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Detailed information for vg0920454686:

Variant ID: vg0920454686 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 20454686
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCCTCACCAGCTTTAGACAAAAAGAACTTACCATCTAGTACACGTTGCAGCAAGGGATCCAACAAAAGATATAAGACTAGAATGTTACGCTCCCGAGAG[G/A]
CCCGAACCTGTATAAACTCCCGTATCTATTGTTTTTTTTGTTTCTGTCCCGACCTCGAATCCTCACACTAGCATCCTGAACGAATCTCAAAAAGGGTTCC

Reverse complement sequence

GGAACCCTTTTTGAGATTCGTTCAGGATGCTAGTGTGAGGATTCGAGGTCGGGACAGAAACAAAAAAAACAATAGATACGGGAGTTTATACAGGTTCGGG[C/T]
CTCTCGGGAGCGTAACATTCTAGTCTTATATCTTTTGTTGGATCCCTTGCTGCAACGTGTACTAGATGGTAAGTTCTTTTTGTCTAAAGCTGGTGAGGAT

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 98.80% 0.50% 0.74% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 96.50% 1.50% 1.98% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 94.00% 2.50% 3.52% 0.00% NA
Tropical Japonica  504 99.00% 0.60% 0.40% 0.00% NA
Japonica Intermediate  241 99.20% 0.40% 0.41% 0.00% NA
VI/Aromatic  96 97.90% 0.00% 2.08% 0.00% NA
Intermediate  90 96.70% 0.00% 3.33% 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
vg0920454686 G -> A LOC_Os09g35590.1 upstream_gene_variant ; 2404.0bp to feature; MODIFIER silent_mutation Average:51.716; most accessible tissue: Callus, score: 76.972 N N N N
vg0920454686 G -> A LOC_Os09g35580.1 downstream_gene_variant ; 3469.0bp to feature; MODIFIER silent_mutation Average:51.716; most accessible tissue: Callus, score: 76.972 N N N N
vg0920454686 G -> A LOC_Os09g35580-LOC_Os09g35590 intergenic_region ; MODIFIER silent_mutation Average:51.716; most accessible tissue: Callus, score: 76.972 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0920454686 1.65E-07 1.98E-10 mr1549 Jap_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
vg0920454686 NA 1.43E-06 mr1550 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
vg0920454686 NA 6.02E-06 mr1686 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
vg0920454686 7.62E-06 6.56E-10 mr1757 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
vg0920454686 NA 2.83E-06 mr1549_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
vg0920454686 NA 7.59E-06 mr1757_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