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Detailed information for vg0125678284:

Variant ID: vg0125678284 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 25678284
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.02, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:


AATGACCATTTAATTGAACCACAGAAAAAACACAGGAATTGGATGAAAGAGATAGCCTCAAAAGAAAGTTAGTAAGAGGTCGAAGCTCTTGCTAAATTTT[T/C]
TCCAAAATCTCTATAGGATTGTCCATTCCATAGGAATTTTAAAGGATTGGATAGGATTCAATCCTTTGTTTCAAAGGACTTCATAGGAAATTTTCCTATA

Reverse complement sequence

TATAGGAAAATTTCCTATGAAGTCCTTTGAAACAAAGGATTGAATCCTATCCAATCCTTTAAAATTCCTATGGAATGGACAATCCTATAGAGATTTTGGA[A/G]
AAAATTTAGCAAGAGCTTCGACCTCTTACTAACTTTCTTTTGAGGCTATCTCTTTCATCCAATTCCTGTGTTTTTTCTGTGGTTCAATTAAATGGTCATT

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 50.60% 49.40% 0.08% 0.00% NA
All Indica  2759 82.80% 17.10% 0.11% 0.00% NA
All Japonica  1512 3.30% 96.70% 0.00% 0.00% NA
Aus  269 4.10% 95.90% 0.00% 0.00% NA
Indica I  595 97.60% 2.40% 0.00% 0.00% NA
Indica II  465 91.40% 8.60% 0.00% 0.00% NA
Indica III  913 67.40% 32.60% 0.00% 0.00% NA
Indica Intermediate  786 84.40% 15.30% 0.38% 0.00% NA
Temperate Japonica  767 0.50% 99.50% 0.00% 0.00% NA
Tropical Japonica  504 5.60% 94.40% 0.00% 0.00% NA
Japonica Intermediate  241 7.50% 92.50% 0.00% 0.00% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 44.40% 54.40% 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
vg0125678284 T -> C LOC_Os01g45250.1 upstream_gene_variant ; 3286.0bp to feature; MODIFIER silent_mutation Average:58.035; most accessible tissue: Zhenshan97 flag leaf, score: 77.203 N N N N
vg0125678284 T -> C LOC_Os01g45220-LOC_Os01g45250 intergenic_region ; MODIFIER silent_mutation Average:58.035; most accessible tissue: Zhenshan97 flag leaf, score: 77.203 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0125678284 NA 1.40E-06 mr1062 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
vg0125678284 NA 7.93E-11 mr1151 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
vg0125678284 NA 3.66E-07 mr1220 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
vg0125678284 NA 3.72E-10 mr1249 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
vg0125678284 NA 4.31E-09 mr1352 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
vg0125678284 2.55E-07 3.52E-08 mr1892 Jap_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
vg0125678284 NA 4.60E-13 mr1940 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