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Detailed information for vg0602036061:

Variant ID: vg0602036061 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 2036061
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: 0.03, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:


AACAGGGGGTGCTATGGACTGTCCAGATTCGTAGTATGTCACATGTTTTTTTTTGACGAATGGAGTATCACGTAGTCAATACTCTATTATGATTTAATTA[T/C]
CTTTACAAATTAGATACGATGTAAAGATGAAAACGGCTATAAAAATTCCCGACCAACCGAGTATCCTTTATGGATAAAGTGCTACCGTTTTCGACCGTAT

Reverse complement sequence

ATACGGTCGAAAACGGTAGCACTTTATCCATAAAGGATACTCGGTTGGTCGGGAATTTTTATAGCCGTTTTCATCTTTACATCGTATCTAATTTGTAAAG[A/G]
TAATTAAATCATAATAGAGTATTGACTACGTGATACTCCATTCGTCAAAAAAAAACATGTGACATACTACGAATCTGGACAGTCCATAGCACCCCCTGTT

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 59.90% 39.50% 0.19% 0.32% NA
All Indica  2759 76.00% 23.50% 0.14% 0.36% NA
All Japonica  1512 22.80% 76.70% 0.20% 0.26% NA
Aus  269 96.30% 3.30% 0.37% 0.00% NA
Indica I  595 94.50% 5.00% 0.17% 0.34% NA
Indica II  465 52.30% 47.30% 0.22% 0.22% NA
Indica III  913 77.10% 22.30% 0.11% 0.44% NA
Indica Intermediate  786 74.70% 24.80% 0.13% 0.38% NA
Temperate Japonica  767 38.20% 61.80% 0.00% 0.00% NA
Tropical Japonica  504 5.00% 94.00% 0.40% 0.60% NA
Japonica Intermediate  241 11.20% 88.00% 0.41% 0.41% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 43.30% 54.40% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0602036061 T -> C LOC_Os06g04670.1 upstream_gene_variant ; 710.0bp to feature; MODIFIER silent_mutation Average:66.878; most accessible tissue: Callus, score: 87.196 N N N N
vg0602036061 T -> C LOC_Os06g04660.1 downstream_gene_variant ; 1248.0bp to feature; MODIFIER silent_mutation Average:66.878; most accessible tissue: Callus, score: 87.196 N N N N
vg0602036061 T -> C LOC_Os06g04680.1 downstream_gene_variant ; 3673.0bp to feature; MODIFIER silent_mutation Average:66.878; most accessible tissue: Callus, score: 87.196 N N N N
vg0602036061 T -> C LOC_Os06g04660.2 downstream_gene_variant ; 1248.0bp to feature; MODIFIER silent_mutation Average:66.878; most accessible tissue: Callus, score: 87.196 N N N N
vg0602036061 T -> C LOC_Os06g04680.2 downstream_gene_variant ; 3241.0bp to feature; MODIFIER silent_mutation Average:66.878; most accessible tissue: Callus, score: 87.196 N N N N
vg0602036061 T -> C LOC_Os06g04660-LOC_Os06g04670 intergenic_region ; MODIFIER silent_mutation Average:66.878; most accessible tissue: Callus, score: 87.196 N N N N
vg0602036061 T -> DEL N N silent_mutation Average:66.878; most accessible tissue: Callus, score: 87.196 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0602036061 5.08E-08 NA Awn_length All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0602036061 NA 1.24E-12 Awn_length Jap_All YES Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0602036061 NA 9.38E-09 mr1050 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
vg0602036061 1.85E-08 5.24E-51 mr1141 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
vg0602036061 4.05E-09 7.36E-24 mr1141 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
vg0602036061 NA 2.79E-11 mr1272 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
vg0602036061 NA 9.21E-06 mr1272 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
vg0602036061 NA 2.80E-06 mr1608 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
vg0602036061 NA 1.19E-08 mr1757 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
vg0602036061 NA 4.53E-20 mr1141_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
vg0602036061 NA 1.39E-09 mr1222_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
vg0602036061 NA 4.88E-07 mr1549_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
vg0602036061 NA 4.34E-06 mr1741_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
vg0602036061 NA 9.20E-09 mr1757_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