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Detailed information for vg1103318925:

Variant ID: vg1103318925 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 3318925
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.02, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


TCAATTTTCTTGCCACAACTTCAGTATAGAAATCAAGTACTCATGTTCTTATTTTGCATCAGGAAGTTTGGTGCCCAAGAATGCATGGTGGATCCACCAT[A/G]
GAGGCTACGGGATCTCGAACACACACTACCAGTGTCGTAACCATGGGAGCTCCCATTAAGCCCCTCTATCTATCATACATCCATCAAAAGAAGGGATTAT

Reverse complement sequence

ATAATCCCTTCTTTTGATGGATGTATGATAGATAGAGGGGCTTAATGGGAGCTCCCATGGTTACGACACTGGTAGTGTGTGTTCGAGATCCCGTAGCCTC[T/C]
ATGGTGGATCCACCATGCATTCTTGGGCACCAAACTTCCTGATGCAAAATAAGAACATGAGTACTTGATTTCTATACTGAAGTTGTGGCAAGAAAATTGA

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 91.70% 6.00% 2.29% 0.00% NA
All Indica  2759 99.70% 0.10% 0.18% 0.00% NA
All Japonica  1512 75.20% 18.10% 6.68% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.00% 0.34% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.10% 0.38% 0.00% NA
Temperate Japonica  767 54.90% 33.90% 11.21% 0.00% NA
Tropical Japonica  504 98.00% 0.20% 1.79% 0.00% NA
Japonica Intermediate  241 92.10% 5.40% 2.49% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 7.80% 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
vg1103318925 A -> G LOC_Os11g06780.1 downstream_gene_variant ; 2633.0bp to feature; MODIFIER silent_mutation Average:52.052; most accessible tissue: Callus, score: 83.809 N N N N
vg1103318925 A -> G LOC_Os11g06780-LOC_Os11g06790 intergenic_region ; MODIFIER silent_mutation Average:52.052; most accessible tissue: Callus, score: 83.809 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1103318925 NA 2.19E-07 mr1163 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
vg1103318925 NA 8.63E-11 mr1010_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
vg1103318925 3.52E-06 NA mr1181_2 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
vg1103318925 NA 7.73E-06 mr1763_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