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Detailed information for vg0203269607:

Variant ID: vg0203269607 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 3269607
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCTCACTCGATTTTCTCACTCAAATTTACAGTGCATTTTCTTGTAAGTTATAGTGTAATTTATGAAACTTACAATGTAACTTTTATAAGTTACACTGTA[A/G]
TTTTTGAATCTTCGCATGTAAATTTTAAATTTTGTATTGGATTTGGTCTTTTTCTTGAGGATATGGTAATTTAGTGTCCATTATAGTGTTTCTTAATTGC

Reverse complement sequence

GCAATTAAGAAACACTATAATGGACACTAAATTACCATATCCTCAAGAAAAAGACCAAATCCAATACAAAATTTAAAATTTACATGCGAAGATTCAAAAA[T/C]
TACAGTGTAACTTATAAAAGTTACATTGTAAGTTTCATAAATTACACTATAACTTACAAGAAAATGCACTGTAAATTTGAGTGAGAAAATCGAGTGAGAG

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 86.50% 13.40% 0.08% 0.00% NA
All Indica  2759 86.70% 13.20% 0.14% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 14.50% 85.50% 0.00% 0.00% NA
Indica I  595 86.70% 13.10% 0.17% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 83.90% 16.00% 0.11% 0.00% NA
Indica Intermediate  786 82.60% 17.20% 0.25% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 72.90% 27.10% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0203269607 A -> G LOC_Os02g06530.1 downstream_gene_variant ; 4001.0bp to feature; MODIFIER silent_mutation Average:43.94; most accessible tissue: Zhenshan97 flag leaf, score: 61.322 N N N N
vg0203269607 A -> G LOC_Os02g06540.1 downstream_gene_variant ; 840.0bp to feature; MODIFIER silent_mutation Average:43.94; most accessible tissue: Zhenshan97 flag leaf, score: 61.322 N N N N
vg0203269607 A -> G LOC_Os02g06550.1 downstream_gene_variant ; 996.0bp to feature; MODIFIER silent_mutation Average:43.94; most accessible tissue: Zhenshan97 flag leaf, score: 61.322 N N N N
vg0203269607 A -> G LOC_Os02g06540-LOC_Os02g06550 intergenic_region ; MODIFIER silent_mutation Average:43.94; most accessible tissue: Zhenshan97 flag leaf, score: 61.322 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0203269607 2.07E-06 NA mr1004 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
vg0203269607 1.29E-06 NA mr1150 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