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Detailed information for vg1227357675:

Variant ID: vg1227357675 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 27357675
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


AAGATTGCTTCTGTAGTTCAGTTAACCCTCCCTTCTCAGGGGTGGCTCTTTTGCTTTCAATTTTTATCCTTGGTTATGTAACAGGGTTTATCCCCTAATT[C/A]
TATTCTTGCTTAATAAAGTTGATGTGTTTTTTTTTAAAAAAAGCAAATCCACCTGCAAAAATACATAGGGGATCCCTGTCAAGACCCGCTAGTGAAAATA

Reverse complement sequence

TATTTTCACTAGCGGGTCTTGACAGGGATCCCCTATGTATTTTTGCAGGTGGATTTGCTTTTTTTAAAAAAAAACACATCAACTTTATTAAGCAAGAATA[G/T]
AATTAGGGGATAAACCCTGTTACATAACCAAGGATAAAAATTGAAAGCAAAAGAGCCACCCCTGAGAAGGGAGGGTTAACTGAACTACAGAAGCAATCTT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.50% 1.50% 0.00% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 95.40% 4.60% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 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  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 91.90% 8.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 96.70% 3.30% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg1227357675 C -> A LOC_Os12g44110.2 downstream_gene_variant ; 1749.0bp to feature; MODIFIER silent_mutation Average:61.768; most accessible tissue: Zhenshan97 flower, score: 81.984 N N N N
vg1227357675 C -> A LOC_Os12g44100-LOC_Os12g44110 intergenic_region ; MODIFIER silent_mutation Average:61.768; most accessible tissue: Zhenshan97 flower, score: 81.984 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1227357675 2.62E-06 2.62E-06 mr1024 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
vg1227357675 NA 8.68E-07 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
vg1227357675 7.40E-08 7.40E-08 mr1024_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
vg1227357675 NA 4.39E-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
vg1227357675 2.16E-06 2.16E-06 mr1915_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