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Detailed information for vg0518987903:

Variant ID: vg0518987903 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 18987903
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.81, A: 0.19, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:


TAAGGTTTGAAAAGAAATACTATGGTGCCCCTCATTAAATGGTGTTTATGTGAGAGTGGAAAGATGGCTGAGGGTAAAATAGGGAGAAATTTAAATGAGA[A/G]
ATGATTGATGGGGTAATTAGTACTCTAGAATTACAATTATTTTGGGATGAATTTTCAATCCTAGAAATATAATTATTTTGGGACGGAGGTAGTACTATTC

Reverse complement sequence

GAATAGTACTACCTCCGTCCCAAAATAATTATATTTCTAGGATTGAAAATTCATCCCAAAATAATTGTAATTCTAGAGTACTAATTACCCCATCAATCAT[T/C]
TCTCATTTAAATTTCTCCCTATTTTACCCTCAGCCATCTTTCCACTCTCACATAAACACCATTTAATGAGGGGCACCATAGTATTTCTTTTCAAACCTTA

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 69.80% 30.10% 0.02% 0.00% NA
All Indica  2759 98.90% 1.10% 0.04% 0.00% NA
All Japonica  1512 15.80% 84.20% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 98.80% 1.20% 0.00% 0.00% NA
Indica Intermediate  786 98.60% 1.30% 0.13% 0.00% NA
Temperate Japonica  767 5.00% 95.00% 0.00% 0.00% NA
Tropical Japonica  504 33.30% 66.70% 0.00% 0.00% NA
Japonica Intermediate  241 13.70% 86.30% 0.00% 0.00% NA
VI/Aromatic  96 7.30% 92.70% 0.00% 0.00% NA
Intermediate  90 66.70% 33.30% 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
vg0518987903 A -> G LOC_Os05g32490-LOC_Os05g32500 intergenic_region ; MODIFIER silent_mutation Average:55.693; most accessible tissue: Zhenshan97 root, score: 83.751 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0518987903 7.31E-07 NA mr1301 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
vg0518987903 5.18E-13 6.20E-14 mr1410 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
vg0518987903 1.08E-07 1.14E-13 mr1410 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
vg0518987903 2.38E-08 NA mr1301_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
vg0518987903 3.12E-16 NA mr1410_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
vg0518987903 2.39E-09 6.56E-14 mr1410_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