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Detailed information for vg1215211990:

Variant ID: vg1215211990 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 15211990
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: 286. )

Flanking Sequence (100 bp) in Reference Genome:


ATATGCTCATCTTCGTAATTTATGTCTCACATGGGATGCTCTAGTATGTCTTTTGTATCACAGAAACAATAAATGTTTCATGTTAAATATGTATATATTT[G/A]
TGGTAATTGTATATATTGGTTTTTCTATAAATTAGTGCTCAGGGATCGGCCTGTGTTTGGTACACTAAATTTGAAGTAAAATTTTCTGGGAACTTAATAT

Reverse complement sequence

ATATTAAGTTCCCAGAAAATTTTACTTCAAATTTAGTGTACCAAACACAGGCCGATCCCTGAGCACTAATTTATAGAAAAACCAATATATACAATTACCA[C/T]
AAATATATACATATTTAACATGAAACATTTATTGTTTCTGTGATACAAAAGACATACTAGAGCATCCCATGTGAGACATAAATTACGAAGATGAGCATAT

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 95.20% 3.90% 0.95% 0.00% NA
All Indica  2759 99.50% 0.30% 0.22% 0.00% NA
All Japonica  1512 87.10% 10.40% 2.45% 0.00% NA
Aus  269 95.50% 4.50% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 98.60% 0.60% 0.76% 0.00% NA
Temperate Japonica  767 94.90% 1.70% 3.39% 0.00% NA
Tropical Japonica  504 78.80% 21.00% 0.20% 0.00% NA
Japonica Intermediate  241 79.70% 16.20% 4.15% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 3.30% 2.22% 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
vg1215211990 G -> A LOC_Os12g26120-LOC_Os12g26140 intergenic_region ; MODIFIER silent_mutation Average:37.745; most accessible tissue: Zhenshan97 young leaf, score: 63.653 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1215211990 3.73E-06 NA mr1016 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
vg1215211990 1.86E-06 NA mr1017 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
vg1215211990 3.57E-06 NA mr1055 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
vg1215211990 7.26E-07 NA mr1022_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
vg1215211990 3.74E-06 NA mr1023_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
vg1215211990 3.71E-07 NA mr1079_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