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Detailed information for vg1220023538:

Variant ID: vg1220023538 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 20023538
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


ATAGGTTCATTAAAGAACTATATACATAGCATAAGTAGCAAAGTCTAATTGTATGATGCATGAATGCAACAAAAAAAATGTCTACATAAATTATCCTATG[C/G]
CACTAAAAATTTTACACAATTCCTTATTTTCAGACTAGTTTTTGGGTGACTAAATATATTATAAGTGGCAAAATTTGCTGCAAGACATTCAAAAAACTTG

Reverse complement sequence

CAAGTTTTTTGAATGTCTTGCAGCAAATTTTGCCACTTATAATATATTTAGTCACCCAAAAACTAGTCTGAAAATAAGGAATTGTGTAAAATTTTTAGTG[G/C]
CATAGGATAATTTATGTAGACATTTTTTTTGTTGCATTCATGCATCATACAATTAGACTTTGCTACTTATGCTATGTATATAGTTCTTTAATGAACCTAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.90% 0.80% 0.30% 0.00% NA
All Indica  2759 99.90% 0.00% 0.07% 0.00% NA
All Japonica  1512 96.90% 2.40% 0.73% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 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 96.10% 2.70% 1.17% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 92.90% 6.20% 0.83% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 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
vg1220023538 C -> G LOC_Os12g33090.1 downstream_gene_variant ; 2236.0bp to feature; MODIFIER silent_mutation Average:80.126; most accessible tissue: Minghui63 root, score: 88.381 N N N N
vg1220023538 C -> G LOC_Os12g33090-LOC_Os12g33100 intergenic_region ; MODIFIER silent_mutation Average:80.126; most accessible tissue: Minghui63 root, score: 88.381 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1220023538 3.34E-06 3.34E-06 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
vg1220023538 NA 4.68E-06 mr1037_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
vg1220023538 8.14E-06 8.14E-06 mr1317_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
vg1220023538 NA 6.87E-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
vg1220023538 2.07E-06 2.07E-06 mr1914_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