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Detailed information for vg0101034362:

Variant ID: vg0101034362 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 1034362
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.73, A: 0.26, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:


GAGGGGCTTAGCAGTACGACGAGCAACCCAATACTGTTTATAATTTAAATTTAAAAAATGGTGAGACGAGTACTCCCTCCATCACTAAATATTTAACGCC[A/G]
TTAAGTTTTTTAAACATGTTTGACCGTCCGTCTTATTAAAAAAGTTTAAGTAATTATTTATTCTTTTCCTATCATTTGATTCATTATTAAATATACTACT

Reverse complement sequence

AGTAGTATATTTAATAATGAATCAAATGATAGGAAAAGAATAAATAATTACTTAAACTTTTTTAATAAGACGGACGGTCAAACATGTTTAAAAAACTTAA[T/C]
GGCGTTAAATATTTAGTGATGGAGGGAGTACTCGTCTCACCATTTTTTAAATTTAAATTATAAACAGTATTGGGTTGCTCGTCGTACTGCTAAGCCCCTC

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 84.30% 15.70% 0.02% 0.00% NA
All Indica  2759 96.80% 3.20% 0.04% 0.00% NA
All Japonica  1512 57.70% 42.30% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 99.30% 0.70% 0.00% 0.00% NA
Indica Intermediate  786 90.80% 9.00% 0.13% 0.00% NA
Temperate Japonica  767 43.50% 56.50% 0.00% 0.00% NA
Tropical Japonica  504 88.50% 11.50% 0.00% 0.00% NA
Japonica Intermediate  241 38.20% 61.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 84.40% 15.60% 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
vg0101034362 A -> G LOC_Os01g02884.1 downstream_gene_variant ; 4250.0bp to feature; MODIFIER silent_mutation Average:50.595; most accessible tissue: Minghui63 root, score: 75.155 N N N N
vg0101034362 A -> G LOC_Os01g02884-LOC_Os01g02890 intergenic_region ; MODIFIER silent_mutation Average:50.595; most accessible tissue: Minghui63 root, score: 75.155 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0101034362 2.05E-06 NA mr1829 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
vg0101034362 4.62E-09 NA mr1354_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
vg0101034362 1.91E-06 NA mr1354_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
vg0101034362 2.27E-08 NA mr1829_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
vg0101034362 1.30E-09 NA mr1902_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