Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0222034653:

Variant ID: vg0222034653 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 22034653
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCAGCTCTTTATTTATACTACACTTCTTTTATGTTATGAGTGTCTTATTTGTTCTTTGTGATGTGATGTTGATTTTATCCTTTTGAGTGCTCACCATGTC[G/A]
TATCTTTTGCATATCATATCTATTCTTACTGCTTATTTGCATCCCAGATGAAGGAAACTCTCTTCGGTTGCTCCCATTAATATATGCATATGAGCTTCAC

Reverse complement sequence

GTGAAGCTCATATGCATATATTAATGGGAGCAACCGAAGAGAGTTTCCTTCATCTGGGATGCAAATAAGCAGTAAGAATAGATATGATATGCAAAAGATA[C/T]
GACATGGTGAGCACTCAAAAGGATAAAATCAACATCACATCACAAAGAACAAATAAGACACTCATAACATAAAAGAAGTGTAGTATAAATAAAGAGCTGC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.80% 37.00% 0.15% 0.00% NA
All Indica  2759 91.70% 8.00% 0.25% 0.00% NA
All Japonica  1512 8.10% 91.90% 0.00% 0.00% NA
Aus  269 95.50% 4.50% 0.00% 0.00% NA
Indica I  595 95.60% 4.20% 0.17% 0.00% NA
Indica II  465 97.20% 2.40% 0.43% 0.00% NA
Indica III  913 90.40% 9.40% 0.22% 0.00% NA
Indica Intermediate  786 87.20% 12.60% 0.25% 0.00% NA
Temperate Japonica  767 1.30% 98.70% 0.00% 0.00% NA
Tropical Japonica  504 19.80% 80.20% 0.00% 0.00% NA
Japonica Intermediate  241 5.00% 95.00% 0.00% 0.00% NA
VI/Aromatic  96 13.50% 86.50% 0.00% 0.00% NA
Intermediate  90 52.20% 47.80% 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
vg0222034653 G -> A LOC_Os02g36470.1 downstream_gene_variant ; 2956.0bp to feature; MODIFIER silent_mutation Average:19.399; most accessible tissue: Minghui63 young leaf, score: 24.836 N N N N
vg0222034653 G -> A LOC_Os02g36480.1 downstream_gene_variant ; 404.0bp to feature; MODIFIER silent_mutation Average:19.399; most accessible tissue: Minghui63 young leaf, score: 24.836 N N N N
vg0222034653 G -> A LOC_Os02g36490.1 downstream_gene_variant ; 3951.0bp to feature; MODIFIER silent_mutation Average:19.399; most accessible tissue: Minghui63 young leaf, score: 24.836 N N N N
vg0222034653 G -> A LOC_Os02g36490.2 downstream_gene_variant ; 3951.0bp to feature; MODIFIER silent_mutation Average:19.399; most accessible tissue: Minghui63 young leaf, score: 24.836 N N N N
vg0222034653 G -> A LOC_Os02g36490.3 downstream_gene_variant ; 3951.0bp to feature; MODIFIER silent_mutation Average:19.399; most accessible tissue: Minghui63 young leaf, score: 24.836 N N N N
vg0222034653 G -> A LOC_Os02g36480-LOC_Os02g36490 intergenic_region ; MODIFIER silent_mutation Average:19.399; most accessible tissue: Minghui63 young leaf, score: 24.836 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0222034653 4.78E-06 4.01E-06 mr1911_2 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