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Detailed information for vg0227637893:

Variant ID: vg0227637893 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 27637893
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGGACCCATATTATATTTTTTGTGTTTTTTATTTCAATAGGATTTGAGAAGCATATTATTTCAATTCTTGTATTTTTCTTATTTATTTGTTTTTCCTATC[C/T]
TGCAAATTAAAGGGACCCTAAATTTTGTTTCAAAATAAATCAATTTCTATATTTTGAATTTTAAAGTTGATTTTGAGATATTCTCAACGTGGTTTTTTTC

Reverse complement sequence

GAAAAAAACCACGTTGAGAATATCTCAAAATCAACTTTAAAATTCAAAATATAGAAATTGATTTATTTTGAAACAAAATTTAGGGTCCCTTTAATTTGCA[G/A]
GATAGGAAAAACAAATAAATAAGAAAAATACAAGAATTGAAATAATATGCTTCTCAAATCCTATTGAAATAAAAAACACAAAAAATATAATATGGGTCCT

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 93.60% 4.70% 1.71% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 80.60% 14.20% 5.22% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 0.00% 0.00% NA
Temperate Japonica  767 69.10% 22.00% 8.87% 0.00% NA
Tropical Japonica  504 99.60% 0.00% 0.40% 0.00% NA
Japonica Intermediate  241 77.20% 19.10% 3.73% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 3.30% 1.11% 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
vg0227637893 C -> T LOC_Os02g45420-LOC_Os02g45440 intergenic_region ; MODIFIER silent_mutation Average:38.586; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0227637893 7.22E-08 NA mr1210 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
vg0227637893 6.51E-06 5.18E-09 mr1210 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
vg0227637893 2.56E-09 NA mr1305 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
vg0227637893 1.37E-06 1.17E-09 mr1305 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
vg0227637893 NA 1.68E-08 mr1585 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
vg0227637893 8.77E-10 NA mr1586 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
vg0227637893 1.79E-06 5.28E-09 mr1586 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
vg0227637893 NA 1.93E-06 mr1305_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
vg0227637893 NA 1.84E-07 mr1585_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