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Detailed information for vg0123696065:

Variant ID: vg0123696065 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 23696065
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


TACGGCTAAACTCAAACAATCTACACGGTGCACTCACTGAGGACCATTTCGTAAATCTTACTAGTCTACAAGTTTTGTGGTTAATATTATAAATGTTAGT[T/C]
GGTAAAACGGAACGACAACTAACTTTATCAATCGCTTCAGTCATTGATCATTTAAGACATGCTAGATGACGGCACGAAAACACATGTATTTATTAACAAA

Reverse complement sequence

TTTGTTAATAAATACATGTGTTTTCGTGCCGTCATCTAGCATGTCTTAAATGATCAATGACTGAAGCGATTGATAAAGTTAGTTGTCGTTCCGTTTTACC[A/G]
ACTAACATTTATAATATTAACCACAAAACTTGTAGACTAGTAAGATTTACGAAATGGTCCTCAGTGAGTGCACCGTGTAGATTGTTTGAGTTTAGCCGTA

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 75.20% 24.30% 0.53% 0.00% NA
All Indica  2759 97.80% 2.00% 0.18% 0.00% NA
All Japonica  1512 28.70% 70.10% 1.19% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 97.60% 2.00% 0.34% 0.00% NA
Indica II  465 98.10% 1.90% 0.00% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 95.90% 3.70% 0.38% 0.00% NA
Temperate Japonica  767 9.50% 88.40% 2.09% 0.00% NA
Tropical Japonica  504 52.00% 48.00% 0.00% 0.00% NA
Japonica Intermediate  241 41.10% 58.10% 0.83% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 68.90% 28.90% 2.22% 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
vg0123696065 T -> C LOC_Os01g41834.1 upstream_gene_variant ; 4034.0bp to feature; MODIFIER silent_mutation Average:54.763; most accessible tissue: Zhenshan97 panicle, score: 76.605 N N N N
vg0123696065 T -> C LOC_Os01g41834-LOC_Os01g41850 intergenic_region ; MODIFIER silent_mutation Average:54.763; most accessible tissue: Zhenshan97 panicle, score: 76.605 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0123696065 NA 3.66E-06 mr1289 Jap_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
vg0123696065 NA 1.48E-11 mr1626 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
vg0123696065 NA 4.32E-06 mr1837 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
vg0123696065 NA 3.46E-10 mr1945 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
vg0123696065 NA 3.05E-15 mr1013_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
vg0123696065 1.24E-06 NA mr1022_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
vg0123696065 NA 5.31E-13 mr1035_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
vg0123696065 7.17E-08 NA mr1079_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