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Detailed information for vg0809823253:

Variant ID: vg0809823253 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 9823253
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTGTGAAAACCAAGCCAAGCTTAAGCCAACCATTCTTGATCTCGAGCGGATAAGGCCGGGAGGAGGGCTCGGTCTCTCCCTGGTCTCCAATTTCTCTCGC[G/A]
CTCCCCTCTCTCTCCCCCGCGCGCGCTCATCTCTCTCTCATCCCAACGGCGGCGGCCGGATCTTGCTGTGGCCCGACAGCAGCGGTACCACCCTCCCCTC

Reverse complement sequence

GAGGGGAGGGTGGTACCGCTGCTGTCGGGCCACAGCAAGATCCGGCCGCCGCCGTTGGGATGAGAGAGAGATGAGCGCGCGCGGGGGAGAGAGAGGGGAG[C/T]
GCGAGAGAAATTGGAGACCAGGGAGAGACCGAGCCCTCCTCCCGGCCTTATCCGCTCGAGATCAAGAATGGTTGGCTTAAGCTTGGCTTGGTTTTCACAG

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 93.50% 6.20% 0.25% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 86.80% 12.40% 0.73% 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 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 96.20% 2.30% 1.43% 0.00% NA
Tropical Japonica  504 70.40% 29.60% 0.00% 0.00% NA
Japonica Intermediate  241 91.30% 8.70% 0.00% 0.00% NA
VI/Aromatic  96 10.40% 89.60% 0.00% 0.00% NA
Intermediate  90 83.30% 15.60% 1.11% 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
vg0809823253 G -> A LOC_Os08g16100.1 upstream_gene_variant ; 4851.0bp to feature; MODIFIER silent_mutation Average:66.37; most accessible tissue: Zhenshan97 young leaf, score: 78.644 N N N N
vg0809823253 G -> A LOC_Os08g16110.1 upstream_gene_variant ; 1633.0bp to feature; MODIFIER silent_mutation Average:66.37; most accessible tissue: Zhenshan97 young leaf, score: 78.644 N N N N
vg0809823253 G -> A LOC_Os08g16120.1 upstream_gene_variant ; 1374.0bp to feature; MODIFIER silent_mutation Average:66.37; most accessible tissue: Zhenshan97 young leaf, score: 78.644 N N N N
vg0809823253 G -> A LOC_Os08g16120.2 upstream_gene_variant ; 1374.0bp to feature; MODIFIER silent_mutation Average:66.37; most accessible tissue: Zhenshan97 young leaf, score: 78.644 N N N N
vg0809823253 G -> A LOC_Os08g16110-LOC_Os08g16120 intergenic_region ; MODIFIER silent_mutation Average:66.37; most accessible tissue: Zhenshan97 young leaf, score: 78.644 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0809823253 1.99E-08 NA Heading_date All YES Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0809823253 NA 3.32E-09 mr1570 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