Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0627802059:

Variant ID: vg0627802059 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 27802059
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


GGCAATTTCCAGGAAAAATGTCAGCATCCTTTCAGAATGTTATGTATGTTGATACCGATGGCCAGCCCTATCCTCCTCCTGTTTGGCCTGCTGGTCTCGA[A/G]
GTTTATGCAAGCAATACGAAATGCTACCAAGCTAGCATTTTTGAGGATAACATGTTTTACTATGTGGGGCCAGGTAGTTGTACTAGTTAAAATTAGAATC

Reverse complement sequence

GATTCTAATTTTAACTAGTACAACTACCTGGCCCCACATAGTAAAACATGTTATCCTCAAAAATGCTAGCTTGGTAGCATTTCGTATTGCTTGCATAAAC[T/C]
TCGAGACCAGCAGGCCAAACAGGAGGAGGATAGGGCTGGCCATCGGTATCAACATACATAACATTCTGAAAGGATGCTGACATTTTTCCTGGAAATTGCC

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 94.30% 5.70% 0.00% 0.00% NA
All Indica  2759 90.40% 9.60% 0.00% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 95.30% 4.70% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 87.60% 12.40% 0.00% 0.00% NA
Indica Intermediate  786 84.40% 15.60% 0.00% 0.00% NA
Temperate Japonica  767 99.50% 0.50% 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 98.90% 1.10% 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
vg0627802059 A -> G LOC_Os06g45920.1 synonymous_variant ; p.Glu209Glu; LOW synonymous_codon Average:72.204; most accessible tissue: Callus, score: 87.029 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0627802059 NA 7.56E-06 mr1442_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
vg0627802059 NA 3.10E-07 mr1533_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
vg0627802059 NA 9.11E-07 mr1980_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