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Detailed information for vg0601508115:

Variant ID: vg0601508115 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 1508115
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:


AGCACAGGAAAGGTGAGGTTCATCATTATTCTCCTTTGATTTTCACTGCCACCTAAGTTGCAAATTCTTTTCCTGAATTTATAGTTTTTATTATACTTAC[T/A]
GCCATTGTACTACCAGAGTTAACTAATTTATTTCTGTATTCTGTAACAAGCTATATGCAGTTTCATATCTAGCGTTTTCAGCATTACCTTTTCTTCGGTG

Reverse complement sequence

CACCGAAGAAAAGGTAATGCTGAAAACGCTAGATATGAAACTGCATATAGCTTGTTACAGAATACAGAAATAAATTAGTTAACTCTGGTAGTACAATGGC[A/T]
GTAAGTATAATAAAAACTATAAATTCAGGAAAAGAATTTGCAACTTAGGTGGCAGTGAAAATCAAAGGAGAATAATGATGAACCTCACCTTTCCTGTGCT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.60% 11.40% 0.00% 0.00% NA
All Indica  2759 80.80% 19.20% 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 72.30% 27.70% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 76.50% 23.50% 0.00% 0.00% NA
Indica Intermediate  786 81.20% 18.80% 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 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 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
vg0601508115 T -> A LOC_Os06g03790.1 upstream_gene_variant ; 4680.0bp to feature; MODIFIER silent_mutation Average:33.898; most accessible tissue: Callus, score: 52.52 N N N N
vg0601508115 T -> A LOC_Os06g03780.1 intron_variant ; MODIFIER silent_mutation Average:33.898; most accessible tissue: Callus, score: 52.52 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0601508115 2.73E-06 NA mr1336 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
vg0601508115 1.30E-06 1.35E-08 mr1336 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
vg0601508115 NA 3.47E-06 mr1740 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
vg0601508115 NA 3.86E-06 mr1319_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