Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0420368452:

Variant ID: vg0420368452 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 20368452
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTAATTAGTATGTAATTTTCGAATTTACATATGTAATTTTAGTACTTACATATGTAATTTTGAGACTTACATTGTAAATACACTAAAATTACATATGTAA[T/G]
TAGGGACTTACAATGTAAATACATGTCGACTATTTTTTTTGATGGAAAATATGGCGCCATAAATATAGCATCTCCTCTCTTGCTTCTGATCACCATTATT

Reverse complement sequence

AATAATGGTGATCAGAAGCAAGAGAGGAGATGCTATATTTATGGCGCCATATTTTCCATCAAAAAAAATAGTCGACATGTATTTACATTGTAAGTCCCTA[A/C]
TTACATATGTAATTTTAGTGTATTTACAATGTAAGTCTCAAAATTACATATGTAAGTACTAAAATTACATATGTAAATTCGAAAATTACATACTAATTAC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.90% 5.10% 0.00% 0.00% NA
All Indica  2759 91.30% 8.70% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 92.70% 7.30% 0.00% 0.00% NA
Indica III  913 82.60% 17.40% 0.00% 0.00% NA
Indica Intermediate  786 94.50% 5.50% 0.00% 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  90 100.00% 0.00% 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
vg0420368452 T -> G LOC_Os04g33620.1 upstream_gene_variant ; 3698.0bp to feature; MODIFIER silent_mutation Average:81.118; most accessible tissue: Zhenshan97 flag leaf, score: 90.298 N N N N
vg0420368452 T -> G LOC_Os04g33640.1 upstream_gene_variant ; 4461.0bp to feature; MODIFIER silent_mutation Average:81.118; most accessible tissue: Zhenshan97 flag leaf, score: 90.298 N N N N
vg0420368452 T -> G LOC_Os04g33640.2 upstream_gene_variant ; 4693.0bp to feature; MODIFIER silent_mutation Average:81.118; most accessible tissue: Zhenshan97 flag leaf, score: 90.298 N N N N
vg0420368452 T -> G LOC_Os04g33630.1 intron_variant ; MODIFIER silent_mutation Average:81.118; most accessible tissue: Zhenshan97 flag leaf, score: 90.298 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0420368452 2.61E-06 2.90E-06 mr1695 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