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Detailed information for vg0234816959:

Variant ID: vg0234816959 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 34816959
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GACCTCAGCGGCGCGCGGCCTCGGAGGCGGCGGGGAGAGCAGGAGTTTGGGTTTAGGCCTGGTTTAGTTCCCAATTTTTTTTTCCAAAAAACATCACATC[G/A]
AATCTTTGGACACATGCATGGAGTATTAAATATAAATAAAAAAATTAATTACACAGTTTGCATGGAAATCGCGAGACGAATCTTTTGAGCCTAATTAGTC

Reverse complement sequence

GACTAATTAGGCTCAAAAGATTCGTCTCGCGATTTCCATGCAAACTGTGTAATTAATTTTTTTATTTATATTTAATACTCCATGCATGTGTCCAAAGATT[C/T]
GATGTGATGTTTTTTGGAAAAAAAAATTGGGAACTAAACCAGGCCTAAACCCAAACTCCTGCTCTCCCCGCCGCCTCCGAGGCCGCGCGCCGCTGAGGTC

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 91.10% 7.50% 1.42% 0.00% NA
All Indica  2759 85.00% 12.70% 2.28% 0.00% NA
All Japonica  1512 99.70% 0.00% 0.26% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 74.10% 21.70% 4.20% 0.00% NA
Indica II  465 83.40% 14.60% 1.94% 0.00% NA
Indica III  913 93.80% 4.90% 1.31% 0.00% NA
Indica Intermediate  786 84.00% 13.90% 2.16% 0.00% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 99.40% 0.00% 0.60% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0234816959 G -> A LOC_Os02g56790.1 upstream_gene_variant ; 4217.0bp to feature; MODIFIER silent_mutation Average:63.463; most accessible tissue: Minghui63 panicle, score: 86.442 N N N N
vg0234816959 G -> A LOC_Os02g56810.1 upstream_gene_variant ; 800.0bp to feature; MODIFIER silent_mutation Average:63.463; most accessible tissue: Minghui63 panicle, score: 86.442 N N N N
vg0234816959 G -> A LOC_Os02g56820.1 upstream_gene_variant ; 4388.0bp to feature; MODIFIER silent_mutation Average:63.463; most accessible tissue: Minghui63 panicle, score: 86.442 N N N N
vg0234816959 G -> A LOC_Os02g56800.1 downstream_gene_variant ; 2269.0bp to feature; MODIFIER silent_mutation Average:63.463; most accessible tissue: Minghui63 panicle, score: 86.442 N N N N
vg0234816959 G -> A LOC_Os02g56800-LOC_Os02g56810 intergenic_region ; MODIFIER silent_mutation Average:63.463; most accessible tissue: Minghui63 panicle, score: 86.442 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0234816959 1.32E-06 2.01E-07 mr1197 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
vg0234816959 NA 7.63E-06 mr1389_2 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
vg0234816959 NA 3.46E-06 mr1389_2 Ind_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