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Detailed information for vg0434699363:

Variant ID: vg0434699363 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 34699363
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.78, A: 0.22, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


TGGTTTTGATGGTCAGCGGATGCTCTGTATGTTGAAATTATAAGCACATAATGATTTAATTTATTCCATAAATAAATCATGACATTGCAGATATAAACTA[G/A]
ATTGAACGCATCATTAGATCTACACATGTAAACTAAGCAGTAAAACATGAACAGATCAAATATGCGTAACATGTCGAACATGTACCGAGGTGGCGGAAAA

Reverse complement sequence

TTTTCCGCCACCTCGGTACATGTTCGACATGTTACGCATATTTGATCTGTTCATGTTTTACTGCTTAGTTTACATGTGTAGATCTAATGATGCGTTCAAT[C/T]
TAGTTTATATCTGCAATGTCATGATTTATTTATGGAATAAATTAAATCATTATGTGCTTATAATTTCAACATACAGAGCATCCGCTGACCATCAAAACCA

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 60.70% 39.00% 0.38% 0.00% NA
All Indica  2759 95.10% 4.30% 0.54% 0.00% NA
All Japonica  1512 13.00% 86.90% 0.07% 0.00% NA
Aus  269 0.40% 99.60% 0.00% 0.00% NA
Indica I  595 97.50% 1.80% 0.67% 0.00% NA
Indica II  465 96.60% 2.80% 0.65% 0.00% NA
Indica III  913 97.00% 2.80% 0.11% 0.00% NA
Indica Intermediate  786 90.30% 8.80% 0.89% 0.00% NA
Temperate Japonica  767 4.40% 95.40% 0.13% 0.00% NA
Tropical Japonica  504 8.10% 91.90% 0.00% 0.00% NA
Japonica Intermediate  241 50.60% 49.40% 0.00% 0.00% NA
VI/Aromatic  96 5.20% 94.80% 0.00% 0.00% NA
Intermediate  90 43.30% 54.40% 2.22% 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
vg0434699363 G -> A LOC_Os04g58280.2 upstream_gene_variant ; 2161.0bp to feature; MODIFIER silent_mutation Average:65.61; most accessible tissue: Minghui63 panicle, score: 86.85 N N N N
vg0434699363 G -> A LOC_Os04g58280.1 upstream_gene_variant ; 2161.0bp to feature; MODIFIER silent_mutation Average:65.61; most accessible tissue: Minghui63 panicle, score: 86.85 N N N N
vg0434699363 G -> A LOC_Os04g58290.1 downstream_gene_variant ; 954.0bp to feature; MODIFIER silent_mutation Average:65.61; most accessible tissue: Minghui63 panicle, score: 86.85 N N N N
vg0434699363 G -> A LOC_Os04g58300.1 downstream_gene_variant ; 3132.0bp to feature; MODIFIER silent_mutation Average:65.61; most accessible tissue: Minghui63 panicle, score: 86.85 N N N N
vg0434699363 G -> A LOC_Os04g58280-LOC_Os04g58290 intergenic_region ; MODIFIER silent_mutation Average:65.61; most accessible tissue: Minghui63 panicle, score: 86.85 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0434699363 NA 8.46E-08 mr1693 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
vg0434699363 NA 6.77E-06 mr1745 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
vg0434699363 NA 2.17E-06 mr1509_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