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Detailed information for vg0825346493:

Variant ID: vg0825346493 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 25346493
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.02, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


GTGTTCAATTGTTAACTCTGTATGTTGCGTGGAAAGAAAGAGGTAAATATACCAACTGACATAATTCAATTTTGGGCTTATCCATTTCCTGAATCTAGGC[A/G]
CTATATAATTATTTGGTGAATTGGTAGAATATATTTTGTGGATTATTCCGTTGTTCATTAGCTAATGCCTTTCAGTTGCAATAGGAATGGAGAACAGTAT

Reverse complement sequence

ATACTGTTCTCCATTCCTATTGCAACTGAAAGGCATTAGCTAATGAACAACGGAATAATCCACAAAATATATTCTACCAATTCACCAAATAATTATATAG[T/C]
GCCTAGATTCAGGAAATGGATAAGCCCAAAATTGAATTATGTCAGTTGGTATATTTACCTCTTTCTTTCCACGCAACATACAGAGTTAACAATTGAACAC

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 85.10% 14.90% 0.02% 0.00% NA
All Indica  2759 81.70% 18.20% 0.04% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 33.10% 66.90% 0.00% 0.00% NA
Indica I  595 81.80% 18.20% 0.00% 0.00% NA
Indica II  465 94.40% 5.60% 0.00% 0.00% NA
Indica III  913 81.10% 18.90% 0.00% 0.00% NA
Indica Intermediate  786 74.90% 24.90% 0.13% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg0825346493 A -> G LOC_Os08g40010.1 downstream_gene_variant ; 2544.0bp to feature; MODIFIER silent_mutation Average:38.736; most accessible tissue: Callus, score: 83.528 N N N N
vg0825346493 A -> G LOC_Os08g40020.1 intron_variant ; MODIFIER silent_mutation Average:38.736; most accessible tissue: Callus, score: 83.528 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0825346493 NA 9.93E-07 mr1587 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
vg0825346493 NA 2.98E-12 mr1918_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
vg0825346493 NA 6.85E-06 mr1965_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