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Detailed information for vg0207312321:

Variant ID: vg0207312321 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 7312321
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, C: 0.01, others allele: 0.00, population size: 130. )

Flanking Sequence (100 bp) in Reference Genome:


GAGACCCGTCTCTGCAAGACATCCAGGAGATCATCAGTTTCAGGTTGTCCTGCAGCAAAAACATCTACATACATCTGCACCAAAGATGGGGTATTACAGG[T/C]
ATGGAGAAGTTGCTTATGTGTTGGCGCAAAAAAACAGAAAAAAAAATTCAGCACTGATGAACTTCGTAATATAAAATCATTGAAGGGGGTGTTTGCTTTG

Reverse complement sequence

CAAAGCAAACACCCCCTTCAATGATTTTATATTACGAAGTTCATCAGTGCTGAATTTTTTTTTCTGTTTTTTTGCGCCAACACATAAGCAACTTCTCCAT[A/G]
CCTGTAATACCCCATCTTTGGTGCAGATGTATGTAGATGTTTTTGCTGCAGGACAACCTGAAACTGATGATCTCCTGGATGTCTTGCAGAGACGGGTCTC

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 91.30% 8.70% 0.00% 0.00% NA
All Indica  2759 85.40% 14.60% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 82.00% 18.00% 0.00% 0.00% NA
Indica II  465 83.70% 16.30% 0.00% 0.00% NA
Indica III  913 84.90% 15.10% 0.00% 0.00% NA
Indica Intermediate  786 89.40% 10.60% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 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 95.60% 4.40% 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
vg0207312321 T -> C LOC_Os02g13640.1 upstream_gene_variant ; 4067.0bp to feature; MODIFIER silent_mutation Average:59.922; most accessible tissue: Callus, score: 88.981 N N N N
vg0207312321 T -> C LOC_Os02g13620.1 downstream_gene_variant ; 1329.0bp to feature; MODIFIER silent_mutation Average:59.922; most accessible tissue: Callus, score: 88.981 N N N N
vg0207312321 T -> C LOC_Os02g13630.1 downstream_gene_variant ; 1777.0bp to feature; MODIFIER silent_mutation Average:59.922; most accessible tissue: Callus, score: 88.981 N N N N
vg0207312321 T -> C LOC_Os02g13620-LOC_Os02g13630 intergenic_region ; MODIFIER silent_mutation Average:59.922; most accessible tissue: Callus, score: 88.981 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0207312321 3.48E-07 1.24E-06 mr1679 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
vg0207312321 6.80E-06 6.80E-06 mr1717 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