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Detailed information for vg0223269173:

Variant ID: vg0223269173 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 23269173
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


ATCATGTCAAACATAATCTGACCATTTCATATGTTCATAAGCAGGATTCAGAATCGGGAATGCTTCTCTCTTTCCCAGACTACGATAACTTTGTTACTGA[A/G]
AGAATGGCAAGCAGCAAAATCAGAAAAAGGAATGTTGATGGTGCTTTGTCCTTCTCTACTGTTGTTGAACAGTTGAGCAACCAAGCTGAATACCTGTCTG

Reverse complement sequence

CAGACAGGTATTCAGCTTGGTTGCTCAACTGTTCAACAACAGTAGAGAAGGACAAAGCACCATCAACATTCCTTTTTCTGATTTTGCTGCTTGCCATTCT[T/C]
TCAGTAACAAAGTTATCGTAGTCTGGGAAAGAGAGAAGCATTCCCGATTCTGAATCCTGCTTATGAACATATGAAATGGTCAGATTATGTTTGACATGAT

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 86.20% 13.70% 0.13% 0.00% NA
All Indica  2759 81.40% 18.30% 0.22% 0.00% NA
All Japonica  1512 99.20% 0.80% 0.00% 0.00% NA
Aus  269 58.00% 42.00% 0.00% 0.00% NA
Indica I  595 70.80% 29.10% 0.17% 0.00% NA
Indica II  465 94.80% 4.90% 0.22% 0.00% NA
Indica III  913 75.60% 24.10% 0.33% 0.00% NA
Indica Intermediate  786 88.40% 11.50% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 97.80% 2.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 90.60% 9.40% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0223269173 A -> G LOC_Os02g38480.1 synonymous_variant ; p.Glu1176Glu; LOW synonymous_codon Average:50.342; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0223269173 NA 5.95E-06 mr1149 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
vg0223269173 8.88E-06 NA mr1072_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
vg0223269173 5.87E-06 1.78E-07 mr1075_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
vg0223269173 5.69E-07 2.96E-09 mr1149_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
vg0223269173 5.17E-06 2.88E-09 mr1441_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