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Detailed information for vg1227357645:

Variant ID: vg1227357645 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 27357645
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.95, A: 0.06, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:


CTCCTTTTTCTGCTGTTAGGTTATTTCAGGAAGATTGCTTCTGTAGTTCAGTTAACCCTCCCTTCTCAGGGGTGGCTCTTTTGCTTTCAATTTTTATCCT[T/A]
GGTTATGTAACAGGGTTTATCCCCTAATTCTATTCTTGCTTAATAAAGTTGATGTGTTTTTTTTTAAAAAAAGCAAATCCACCTGCAAAAATACATAGGG

Reverse complement sequence

CCCTATGTATTTTTGCAGGTGGATTTGCTTTTTTTAAAAAAAAACACATCAACTTTATTAAGCAAGAATAGAATTAGGGGATAAACCCTGTTACATAACC[A/T]
AGGATAAAAATTGAAAGCAAAAGAGCCACCCCTGAGAAGGGAGGGTTAACTGAACTACAGAAGCAATCTTCCTGAAATAACCTAACAGCAGAAAAAGGAG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 74.00% 25.90% 0.11% 0.00% NA
All Indica  2759 59.30% 40.60% 0.14% 0.00% NA
All Japonica  1512 94.90% 5.00% 0.07% 0.00% NA
Aus  269 94.40% 5.60% 0.00% 0.00% NA
Indica I  595 79.00% 20.80% 0.17% 0.00% NA
Indica II  465 79.10% 20.90% 0.00% 0.00% NA
Indica III  913 38.90% 61.00% 0.11% 0.00% NA
Indica Intermediate  786 56.40% 43.40% 0.25% 0.00% NA
Temperate Japonica  767 91.40% 8.50% 0.13% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 95.90% 4.10% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 86.70% 13.30% 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
vg1227357645 T -> A LOC_Os12g44110.2 downstream_gene_variant ; 1779.0bp to feature; MODIFIER silent_mutation Average:60.699; most accessible tissue: Zhenshan97 flower, score: 83.915 N N N N
vg1227357645 T -> A LOC_Os12g44100-LOC_Os12g44110 intergenic_region ; MODIFIER silent_mutation Average:60.699; most accessible tissue: Zhenshan97 flower, score: 83.915 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1227357645 2.86E-06 2.86E-06 mr1024 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
vg1227357645 NA 2.14E-06 mr1565 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
vg1227357645 NA 4.65E-06 mr1922 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
vg1227357645 NA 1.77E-06 mr1940 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
vg1227357645 2.13E-07 2.13E-07 mr1024_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
vg1227357645 NA 2.83E-07 mr1565_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
vg1227357645 1.66E-06 1.66E-06 mr1915_2 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