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Detailed information for vg0335946674:

Variant ID: vg0335946674 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 35946674
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAGAAGAGCAGCGGGCTACAGATTTATAGCCAGCTGTAGCATGGACTCAAAGACACAGTGTTTGTATGACAGGTGGGACCAGGTATTAATAGTGTAGTAT[G/A]
TAACTATTGTATGAATGAGCTATTAGATTGGCTATGGATGAATTGAATCTATAAAATCGAACTTTCAGTGCATTAACTTACAAGAAGATCGAGGAAATTA

Reverse complement sequence

TAATTTCCTCGATCTTCTTGTAAGTTAATGCACTGAAAGTTCGATTTTATAGATTCAATTCATCCATAGCCAATCTAATAGCTCATTCATACAATAGTTA[C/T]
ATACTACACTATTAATACCTGGTCCCACCTGTCATACAAACACTGTGTCTTTGAGTCCATGCTACAGCTGGCTATAAATCTGTAGCCCGCTGCTCTTCTC

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 94.50% 5.50% 0.00% 0.00% NA
All Indica  2759 92.70% 7.30% 0.00% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 80.70% 19.30% 0.00% 0.00% NA
Indica I  595 96.30% 3.70% 0.00% 0.00% NA
Indica II  465 93.30% 6.70% 0.00% 0.00% NA
Indica III  913 93.60% 6.40% 0.00% 0.00% NA
Indica Intermediate  786 88.40% 11.60% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0335946674 G -> A LOC_Os03g63644.1 downstream_gene_variant ; 1589.0bp to feature; MODIFIER silent_mutation Average:54.516; most accessible tissue: Minghui63 panicle, score: 87.605 N N N N
vg0335946674 G -> A LOC_Os03g63640-LOC_Os03g63644 intergenic_region ; MODIFIER silent_mutation Average:54.516; most accessible tissue: Minghui63 panicle, score: 87.605 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0335946674 4.91E-06 NA mr1148_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
vg0335946674 3.28E-07 NA mr1151_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
vg0335946674 2.94E-07 NA mr1248_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
vg0335946674 7.09E-06 8.58E-09 mr1252_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
vg0335946674 NA 1.49E-07 mr1263_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
vg0335946674 2.70E-06 NA mr1377_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
vg0335946674 NA 5.70E-07 mr1702_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
vg0335946674 2.03E-06 9.61E-11 mr1844_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