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Detailed information for vg0325243401:

Variant ID: vg0325243401 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 25243401
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGACTTTCTTAGATTTAATGCATAACTCTCAATTCTTCCACACAAGATTGGCTATATGGGCATCGAGAAATGTAAATATTAATGAATCGCTTGTTTACGA[G/A]
GAATAACTAGTAGCATGTTTAAATAGATGATGAGTATAATTACTTATCCTTAATCTATGTGCCAAGATGATTGGAGTACAATAGATCAACTTTTTTTTTT

Reverse complement sequence

AAAAAAAAAAGTTGATCTATTGTACTCCAATCATCTTGGCACATAGATTAAGGATAAGTAATTATACTCATCATCTATTTAAACATGCTACTAGTTATTC[C/T]
TCGTAAACAAGCGATTCATTAATATTTACATTTCTCGATGCCCATATAGCCAATCTTGTGTGGAAGAATTGAGAGTTATGCATTAAATCTAAGAAAGTCA

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 83.30% 16.60% 0.08% 0.00% NA
All Indica  2759 94.20% 5.80% 0.04% 0.00% NA
All Japonica  1512 75.60% 24.20% 0.20% 0.00% NA
Aus  269 8.60% 91.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 87.40% 12.60% 0.00% 0.00% NA
Indica Intermediate  786 94.70% 5.20% 0.13% 0.00% NA
Temperate Japonica  767 82.10% 17.50% 0.39% 0.00% NA
Tropical Japonica  504 73.00% 27.00% 0.00% 0.00% NA
Japonica Intermediate  241 60.20% 39.80% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0325243401 G -> A LOC_Os03g44760.1 downstream_gene_variant ; 3182.0bp to feature; MODIFIER silent_mutation Average:37.794; most accessible tissue: Minghui63 panicle, score: 71.773 N N N N
vg0325243401 G -> A LOC_Os03g44760.4 downstream_gene_variant ; 3244.0bp to feature; MODIFIER silent_mutation Average:37.794; most accessible tissue: Minghui63 panicle, score: 71.773 N N N N
vg0325243401 G -> A LOC_Os03g44760.2 downstream_gene_variant ; 3182.0bp to feature; MODIFIER silent_mutation Average:37.794; most accessible tissue: Minghui63 panicle, score: 71.773 N N N N
vg0325243401 G -> A LOC_Os03g44760.5 downstream_gene_variant ; 3244.0bp to feature; MODIFIER silent_mutation Average:37.794; most accessible tissue: Minghui63 panicle, score: 71.773 N N N N
vg0325243401 G -> A LOC_Os03g44760.3 downstream_gene_variant ; 3244.0bp to feature; MODIFIER silent_mutation Average:37.794; most accessible tissue: Minghui63 panicle, score: 71.773 N N N N
vg0325243401 G -> A LOC_Os03g44760-LOC_Os03g44780 intergenic_region ; MODIFIER silent_mutation Average:37.794; most accessible tissue: Minghui63 panicle, score: 71.773 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0325243401 1.49E-08 NA mr1745 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
vg0325243401 NA 4.50E-07 mr1745 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
vg0325243401 4.37E-08 NA mr1745_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
vg0325243401 NA 1.18E-09 mr1745_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