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Detailed information for vg0207335149:

Variant ID: vg0207335149 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 7335149
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: 227. )

Flanking Sequence (100 bp) in Reference Genome:


GGTAATCAGGATCCAATCTGACCTATTAAATACGGGTTTTGGAGCTAATATCATCATAGTCTTAAGGAAGTAAAGGAAAAAAAATATATAATTATGCATT[A/G]
TCGGCCACCGTAATATATACTCCCTCATGTCACAATTAAATTCTTAGGTTTCAGACAAATTCTGGTTAAACTTTGACTATCATTGACTTTAATTACTTAA

Reverse complement sequence

TTAAGTAATTAAAGTCAATGATAGTCAAAGTTTAACCAGAATTTGTCTGAAACCTAAGAATTTAATTGTGACATGAGGGAGTATATATTACGGTGGCCGA[T/C]
AATGCATAATTATATATTTTTTTTCCTTTACTTCCTTAAGACTATGATGATATTAGCTCCAAAACCCGTATTTAATAGGTCAGATTGGATCCTGATTACC

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 97.50% 2.50% 0.00% 0.00% NA
All Indica  2759 97.00% 3.00% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 88.10% 11.90% 0.00% 0.00% NA
Indica I  595 88.70% 11.30% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 98.10% 1.90% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 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 97.80% 2.20% 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
vg0207335149 A -> G LOC_Os02g13670.1 upstream_gene_variant ; 1063.0bp to feature; MODIFIER silent_mutation Average:33.244; most accessible tissue: Zhenshan97 young leaf, score: 51.997 N N N N
vg0207335149 A -> G LOC_Os02g13670-LOC_Os02g13690 intergenic_region ; MODIFIER silent_mutation Average:33.244; most accessible tissue: Zhenshan97 young leaf, score: 51.997 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0207335149 2.16E-06 2.74E-08 mr1053_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
vg0207335149 3.11E-06 2.07E-06 mr1128_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
vg0207335149 NA 3.85E-07 mr1147_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
vg0207335149 NA 5.35E-06 mr1204_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