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Detailed information for vg1226996981:

Variant ID: vg1226996981 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 26996981
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


ACTTGGCAGTGTGAAAAAATATTGCAGGCATACCATCTTGTAGTTTCAGCTTTACATTGCAATTTATTTTGCAAGTATGGATTTTCTGGAGGGATCTAAT[G/A]
GGTTTTATAGGTTTTATTCTGCATATTCTGTAGCTCTAGATCTGTGCCTCGCACCTAAAAATTTCCAGATGCCTTCCATGCCTATTCGTAGTAGTGTAGA

Reverse complement sequence

TCTACACTACTACGAATAGGCATGGAAGGCATCTGGAAATTTTTAGGTGCGAGGCACAGATCTAGAGCTACAGAATATGCAGAATAAAACCTATAAAACC[C/T]
ATTAGATCCCTCCAGAAAATCCATACTTGCAAAATAAATTGCAATGTAAAGCTGAAACTACAAGATGGTATGCCTGCAATATTTTTTCACACTGCCAAGT

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 86.10% 13.90% 0.00% 0.00% NA
All Indica  2759 76.90% 23.10% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 96.70% 3.30% 0.00% 0.00% NA
Indica I  595 96.50% 3.50% 0.00% 0.00% NA
Indica II  465 88.20% 11.80% 0.00% 0.00% NA
Indica III  913 62.00% 38.00% 0.00% 0.00% NA
Indica Intermediate  786 72.80% 27.20% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 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 99.00% 1.00% 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
vg1226996981 G -> A LOC_Os12g43520.1 downstream_gene_variant ; 532.0bp to feature; MODIFIER silent_mutation Average:71.654; most accessible tissue: Callus, score: 86.365 N N N N
vg1226996981 G -> A LOC_Os12g43510-LOC_Os12g43520 intergenic_region ; MODIFIER silent_mutation Average:71.654; most accessible tissue: Callus, score: 86.365 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1226996981 NA 4.43E-07 mr1515 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
vg1226996981 3.48E-07 2.23E-06 mr1047_2 Ind_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
vg1226996981 NA 5.68E-06 mr1834_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