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Detailed information for vg0324228701:

Variant ID: vg0324228701 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 24228701
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CATGTACACATATAGTTTTACAAATTTCACAATTTTTTTTTAAATAAGACGAACGATCAAACATGTGCTAAAAAGGCAACGGTGTCAAACATTTTAAAAC[G/A]
GAGGGAGTAACAGTTACACAATGAGTGTATAGTATACCATCTTCCTTAGATACAACCTCTTAACTAAAATCTAACCTAGGGCCAGTTTGGTTTAGTGCCA

Reverse complement sequence

TGGCACTAAACCAAACTGGCCCTAGGTTAGATTTTAGTTAAGAGGTTGTATCTAAGGAAGATGGTATACTATACACTCATTGTGTAACTGTTACTCCCTC[C/T]
GTTTTAAAATGTTTGACACCGTTGCCTTTTTAGCACATGTTTGATCGTTCGTCTTATTTAAAAAAAAATTGTGAAATTTGTAAAACTATATGTGTACATG

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 76.70% 21.30% 2.01% 0.00% NA
All Indica  2759 99.10% 0.60% 0.29% 0.00% NA
All Japonica  1512 36.40% 58.30% 5.29% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.70% 0.00% 0.34% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 99.70% 0.10% 0.22% 0.00% NA
Indica Intermediate  786 98.00% 1.50% 0.51% 0.00% NA
Temperate Japonica  767 58.50% 34.30% 7.17% 0.00% NA
Tropical Japonica  504 9.90% 87.70% 2.38% 0.00% NA
Japonica Intermediate  241 21.20% 73.40% 5.39% 0.00% NA
VI/Aromatic  96 10.40% 87.50% 2.08% 0.00% NA
Intermediate  90 68.90% 25.60% 5.56% 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
vg0324228701 G -> A LOC_Os03g43440.1 upstream_gene_variant ; 771.0bp to feature; MODIFIER silent_mutation Average:39.517; most accessible tissue: Callus, score: 59.228 N N N N
vg0324228701 G -> A LOC_Os03g43440-LOC_Os03g43460 intergenic_region ; MODIFIER silent_mutation Average:39.517; most accessible tissue: Callus, score: 59.228 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0324228701 1.70E-06 NA mr1585 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
vg0324228701 7.74E-06 NA mr1586 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
vg0324228701 NA 2.94E-12 mr1379_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
vg0324228701 NA 7.50E-06 mr1379_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
vg0324228701 NA 1.52E-14 mr1454_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
vg0324228701 NA 4.15E-08 mr1559_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
vg0324228701 1.85E-07 NA mr1585_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