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Detailed information for vg0505612533:

Variant ID: vg0505612533 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 5612533
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGACCAAAACAGACTCTTCACAACATTATTCTCATCAGTTCTGAATCTGAAATAAAATAATGGATCCTCTGATATTTTCTTCTCAAAAAAATCCAAACAC[T/A]
GCATCATGTCATTTTTCCCACTTTCTCTTCTAACAAAATCTCTATAATTGCTCATAGCCTTTTTTGTGTAAGGAACTGCAAACAAGCCACCCCTAACATA

Reverse complement sequence

TATGTTAGGGGTGGCTTGTTTGCAGTTCCTTACACAAAAAAGGCTATGAGCAATTATAGAGATTTTGTTAGAAGAGAAAGTGGGAAAAATGACATGATGC[A/T]
GTGTTTGGATTTTTTTGAGAAGAAAATATCAGAGGATCCATTATTTTATTTCAGATTCAGAACTGATGAGAATAATGTTGTGAAGAGTCTGTTTTGGTCC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.00% 2.00% 0.02% 0.00% NA
All Indica  2759 96.60% 3.30% 0.04% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 94.50% 5.50% 0.00% 0.00% NA
Indica Intermediate  786 95.50% 4.30% 0.13% 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  241 100.00% 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
vg0505612533 T -> A LOC_Os05g10270.1 downstream_gene_variant ; 2899.0bp to feature; MODIFIER silent_mutation Average:17.422; most accessible tissue: Callus, score: 31.877 N N N N
vg0505612533 T -> A LOC_Os05g10270-LOC_Os05g10290 intergenic_region ; MODIFIER silent_mutation Average:17.422; most accessible tissue: Callus, score: 31.877 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0505612533 4.28E-06 4.18E-06 mr1245 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
vg0505612533 4.14E-06 4.14E-06 mr1373 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
vg0505612533 1.59E-13 7.28E-16 mr1697 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