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Detailed information for vg0505850932:

Variant ID: vg0505850932 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 5850932
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCGCGAGCATGGAAAAAGCACAAGACACGGGCGATGTATACAGGTTCGGGCCGCTGAGAAGCGTAATACCCTACTCCTGTGTTTTGGTGGATCTGTGTAT[G/A]
AAGAAGCTACAAAATGCCAGCCAGCCCCCGATCGTTCTCTTCTTTTTCTTCCTAAAAATCCTCCCCCATCTTTCTAAGTGGGCAAGGTCCTCCTTTTATA

Reverse complement sequence

TATAAAAGGAGGACCTTGCCCACTTAGAAAGATGGGGGAGGATTTTTAGGAAGAAAAAGAAGAGAACGATCGGGGGCTGGCTGGCATTTTGTAGCTTCTT[C/T]
ATACACAGATCCACCAAAACACAGGAGTAGGGTATTACGCTTCTCAGCGGCCCGAACCTGTATACATCGCCCGTGTCTTGTGCTTTTTCCATGCTCGCGA

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 28.40% 9.10% 4.40% 58.13% NA
All Indica  2759 20.70% 5.40% 2.54% 71.37% NA
All Japonica  1512 40.70% 17.70% 8.00% 33.60% NA
Aus  269 19.70% 0.40% 0.37% 79.55% NA
Indica I  595 25.40% 3.70% 5.38% 65.55% NA
Indica II  465 7.70% 3.20% 1.29% 87.74% NA
Indica III  913 22.10% 7.40% 0.77% 69.66% NA
Indica Intermediate  786 23.00% 5.70% 3.18% 68.07% NA
Temperate Japonica  767 62.30% 30.10% 0.91% 6.65% NA
Tropical Japonica  504 7.30% 3.80% 18.06% 70.83% NA
Japonica Intermediate  241 41.50% 7.50% 9.54% 41.49% NA
VI/Aromatic  96 82.30% 1.00% 6.25% 10.42% NA
Intermediate  90 28.90% 8.90% 11.11% 51.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0505850932 G -> DEL N N silent_mutation Average:13.365; most accessible tissue: Callus, score: 34.215 N N N N
vg0505850932 G -> A LOC_Os05g10670.1 upstream_gene_variant ; 2641.0bp to feature; MODIFIER silent_mutation Average:13.365; most accessible tissue: Callus, score: 34.215 N N N N
vg0505850932 G -> A LOC_Os05g10670-LOC_Os05g10680 intergenic_region ; MODIFIER silent_mutation Average:13.365; most accessible tissue: Callus, score: 34.215 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0505850932 NA 7.07E-09 mr1002 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
vg0505850932 2.13E-07 2.13E-07 mr1190 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
vg0505850932 8.93E-08 1.47E-07 mr1245 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
vg0505850932 2.94E-07 2.94E-07 mr1373 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
vg0505850932 8.36E-07 8.36E-07 mr1652 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
vg0505850932 2.42E-07 3.09E-08 mr1697 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
vg0505850932 8.86E-13 1.13E-14 mr1697 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
vg0505850932 NA 3.95E-06 mr1164_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
vg0505850932 NA 4.06E-06 mr1330_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
vg0505850932 NA 2.86E-07 mr1627_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
vg0505850932 NA 6.12E-07 mr1880_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