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Detailed information for vg0142773064:

Variant ID: vg0142773064 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 42773064
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGCAGCTTTTGACAGTGTGAGGGACAGATTTCGATCAAGGTTTTCTGAGTTGCAGCAATTTAAGAAAACGCAATGCTGATGGAGACACAGTGGACACCAC[T/A]
ATTACTTTTCTTTTTGTTCGGCAGTTTTATACTGTTGAACACGAACAGTATTTAAGTAGTTTTAAACACAATACTGTTGGAGTAGTTTTGTTTGCCGTGG

Reverse complement sequence

CCACGGCAAACAAAACTACTCCAACAGTATTGTGTTTAAAACTACTTAAATACTGTTCGTGTTCAACAGTATAAAACTGCCGAACAAAAAGAAAAGTAAT[A/T]
GTGGTGTCCACTGTGTCTCCATCAGCATTGCGTTTTCTTAAATTGCTGCAACTCAGAAAACCTTGATCGAAATCTGTCCCTCACACTGTCAAAAGCTGCT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.20% 3.20% 0.97% 2.67% NA
All Indica  2759 92.10% 5.40% 1.49% 1.01% NA
All Japonica  1512 93.50% 0.00% 0.20% 6.28% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 75.00% 19.30% 5.71% 0.00% NA
Indica II  465 98.10% 1.30% 0.22% 0.43% NA
Indica III  913 97.20% 0.10% 0.22% 2.52% NA
Indica Intermediate  786 95.80% 3.30% 0.51% 0.38% NA
Temperate Japonica  767 99.90% 0.00% 0.00% 0.13% NA
Tropical Japonica  504 81.20% 0.00% 0.60% 18.25% NA
Japonica Intermediate  241 99.20% 0.00% 0.00% 0.83% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 1.10% 2.22% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0142773064 T -> A LOC_Os01g73830.1 downstream_gene_variant ; 22.0bp to feature; MODIFIER silent_mutation Average:65.314; most accessible tissue: Callus, score: 87.766 N N N N
vg0142773064 T -> A LOC_Os01g73840.2 downstream_gene_variant ; 1770.0bp to feature; MODIFIER silent_mutation Average:65.314; most accessible tissue: Callus, score: 87.766 N N N N
vg0142773064 T -> A LOC_Os01g73840.1 downstream_gene_variant ; 1770.0bp to feature; MODIFIER silent_mutation Average:65.314; most accessible tissue: Callus, score: 87.766 N N N N
vg0142773064 T -> A LOC_Os01g73830-LOC_Os01g73840 intergenic_region ; MODIFIER silent_mutation Average:65.314; most accessible tissue: Callus, score: 87.766 N N N N
vg0142773064 T -> DEL N N silent_mutation Average:65.314; most accessible tissue: Callus, score: 87.766 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0142773064 NA 1.76E-11 mr1201 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
vg0142773064 NA 8.13E-11 mr1201 Ind_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
vg0142773064 NA 2.36E-08 mr1219 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
vg0142773064 NA 1.96E-08 mr1219 Ind_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
vg0142773064 NA 2.66E-10 mr1274 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
vg0142773064 NA 1.92E-08 mr1274 Ind_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
vg0142773064 NA 1.52E-06 mr1662 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
vg0142773064 NA 4.98E-07 mr1662 Ind_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
vg0142773064 8.67E-06 NA mr1075_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
vg0142773064 7.55E-06 NA mr1075_2 Ind_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
vg0142773064 1.81E-06 NA mr1124_2 Ind_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
vg0142773064 NA 1.41E-13 mr1201_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
vg0142773064 NA 8.54E-13 mr1201_2 Ind_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
vg0142773064 NA 1.14E-09 mr1219_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
vg0142773064 NA 3.57E-10 mr1219_2 Ind_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
vg0142773064 NA 1.16E-12 mr1274_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
vg0142773064 NA 1.11E-11 mr1274_2 Ind_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
vg0142773064 NA 4.97E-06 mr1592_2 Ind_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