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Detailed information for vg0201493818:

Variant ID: vg0201493818 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 1493818
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.90, G: 0.09, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


CGACACTATGGAATTAATTGATGTCTCACCCACATGTGTGCTATCGTTTTAGTTTAGACCATAAGAAACCTACATCAGCAGACTGACTGTAGTGATCTAC[A/G]
CATCAAACTTATAATCACTACACATCAAACCTATATGTAGGTGAAAGAGAGTGGAAGACAGAAGAAAGAAGCACTGGCAAACTTTCTTAACGTTTGCCTA

Reverse complement sequence

TAGGCAAACGTTAAGAAAGTTTGCCAGTGCTTCTTTCTTCTGTCTTCCACTCTCTTTCACCTACATATAGGTTTGATGTGTAGTGATTATAAGTTTGATG[T/C]
GTAGATCACTACAGTCAGTCTGCTGATGTAGGTTTCTTATGGTCTAAACTAAAACGATAGCACACATGTGGGTGAGACATCAATTAATTCCATAGTGTCG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 80.70% 19.20% 0.04% 0.00% NA
All Indica  2759 75.80% 24.20% 0.04% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 13.40% 86.60% 0.00% 0.00% NA
Indica I  595 95.80% 4.20% 0.00% 0.00% NA
Indica II  465 87.10% 12.90% 0.00% 0.00% NA
Indica III  913 53.10% 46.90% 0.00% 0.00% NA
Indica Intermediate  786 80.20% 19.70% 0.13% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 6.70% 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
vg0201493818 A -> G LOC_Os02g03620-LOC_Os02g03630 intergenic_region ; MODIFIER silent_mutation Average:59.342; most accessible tissue: Callus, score: 99.364 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0201493818 NA 2.09E-06 mr1286 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
vg0201493818 NA 1.64E-06 mr1320 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
vg0201493818 NA 6.90E-06 mr1331 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
vg0201493818 NA 1.32E-06 mr1420 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
vg0201493818 NA 5.68E-06 mr1445 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
vg0201493818 NA 6.03E-09 mr1523 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
vg0201493818 NA 3.71E-07 mr1556 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
vg0201493818 NA 1.98E-06 mr1574 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