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Detailed information for vg0417551912:

Variant ID: vg0417551912 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 17551912
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGAGAGATATGATAGATCCGATCAAGCGCTGAGCTAGAACGGACTTACAGCGCTTTTCGTTACTCAGCTCATCATCACAGCATGTACACCTGCTCAGTGA[G/A]
CTGAGGGGACGACAAGGATAAACGTCTTCGTTGAATTGTAGCCCTTTTTGTTTTGACATTATAAGTCTACGACGACGATCGTCCTGAAAGCTAGGTCTAT

Reverse complement sequence

ATAGACCTAGCTTTCAGGACGATCGTCGTCGTAGACTTATAATGTCAAAACAAAAAGGGCTACAATTCAACGAAGACGTTTATCCTTGTCGTCCCCTCAG[C/T]
TCACTGAGCAGGTGTACATGCTGTGATGATGAGCTGAGTAACGAAAAGCGCTGTAAGTCCGTTCTAGCTCAGCGCTTGATCGGATCTATCATATCTCTCT

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 59.70% 4.80% 1.52% 33.96% NA
All Indica  2759 56.80% 1.10% 1.56% 40.59% NA
All Japonica  1512 63.20% 12.60% 1.12% 23.08% NA
Aus  269 61.30% 0.00% 2.97% 35.69% NA
Indica I  595 78.30% 0.20% 1.01% 20.50% NA
Indica II  465 55.50% 4.50% 1.29% 38.71% NA
Indica III  913 38.40% 0.30% 1.86% 59.36% NA
Indica Intermediate  786 62.50% 0.60% 1.78% 35.11% NA
Temperate Japonica  767 59.70% 0.30% 1.04% 38.98% NA
Tropical Japonica  504 61.50% 36.10% 1.79% 0.60% NA
Japonica Intermediate  241 77.60% 2.90% 0.00% 19.50% NA
VI/Aromatic  96 76.00% 0.00% 1.04% 22.92% NA
Intermediate  90 70.00% 6.70% 3.33% 20.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0417551912 G -> DEL N N silent_mutation Average:32.617; most accessible tissue: Callus, score: 71.449 N N N N
vg0417551912 G -> A LOC_Os04g29540.1 upstream_gene_variant ; 2659.0bp to feature; MODIFIER silent_mutation Average:32.617; most accessible tissue: Callus, score: 71.449 N N N N
vg0417551912 G -> A LOC_Os04g29530-LOC_Os04g29540 intergenic_region ; MODIFIER silent_mutation Average:32.617; most accessible tissue: Callus, score: 71.449 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0417551912 NA 8.96E-07 mr1082 Jap_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
vg0417551912 NA 2.76E-06 mr1226 Jap_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
vg0417551912 2.43E-07 4.31E-10 mr1082_2 Jap_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
vg0417551912 6.36E-06 7.87E-09 mr1083_2 Jap_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
vg0417551912 NA 9.20E-06 mr1103_2 Jap_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
vg0417551912 NA 1.12E-07 mr1226_2 Jap_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
vg0417551912 NA 2.11E-06 mr1408_2 Jap_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