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Detailed information for vg0139856883:

Variant ID: vg0139856883 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 39856883
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATGTACACCTCAGTCTTTAAGAAAAAGATAAATGCATATTCTGAATAGATATTCAGGTTTCATTGCTAGAATTGAGTATTTCGAGTAAAGTCCATTACC[G/A]
GTCCCTAAACTTGTACCGTTGTGTCATCCCGATCCCTAAACTCACAAATCAACCGTTTAGGTCCTCAAACTTGTTTGACTGTGTCATCCCGGTCACTCGT

Reverse complement sequence

ACGAGTGACCGGGATGACACAGTCAAACAAGTTTGAGGACCTAAACGGTTGATTTGTGAGTTTAGGGATCGGGATGACACAACGGTACAAGTTTAGGGAC[C/T]
GGTAATGGACTTTACTCGAAATACTCAATTCTAGCAATGAAACCTGAATATCTATTCAGAATATGCATTTATCTTTTTCTTAAAGACTGAGGTGTACATA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.50% 8.50% 0.02% 0.00% NA
All Indica  2759 90.50% 9.40% 0.04% 0.00% NA
All Japonica  1512 97.90% 2.10% 0.00% 0.00% NA
Aus  269 66.20% 33.80% 0.00% 0.00% NA
Indica I  595 97.50% 2.50% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 87.20% 12.80% 0.00% 0.00% NA
Indica Intermediate  786 83.60% 16.30% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 97.20% 2.80% 0.00% 0.00% NA
Japonica Intermediate  241 92.90% 7.10% 0.00% 0.00% NA
VI/Aromatic  96 83.30% 16.70% 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
vg0139856883 G -> A LOC_Os01g68630.1 upstream_gene_variant ; 921.0bp to feature; MODIFIER silent_mutation Average:41.055; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N
vg0139856883 G -> A LOC_Os01g68620.1 downstream_gene_variant ; 835.0bp to feature; MODIFIER silent_mutation Average:41.055; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N
vg0139856883 G -> A LOC_Os01g68620-LOC_Os01g68630 intergenic_region ; MODIFIER silent_mutation Average:41.055; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0139856883 NA 8.73E-06 mr1138 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
vg0139856883 NA 8.17E-08 mr1027_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
vg0139856883 NA 2.35E-06 mr1364_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
vg0139856883 NA 8.38E-06 mr1428_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
vg0139856883 NA 2.85E-08 mr1469_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
vg0139856883 NA 5.29E-07 mr1469_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
vg0139856883 NA 1.68E-06 mr1539_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