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Detailed information for vg1218863509:

Variant ID: vg1218863509 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 18863509
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.75, G: 0.23, others allele: 0.00, population size: 159. )

Flanking Sequence (100 bp) in Reference Genome:


CTTGTGCTTTTGCCATTTATATTGAGCTCCACCTTGCTAGTAATAAATTACTATACCTATTGTTTTTCTATTTAACATGACATGAATGAATGAACAAATA[G/A]
CCACATTAAAATAACATTATGTTAACAGGGGCATGTGCTCCCATTCTTTTCTCTCCATTAAATATTATTGGGTCATAAGGGGCAATATGCCCCCTCTAAT

Reverse complement sequence

ATTAGAGGGGGCATATTGCCCCTTATGACCCAATAATATTTAATGGAGAGAAAAGAATGGGAGCACATGCCCCTGTTAACATAATGTTATTTTAATGTGG[C/T]
TATTTGTTCATTCATTCATGTCATGTTAAATAGAAAAACAATAGGTATAGTAATTTATTACTAGCAAGGTGGAGCTCAATATAAATGGCAAAAGCACAAG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 61.30% 38.50% 0.21% 0.00% NA
All Indica  2759 90.60% 9.30% 0.11% 0.00% NA
All Japonica  1512 7.20% 92.50% 0.26% 0.00% NA
Aus  269 88.50% 11.50% 0.00% 0.00% NA
Indica I  595 95.60% 4.40% 0.00% 0.00% NA
Indica II  465 78.30% 21.70% 0.00% 0.00% NA
Indica III  913 94.70% 5.10% 0.11% 0.00% NA
Indica Intermediate  786 89.20% 10.60% 0.25% 0.00% NA
Temperate Japonica  767 2.00% 97.90% 0.13% 0.00% NA
Tropical Japonica  504 5.80% 94.00% 0.20% 0.00% NA
Japonica Intermediate  241 27.00% 72.20% 0.83% 0.00% NA
VI/Aromatic  96 21.90% 78.10% 0.00% 0.00% NA
Intermediate  90 32.20% 64.40% 3.33% 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
vg1218863509 G -> A LOC_Os12g31350.1 upstream_gene_variant ; 2862.0bp to feature; MODIFIER silent_mutation Average:28.486; most accessible tissue: Callus, score: 78.828 N N N N
vg1218863509 G -> A LOC_Os12g31350-LOC_Os12g31370 intergenic_region ; MODIFIER silent_mutation Average:28.486; most accessible tissue: Callus, score: 78.828 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218863509 NA 2.78E-06 mr1118 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
vg1218863509 NA 2.58E-08 mr1242 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
vg1218863509 NA 4.11E-21 mr1254 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
vg1218863509 NA 3.03E-15 mr1361 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
vg1218863509 NA 2.73E-08 mr1442 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
vg1218863509 NA 7.80E-08 mr1458 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
vg1218863509 NA 1.85E-11 mr1553 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
vg1218863509 NA 1.08E-07 mr1646 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
vg1218863509 1.34E-06 1.34E-06 mr1750 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
vg1218863509 NA 9.35E-07 mr1797 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
vg1218863509 NA 9.35E-07 mr1801 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
vg1218863509 NA 1.77E-07 mr1835 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
vg1218863509 NA 1.83E-06 mr1944 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
vg1218863509 3.10E-08 3.10E-08 mr1987 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
vg1218863509 NA 8.53E-06 mr1457_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
vg1218863509 7.77E-06 NA mr1458_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
vg1218863509 3.40E-08 2.99E-09 mr1458_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