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Detailed information for vg0133799491:

Variant ID: vg0133799491 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 33799491
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.07, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


AAGGTCGCTCAACTTGTCATCGAGTTACAAAATCGTCCCCTAACCGTAAAATTGGATACAACGCATCCCTGGTAACAACCAAATTTGGTAATATCAGCAT[T/C]
GGAAAAGAGAATTAGATCGAAGTGGAGTCGAAGGCGGAGATCGATTCGAGAACAGAGCAAGAATCGGCTGGAGTTCGGATCAGCTACGATTGGATTGGCT

Reverse complement sequence

AGCCAATCCAATCGTAGCTGATCCGAACTCCAGCCGATTCTTGCTCTGTTCTCGAATCGATCTCCGCCTTCGACTCCACTTCGATCTAATTCTCTTTTCC[A/G]
ATGCTGATATTACCAAATTTGGTTGTTACCAGGGATGCGTTGTATCCAATTTTACGGTTAGGGGACGATTTTGTAACTCGATGACAAGTTGAGCGACCTT

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 64.60% 35.10% 0.19% 0.02% NA
All Indica  2759 97.10% 2.80% 0.04% 0.04% NA
All Japonica  1512 6.40% 93.50% 0.07% 0.00% NA
Aus  269 89.60% 7.80% 2.60% 0.00% NA
Indica I  595 96.30% 3.70% 0.00% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 98.70% 1.20% 0.00% 0.11% NA
Indica Intermediate  786 95.00% 4.80% 0.13% 0.00% NA
Temperate Japonica  767 8.20% 91.70% 0.13% 0.00% NA
Tropical Japonica  504 2.20% 97.80% 0.00% 0.00% NA
Japonica Intermediate  241 9.50% 90.50% 0.00% 0.00% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 37.80% 62.20% 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
vg0133799491 T -> DEL N N silent_mutation Average:44.714; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg0133799491 T -> C LOC_Os01g58470.1 upstream_gene_variant ; 3663.0bp to feature; MODIFIER silent_mutation Average:44.714; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg0133799491 T -> C LOC_Os01g58459-LOC_Os01g58470 intergenic_region ; MODIFIER silent_mutation Average:44.714; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0133799491 NA 1.10E-08 mr1005 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
vg0133799491 1.53E-09 3.03E-112 mr1008 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
vg0133799491 1.43E-07 2.59E-10 mr1008 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
vg0133799491 7.10E-09 5.60E-109 mr1009 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
vg0133799491 2.76E-07 9.84E-10 mr1009 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
vg0133799491 NA 2.57E-69 mr1014 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
vg0133799491 NA 8.00E-13 mr1239 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
vg0133799491 2.32E-11 2.99E-114 mr1008_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
vg0133799491 NA 5.98E-08 mr1008_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
vg0133799491 NA 3.94E-06 mr1008_2 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
vg0133799491 NA 5.61E-06 mr1057_2 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