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Detailed information for vg1200672282:

Variant ID: vg1200672282 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 672282
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGTTGTTGGGCGTCTTCATCTTCACTGCTAGCTGACCTAACTGCTGCCGACTGGTTTCTTCGCCTCCATGGCTATGCGACTTCATCATCTTTGATTGGT[G/A]
TCACCGTTTTTACCACCACCAACATTTTTGTCACCTCTGACGGGCGATATCATCCCCATGTTCATCATCTTGCCTTCATGTCGACTGCATCAGCTATTGC

Reverse complement sequence

GCAATAGCTGATGCAGTCGACATGAAGGCAAGATGATGAACATGGGGATGATATCGCCCGTCAGAGGTGACAAAAATGTTGGTGGTGGTAAAAACGGTGA[C/T]
ACCAATCAAAGATGATGAAGTCGCATAGCCATGGAGGCGAAGAAACCAGTCGGCAGCAGTTAGGTCAGCTAGCAGTGAAGATGAAGACGCCCAACAACAA

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 55.40% 44.60% 0.02% 0.00% NA
All Indica  2759 90.10% 9.90% 0.00% 0.00% NA
All Japonica  1512 4.00% 95.90% 0.07% 0.00% NA
Aus  269 10.40% 89.60% 0.00% 0.00% NA
Indica I  595 74.10% 25.90% 0.00% 0.00% NA
Indica II  465 97.20% 2.80% 0.00% 0.00% NA
Indica III  913 94.90% 5.10% 0.00% 0.00% NA
Indica Intermediate  786 92.60% 7.40% 0.00% 0.00% NA
Temperate Japonica  767 6.00% 94.00% 0.00% 0.00% NA
Tropical Japonica  504 2.40% 97.60% 0.00% 0.00% NA
Japonica Intermediate  241 1.20% 98.30% 0.41% 0.00% NA
VI/Aromatic  96 9.40% 90.60% 0.00% 0.00% NA
Intermediate  90 34.40% 65.60% 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
vg1200672282 G -> A LOC_Os12g02180.1 downstream_gene_variant ; 1800.0bp to feature; MODIFIER silent_mutation Average:22.657; most accessible tissue: Callus, score: 47.846 N N N N
vg1200672282 G -> A LOC_Os12g02170-LOC_Os12g02180 intergenic_region ; MODIFIER silent_mutation Average:22.657; most accessible tissue: Callus, score: 47.846 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1200672282 NA 3.27E-12 mr1172_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
vg1200672282 NA 4.33E-10 mr1338_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
vg1200672282 NA 2.39E-06 mr1359_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
vg1200672282 NA 1.63E-11 mr1449_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
vg1200672282 NA 3.44E-06 mr1449_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
vg1200672282 NA 1.60E-12 mr1514_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
vg1200672282 NA 1.38E-11 mr1734_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
vg1200672282 NA 4.22E-10 mr1782_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
vg1200672282 NA 6.52E-09 mr1851_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