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Detailed information for vg1223872471:

Variant ID: vg1223872471 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 23872471
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: 128. )

Flanking Sequence (100 bp) in Reference Genome:


ATCACATCCAAAACTTTCCTACACACATAAACTTCCAACTTTTTTTTTCCAAACTTCCAACTTTTCCTAAACTTTCAACTTTTTTCATTAACTAAACACA[G/A]
CCCAAACTTCTAATTTTGGTTTGAACTAACCACATTCTTCTTCTTTCAAACACTCGCTAGCGAGAAGATGTACGTTCATTCAGAGATCTTGCAGCAGGGT

Reverse complement sequence

ACCCTGCTGCAAGATCTCTGAATGAACGTACATCTTCTCGCTAGCGAGTGTTTGAAAGAAGAAGAATGTGGTTAGTTCAAACCAAAATTAGAAGTTTGGG[C/T]
TGTGTTTAGTTAATGAAAAAAGTTGAAAGTTTAGGAAAAGTTGGAAGTTTGGAAAAAAAAAGTTGGAAGTTTATGTGTGTAGGAAAGTTTTGGATGTGAT

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 97.10% 2.40% 0.57% 0.00% NA
All Indica  2759 95.00% 4.00% 0.98% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 83.20% 12.80% 4.03% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 95.50% 4.10% 0.38% 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  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg1223872471 G -> A LOC_Os12g38840-LOC_Os12g38850 intergenic_region ; MODIFIER silent_mutation Average:39.294; most accessible tissue: Callus, score: 69.841 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1223872471 1.91E-06 1.05E-13 mr1038 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
vg1223872471 5.57E-06 NA mr1141 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
vg1223872471 1.70E-08 5.29E-17 mr1389 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
vg1223872471 8.43E-07 2.32E-14 mr1038_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
vg1223872471 3.62E-06 2.25E-13 mr1389_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
vg1223872471 4.99E-06 4.99E-06 mr1416_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