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Detailed information for vg0205621590:

Variant ID: vg0205621590 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 5621590
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCTCCGGCGAAGGGATAAGTCCAATGTTCCGCCGGTCCAGGCAATTGTATCGTCTACGTCGGCGTCGTTCAAGACTGCATCAATACATTCGACCTCTTG[G/A]
ATTGCTCTGGTTTGGATGATATATTTACCTACCTATTTATCATATGTCTCTGATAATCTAGTCTTAGTATGTCAATTTAGCTCTATCGACTGCTTCTCGT

Reverse complement sequence

ACGAGAAGCAGTCGATAGAGCTAAATTGACATACTAAGACTAGATTATCAGAGACATATGATAAATAGGTAGGTAAATATATCATCCAAACCAGAGCAAT[C/T]
CAAGAGGTCGAATGTATTGATGCAGTCTTGAACGACGCCGACGTAGACGATACAATTGCCTGGACCGGCGGAACATTGGACTTATCCCTTCGCCGGAGAT

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 90.80% 9.20% 0.06% 0.00% NA
All Indica  2759 85.10% 14.90% 0.07% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 93.70% 5.90% 0.37% 0.00% NA
Indica I  595 98.00% 2.00% 0.00% 0.00% NA
Indica II  465 84.10% 15.90% 0.00% 0.00% NA
Indica III  913 78.80% 21.20% 0.00% 0.00% NA
Indica Intermediate  786 83.20% 16.50% 0.25% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0205621590 G -> A LOC_Os02g10690.1 upstream_gene_variant ; 1762.0bp to feature; MODIFIER silent_mutation Average:43.707; most accessible tissue: Zhenshan97 flag leaf, score: 75.455 N N N N
vg0205621590 G -> A LOC_Os02g10690.2 upstream_gene_variant ; 1762.0bp to feature; MODIFIER silent_mutation Average:43.707; most accessible tissue: Zhenshan97 flag leaf, score: 75.455 N N N N
vg0205621590 G -> A LOC_Os02g10670.1 downstream_gene_variant ; 1639.0bp to feature; MODIFIER silent_mutation Average:43.707; most accessible tissue: Zhenshan97 flag leaf, score: 75.455 N N N N
vg0205621590 G -> A LOC_Os02g10680.1 downstream_gene_variant ; 932.0bp to feature; MODIFIER silent_mutation Average:43.707; most accessible tissue: Zhenshan97 flag leaf, score: 75.455 N N N N
vg0205621590 G -> A LOC_Os02g10670-LOC_Os02g10680 intergenic_region ; MODIFIER silent_mutation Average:43.707; most accessible tissue: Zhenshan97 flag leaf, score: 75.455 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0205621590 NA 2.11E-07 mr1619_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
vg0205621590 4.83E-06 NA mr1705_2 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
vg0205621590 NA 8.70E-07 mr1705_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