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Detailed information for vg0116370525:

Variant ID: vg0116370525 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 16370525
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCAACTGTGCAGATTGCCGGTATTAATATATTGTTTGAATATAATGCTCAGATCTACTTTAGATATGCCATTCAGAGTTCCCTCAATTAATAATGGTGG[T/C]
GCTTGTGTGTTTGGATGGTTATGGATTATTATATTATATTTAATATTGTTGAAAACTCAAAATGAGTAACTAAAGTGAAGTAACATGTGATGCAATGTAC

Reverse complement sequence

GTACATTGCATCACATGTTACTTCACTTTAGTTACTCATTTTGAGTTTTCAACAATATTAAATATAATATAATAATCCATAACCATCCAAACACACAAGC[A/G]
CCACCATTATTAATTGAGGGAACTCTGAATGGCATATCTAAAGTAGATCTGAGCATTATATTCAAACAATATATTAATACCGGCAATCTGCACAGTTGAT

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 87.60% 9.90% 2.52% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 62.50% 29.90% 7.61% 0.00% NA
Aus  269 98.50% 0.70% 0.74% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 37.30% 51.40% 11.34% 0.00% NA
Tropical Japonica  504 96.20% 0.60% 3.17% 0.00% NA
Japonica Intermediate  241 72.20% 22.80% 4.98% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 6.70% 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
vg0116370525 T -> C LOC_Os01g29220.1 downstream_gene_variant ; 668.0bp to feature; MODIFIER silent_mutation Average:48.003; most accessible tissue: Callus, score: 67.104 N N N N
vg0116370525 T -> C LOC_Os01g29220-LOC_Os01g29230 intergenic_region ; MODIFIER silent_mutation Average:48.003; most accessible tissue: Callus, score: 67.104 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0116370525 NA 1.49E-07 mr1002 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
vg0116370525 NA 2.10E-06 mr1013 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
vg0116370525 NA 1.72E-06 mr1031 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
vg0116370525 NA 5.49E-13 mr1034 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
vg0116370525 NA 4.99E-07 mr1034 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
vg0116370525 NA 9.77E-06 mr1077 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
vg0116370525 5.82E-06 5.55E-07 mr1170 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
vg0116370525 NA 3.06E-07 mr1202 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
vg0116370525 NA 1.11E-07 mr1252 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
vg0116370525 NA 5.36E-06 mr1548 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
vg0116370525 NA 2.42E-06 mr1555 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
vg0116370525 NA 7.63E-07 mr1576 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
vg0116370525 NA 1.26E-06 mr1013_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