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Detailed information for vg0819862457:

Variant ID: vg0819862457 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 19862457
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AACCCTGACAGTAGCCCCCCGACTTCTGCTTAAATGAACTCGTGAGACCGATCGCAACTTCTGATGTCGGAGTTGTCGTTGTTCTCGATGTGAGGACCGA[G/A]
AGACGAGGAGTGATCGACAACGTCGGGTGAAGCTTCAACGGTCATGAGTGAATTTAAATTGAAGTCTGAAAAATTGCCGCGTGTAACGGACCCAGAAATT

Reverse complement sequence

AATTTCTGGGTCCGTTACACGCGGCAATTTTTCAGACTTCAATTTAAATTCACTCATGACCGTTGAAGCTTCACCCGACGTTGTCGATCACTCCTCGTCT[C/T]
TCGGTCCTCACATCGAGAACAACGACAACTCCGACATCAGAAGTTGCGATCGGTCTCACGAGTTCATTTAAGCAGAAGTCGGGGGGCTACTGTCAGGGTT

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 94.20% 5.60% 0.17% 0.04% NA
All Indica  2759 97.80% 2.10% 0.04% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 27.90% 68.80% 2.60% 0.74% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 97.60% 2.40% 0.00% 0.00% NA
Indica III  913 98.50% 1.50% 0.00% 0.00% NA
Indica Intermediate  786 95.50% 4.30% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 90.60% 9.40% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0819862457 G -> A LOC_Os08g32010.1 upstream_gene_variant ; 3004.0bp to feature; MODIFIER silent_mutation Average:30.854; most accessible tissue: Zhenshan97 root, score: 69.506 N N N N
vg0819862457 G -> A LOC_Os08g32020.1 upstream_gene_variant ; 297.0bp to feature; MODIFIER silent_mutation Average:30.854; most accessible tissue: Zhenshan97 root, score: 69.506 N N N N
vg0819862457 G -> A LOC_Os08g32030.1 downstream_gene_variant ; 3953.0bp to feature; MODIFIER silent_mutation Average:30.854; most accessible tissue: Zhenshan97 root, score: 69.506 N N N N
vg0819862457 G -> A LOC_Os08g32010-LOC_Os08g32020 intergenic_region ; MODIFIER silent_mutation Average:30.854; most accessible tissue: Zhenshan97 root, score: 69.506 N N N N
vg0819862457 G -> DEL N N silent_mutation Average:30.854; most accessible tissue: Zhenshan97 root, score: 69.506 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0819862457 1.43E-07 NA mr1248 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
vg0819862457 NA 1.57E-08 mr1465 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