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Detailed information for vg0127893586:

Variant ID: vg0127893586 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 27893586
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.67, G: 0.31, others allele: 0.00, population size: 45. )

Flanking Sequence (100 bp) in Reference Genome:


GGTCGCACGCTTAATGGGTCGGAATAAGGGGATTGGATGGAGATCCAATATGAGCTTACTTCGGATAGGGATCCGAATAGGAGTCCTACGGGCTTTGAAG[G/A]
CCCGAGTGATGGATCCTATATATTCGTGAGAGGTGTGACCGGCGGAGGCATTGCATCACGTGAGAAACCCTAGCCGTCACTTCCCTCCCCGAGCAAAACC

Reverse complement sequence

GGTTTTGCTCGGGGAGGGAAGTGACGGCTAGGGTTTCTCACGTGATGCAATGCCTCCGCCGGTCACACCTCTCACGAATATATAGGATCCATCACTCGGG[C/T]
CTTCAAAGCCCGTAGGACTCCTATTCGGATCCCTATCCGAAGTAAGCTCATATTGGATCTCCATCCAATCCCCTTATTCCGACCCATTAAGCGTGCGACC

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 70.60% 29.30% 0.04% 0.00% NA
All Indica  2759 98.70% 1.30% 0.00% 0.00% NA
All Japonica  1512 13.80% 86.20% 0.00% 0.00% NA
Aus  269 96.70% 3.30% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 96.80% 3.20% 0.00% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 98.20% 1.80% 0.00% 0.00% NA
Temperate Japonica  767 0.30% 99.70% 0.00% 0.00% NA
Tropical Japonica  504 37.90% 62.10% 0.00% 0.00% NA
Japonica Intermediate  241 6.60% 93.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 55.60% 42.20% 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
vg0127893586 G -> A LOC_Os01g48660.1 upstream_gene_variant ; 2768.0bp to feature; MODIFIER silent_mutation Average:56.015; most accessible tissue: Minghui63 panicle, score: 77.956 N N N N
vg0127893586 G -> A LOC_Os01g48650.1 intron_variant ; MODIFIER silent_mutation Average:56.015; most accessible tissue: Minghui63 panicle, score: 77.956 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0127893586 NA 9.90E-15 mr1361 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
vg0127893586 9.09E-07 NA mr1103_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
vg0127893586 8.09E-06 NA mr1104_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
vg0127893586 NA 7.69E-24 mr1308_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
vg0127893586 NA 7.97E-23 mr1361_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
vg0127893586 NA 6.27E-28 mr1584_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
vg0127893586 NA 2.09E-07 mr1607_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
vg0127893586 NA 9.43E-17 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