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Detailed information for vg0301926245:

Variant ID: vg0301926245 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 1926245
Reference Allele: GAlternative Allele: A,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAATTGAAACCATGCCATTATAATTTTGCAAAATTTAAGATATGCCATCCTGACCCACATGTCATTGACTCATGTGGGTCCTATATGTCATTGAGATATC[G/A,T]
ATGGCATATCTCAAACTTTGTAAAATTATAATGGCATGGTTCTAAATTACCCAATTAGAAACCCACCATTGAAGCACCGATCATGAGCCTCGGCGGCCGC

Reverse complement sequence

GCGGCCGCCGAGGCTCATGATCGGTGCTTCAATGGTGGGTTTCTAATTGGGTAATTTAGAACCATGCCATTATAATTTTACAAAGTTTGAGATATGCCAT[C/T,A]
GATATCTCAATGACATATAGGACCCACATGAGTCAATGACATGTGGGTCAGGATGGCATATCTTAAATTTTGCAAAATTATAATGGCATGGTTTCAATTT

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 99.60% 0.30% 0.11% 0.00% T: 0.02%
All Indica  2759 100.00% 0.00% 0.00% 0.00% T: 0.04%
All Japonica  1512 99.50% 0.30% 0.26% 0.00% NA
Aus  269 99.60% 0.40% 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 99.90% 0.00% 0.00% 0.00% T: 0.11%
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 99.00% 0.50% 0.52% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 6.20% 1.04% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0301926245 G -> T LOC_Os03g04190.1 upstream_gene_variant ; 4349.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0301926245 G -> T LOC_Os03g04195.1 upstream_gene_variant ; 14.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0301926245 G -> T LOC_Os03g04190-LOC_Os03g04195 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0301926245 G -> A LOC_Os03g04190.1 upstream_gene_variant ; 4349.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0301926245 G -> A LOC_Os03g04195.1 upstream_gene_variant ; 14.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0301926245 G -> A LOC_Os03g04190-LOC_Os03g04195 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0301926245 1.38E-06 1.38E-06 mr1394 Ind_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