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Detailed information for vg0112438971:

Variant ID: vg0112438971 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 12438971
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, T: 0.05, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:


CCGTTTATTTTATTTTGCGCTGCTTAGATCTTTATTGTTTGAGAGGAACTATCTACCTCTGTAATGACTTTATATTCGCTTATTAATTAGAGTAACAATT[T/G]
TACTCTATTATCAATTTGTTATTGTGTGCCTCGGCTGATTCCTGGATGAGGGTTTACATACATGTAAGCGTTTGGAATTTTGGATAGAAATTCCGGGCGT

Reverse complement sequence

ACGCCCGGAATTTCTATCCAAAATTCCAAACGCTTACATGTATGTAAACCCTCATCCAGGAATCAGCCGAGGCACACAATAACAAATTGATAATAGAGTA[A/C]
AATTGTTACTCTAATTAATAAGCGAATATAAAGTCATTACAGAGGTAGATAGTTCCTCTCAAACAATAAAGATCTAAGCAGCGCAAAATAAAATAAACGG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 68.20% 31.00% 0.04% 0.72% NA
All Indica  2759 96.70% 3.30% 0.04% 0.00% NA
All Japonica  1512 13.60% 84.10% 0.00% 2.25% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.00% 1.00% 0.00% 0.00% NA
Indica II  465 95.30% 4.70% 0.00% 0.00% NA
Indica III  913 95.60% 4.40% 0.00% 0.00% NA
Indica Intermediate  786 97.10% 2.80% 0.13% 0.00% NA
Temperate Japonica  767 6.10% 93.90% 0.00% 0.00% NA
Tropical Japonica  504 12.70% 80.60% 0.00% 6.75% NA
Japonica Intermediate  241 39.40% 60.60% 0.00% 0.00% NA
VI/Aromatic  96 31.20% 68.80% 0.00% 0.00% NA
Intermediate  90 57.80% 41.10% 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
vg0112438971 T -> G LOC_Os01g22140.1 downstream_gene_variant ; 54.0bp to feature; MODIFIER silent_mutation Average:25.861; most accessible tissue: Minghui63 root, score: 33.152 N N N N
vg0112438971 T -> G LOC_Os01g22120-LOC_Os01g22140 intergenic_region ; MODIFIER silent_mutation Average:25.861; most accessible tissue: Minghui63 root, score: 33.152 N N N N
vg0112438971 T -> DEL N N silent_mutation Average:25.861; most accessible tissue: Minghui63 root, score: 33.152 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0112438971 NA 2.61E-06 mr1066 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
vg0112438971 NA 9.04E-19 mr1242 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
vg0112438971 NA 2.57E-14 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
vg0112438971 NA 1.10E-18 mr1168_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
vg0112438971 NA 5.67E-19 mr1657_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