LOC_Os02g32630-LOC_Os02g32650 intergenic_region ; MODIFIER silent_mutation Average:45.965; most accessible tissue: Minghui63 root, score: 81.681 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0219348866 NA 2.26E-07 mr1201_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
vg0219348866 NA 1.56E-08 mr1219_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
vg0219348866 NA 5.06E-08 mr1274_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
vg0219348866 4.52E-06 4.76E-10 mr1793_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