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Detailed information for vg0808194223:

Variant ID: vg0808194223 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 8194223
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GATGTTTAGATTCAGTGGTGTAAAGTTTTGGCATGTCATATCGGATATTATATAGGGTGTTATATGGGGTGTTGAGACACTAATAAAAAAACTAATTATA[G/T]
AATCCGTCAGTAAATCGCGAGACGAATTTATTAAGTCTAATTAATCCGTCATTAGTAAATGTTTACAGTAGCACTACATTGTCAAATCATGGAGCAATTA

Reverse complement sequence

TAATTGCTCCATGATTTGACAATGTAGTGCTACTGTAAACATTTACTAATGACGGATTAATTAGACTTAATAAATTCGTCTCGCGATTTACTGACGGATT[C/A]
TATAATTAGTTTTTTTATTAGTGTCTCAACACCCCATATAACACCCTATATAATATCCGATATGACATGCCAAAACTTTACACCACTGAATCTAAACATC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.40% 0.80% 0.55% 2.26% NA
All Indica  2759 99.20% 0.40% 0.40% 0.00% NA
All Japonica  1512 90.50% 1.70% 0.86% 6.94% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.80% 2.00% 1.18% 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 99.50% 0.00% 0.51% 0.00% NA
Temperate Japonica  767 91.50% 3.40% 1.69% 3.39% NA
Tropical Japonica  504 96.80% 0.00% 0.00% 3.17% NA
Japonica Intermediate  241 73.90% 0.00% 0.00% 26.14% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 0.00% 2.22% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0808194223 G -> T LOC_Os08g13730.1 upstream_gene_variant ; 4136.0bp to feature; MODIFIER silent_mutation Average:59.974; most accessible tissue: Callus, score: 79.596 N N N N
vg0808194223 G -> T LOC_Os08g13740.1 upstream_gene_variant ; 1970.0bp to feature; MODIFIER silent_mutation Average:59.974; most accessible tissue: Callus, score: 79.596 N N N N
vg0808194223 G -> T LOC_Os08g13750.1 upstream_gene_variant ; 896.0bp to feature; MODIFIER silent_mutation Average:59.974; most accessible tissue: Callus, score: 79.596 N N N N
vg0808194223 G -> T LOC_Os08g13740-LOC_Os08g13750 intergenic_region ; MODIFIER silent_mutation Average:59.974; most accessible tissue: Callus, score: 79.596 N N N N
vg0808194223 G -> DEL N N silent_mutation Average:59.974; most accessible tissue: Callus, score: 79.596 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0808194223 2.52E-07 1.67E-14 Awn_length Jap_All Not 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
vg0808194223 1.79E-06 1.54E-07 mr1201 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
vg0808194223 4.85E-06 9.83E-07 mr1219 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
vg0808194223 2.80E-07 6.80E-08 mr1274 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
vg0808194223 2.56E-06 2.35E-07 mr1274_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