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Detailed information for vg1227323057:

Variant ID: vg1227323057 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 27323057
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:


TCCTTATCCGGAACTCCTTCTATATACGAGATTACGAGGTTTGTTTCCGTATAGAACATGGTATGTGGTGGGCCTCACCGAGCTTAGTCGATTACTATTG[G/A]
GTATGTGGTATCAATAACCCTTATAGTATGCATGCAACCAATAAGTACTAAGATGACATTTTGGGTTCCGGTCAACAATTTAATTTAGCACATAGAGATT

Reverse complement sequence

AATCTCTATGTGCTAAATTAAATTGTTGACCGGAACCCAAAATGTCATCTTAGTACTTATTGGTTGCATGCATACTATAAGGGTTATTGATACCACATAC[C/T]
CAATAGTAATCGACTAAGCTCGGTGAGGCCCACCACATACCATGTTCTATACGGAAACAAACCTCGTAATCTCGTATATAGAAGGAGTTCCGGATAAGGA

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 72.80% 26.90% 0.32% 0.00% NA
All Indica  2759 54.70% 44.90% 0.47% 0.00% NA
All Japonica  1512 99.30% 0.70% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 81.20% 17.80% 1.01% 0.00% NA
Indica II  465 27.70% 72.30% 0.00% 0.00% NA
Indica III  913 52.40% 47.10% 0.55% 0.00% NA
Indica Intermediate  786 53.20% 46.60% 0.25% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 75.60% 22.20% 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
vg1227323057 G -> A LOC_Os12g44060.1 upstream_gene_variant ; 1547.0bp to feature; MODIFIER silent_mutation Average:51.285; most accessible tissue: Callus, score: 70.329 N N N N
vg1227323057 G -> A LOC_Os12g44050-LOC_Os12g44060 intergenic_region ; MODIFIER silent_mutation Average:51.285; most accessible tissue: Callus, score: 70.329 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1227323057 NA 6.38E-09 mr1174 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
vg1227323057 NA 1.79E-11 mr1174_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
vg1227323057 NA 3.96E-12 mr1330_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
vg1227323057 NA 6.89E-06 mr1341_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
vg1227323057 NA 2.42E-08 mr1347_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
vg1227323057 2.15E-06 NA mr1350_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
vg1227323057 NA 9.99E-06 mr1350_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
vg1227323057 NA 1.09E-06 mr1418_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
vg1227323057 NA 1.23E-08 mr1449_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
vg1227323057 NA 2.30E-06 mr1558_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
vg1227323057 NA 6.99E-06 mr1779_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
vg1227323057 NA 4.16E-07 mr1992_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