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Detailed information for vg0206037677:

Variant ID: vg0206037677 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 6037677
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


CCAAGCTATAACAAAATTATATTTTACTCCCTCCGTCCCATAATATAAACAGTTTTGAACTTCGACGTAGTTTTCGAGATGCTATTTTAACCAATAATAT[C/T]
TATAAAAGTAAAATGTTTTAAATAAAAAGAATTGCATATTATGATAGTTTGTTTAATGATAAATCCAGTAACATCAATTTTACACGATTGATCTTTATTG

Reverse complement sequence

CAATAAAGATCAATCGTGTAAAATTGATGTTACTGGATTTATCATTAAACAAACTATCATAATATGCAATTCTTTTTATTTAAAACATTTTACTTTTATA[G/A]
ATATTATTGGTTAAAATAGCATCTCGAAAACTACGTCGAAGTTCAAAACTGTTTATATTATGGGACGGAGGGAGTAAAATATAATTTTGTTATAGCTTGG

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 92.60% 7.40% 0.00% 0.00% NA
All Indica  2759 87.50% 12.50% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 72.40% 27.60% 0.00% 0.00% NA
Indica II  465 89.00% 11.00% 0.00% 0.00% NA
Indica III  913 94.90% 5.10% 0.00% 0.00% NA
Indica Intermediate  786 89.60% 10.40% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0206037677 C -> T LOC_Os02g11730.1 upstream_gene_variant ; 3930.0bp to feature; MODIFIER silent_mutation Average:48.258; most accessible tissue: Callus, score: 93.534 N N N N
vg0206037677 C -> T LOC_Os02g11720.1 downstream_gene_variant ; 545.0bp to feature; MODIFIER silent_mutation Average:48.258; most accessible tissue: Callus, score: 93.534 N N N N
vg0206037677 C -> T LOC_Os02g11710-LOC_Os02g11720 intergenic_region ; MODIFIER silent_mutation Average:48.258; most accessible tissue: Callus, score: 93.534 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0206037677 NA 1.90E-06 mr1170 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
vg0206037677 6.11E-06 NA mr1714 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
vg0206037677 3.17E-06 3.17E-06 mr1714 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
vg0206037677 4.29E-06 NA mr1714_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
vg0206037677 3.02E-06 9.02E-06 mr1714_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