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Detailed information for vg0127954494:

Variant ID: vg0127954494 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 27954494
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.55, G: 0.45, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTAAAATTATTATTTTTTTTTACTTACTTTATTATCCAAAGTACTTTAAGCATAACTTTTCGTTTTTTATATTTGCACAAAATTTTTTTAAATAAGAC[A/G]
AGTAGTCAAACAGTGAAAGAAAAACTTAAAATCTCTTATATTATGGGACGTAGGGAGTAGTTAGTAGATGCTACTAGCACATATTTTCTCCGTCCCATAA

Reverse complement sequence

TTATGGGACGGAGAAAATATGTGCTAGTAGCATCTACTAACTACTCCCTACGTCCCATAATATAAGAGATTTTAAGTTTTTCTTTCACTGTTTGACTACT[T/C]
GTCTTATTTAAAAAAATTTTGTGCAAATATAAAAAACGAAAAGTTATGCTTAAAGTACTTTGGATAATAAAGTAAGTAAAAAAAAATAATAATTTTAAAA

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 71.50% 28.40% 0.06% 0.00% NA
All Indica  2759 99.00% 0.90% 0.04% 0.00% NA
All Japonica  1512 15.20% 84.70% 0.07% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 97.20% 2.80% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 98.70% 1.30% 0.00% 0.00% NA
Temperate Japonica  767 0.70% 99.30% 0.00% 0.00% NA
Tropical Japonica  504 41.10% 58.90% 0.00% 0.00% NA
Japonica Intermediate  241 7.50% 92.10% 0.41% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 60.00% 38.90% 1.11% 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
vg0127954494 A -> G LOC_Os01g48740.1 upstream_gene_variant ; 2159.0bp to feature; MODIFIER silent_mutation Average:45.977; most accessible tissue: Zhenshan97 flower, score: 75.883 N N N N
vg0127954494 A -> G LOC_Os01g48720-LOC_Os01g48740 intergenic_region ; MODIFIER silent_mutation Average:45.977; most accessible tissue: Zhenshan97 flower, score: 75.883 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0127954494 NA 7.75E-58 mr1019 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
vg0127954494 NA 1.30E-70 mr1019_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
vg0127954494 NA 2.29E-51 mr1261_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
vg0127954494 1.71E-06 NA mr1517_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
vg0127954494 NA 1.52E-17 mr1682_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
vg0127954494 NA 7.28E-18 mr1730_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