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Detailed information for vg0226331103:

Variant ID: vg0226331103 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 26331103
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCGGATCAAACATGTCACCGGATCCGCGCCGTGATGCCTCGCCTCCAGAGTGATGGATGCCGAGCTCCGCCTAGTCGCTTGCTTTGGATCCGGCCTTCTC[G/A]
CCAGTTGTCGGCGCCGCATCTGACCTCCTCACCGCCGGATCGGCTCTACGCCGCCTCGCCGCCGGAGTGATGGATGTCGAGCTCCGCCCTGGCACCGGTG

Reverse complement sequence

CACCGGTGCCAGGGCGGAGCTCGACATCCATCACTCCGGCGGCGAGGCGGCGTAGAGCCGATCCGGCGGTGAGGAGGTCAGATGCGGCGCCGACAACTGG[C/T]
GAGAAGGCCGGATCCAAAGCAAGCGACTAGGCGGAGCTCGGCATCCATCACTCTGGAGGCGAGGCATCACGGCGCGGATCCGGTGACATGTTTGATCCGG

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 96.70% 2.40% 0.91% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 89.70% 7.40% 2.84% 0.00% NA
Aus  269 100.00% 0.00% 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  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 80.10% 14.60% 5.35% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.00% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 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
vg0226331103 G -> A LOC_Os02g43630.1 upstream_gene_variant ; 1660.0bp to feature; MODIFIER silent_mutation Average:61.617; most accessible tissue: Zhenshan97 young leaf, score: 80.589 N N N N
vg0226331103 G -> A LOC_Os02g43620.1 downstream_gene_variant ; 4968.0bp to feature; MODIFIER silent_mutation Average:61.617; most accessible tissue: Zhenshan97 young leaf, score: 80.589 N N N N
vg0226331103 G -> A LOC_Os02g43640.1 downstream_gene_variant ; 4375.0bp to feature; MODIFIER silent_mutation Average:61.617; most accessible tissue: Zhenshan97 young leaf, score: 80.589 N N N N
vg0226331103 G -> A LOC_Os02g43630-LOC_Os02g43640 intergenic_region ; MODIFIER silent_mutation Average:61.617; most accessible tissue: Zhenshan97 young leaf, score: 80.589 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0226331103 NA 8.70E-06 mr1321_2 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
vg0226331103 NA 6.83E-07 mr1330_2 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
vg0226331103 NA 7.01E-06 mr1332_2 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
vg0226331103 NA 6.16E-06 mr1446_2 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
vg0226331103 2.20E-07 2.20E-07 mr1499_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
vg0226331103 NA 8.41E-06 mr1996_2 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