Search for Variation information by Variation ID:

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

Detailed information for vg0626042692:

Variant ID: vg0626042692 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 26042692
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTAATTATTACAAACTTAAAAAATAGATTAATATGATATTTTAGAGCAACTTTCATATAGAAAATTTTCACACAAAACACATCGTTTAGAAGTTTGAAAA[G/A]
CGTTCCACGAAAATCTTAATCTTCATTCAACTTTTGTGGGAGAAAATAACGGGACCATAGTCCTGTCCGTGGATGATTATTTTTGTAACTACTAGTGCTT

Reverse complement sequence

AAGCACTAGTAGTTACAAAAATAATCATCCACGGACAGGACTATGGTCCCGTTATTTTCTCCCACAAAAGTTGAATGAAGATTAAGATTTTCGTGGAACG[C/T]
TTTTCAAACTTCTAAACGATGTGTTTTGTGTGAAAATTTTCTATATGAAAGTTGCTCTAAAATATCATATTAATCTATTTTTTAAGTTTGTAATAATTAA

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 92.90% 7.00% 0.04% 0.00% NA
All Indica  2759 99.40% 0.60% 0.00% 0.00% NA
All Japonica  1512 79.70% 20.20% 0.07% 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 97.60% 2.40% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 96.50% 3.50% 0.00% 0.00% NA
Tropical Japonica  504 48.60% 51.20% 0.20% 0.00% NA
Japonica Intermediate  241 91.30% 8.70% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 87.80% 11.10% 1.11% 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
vg0626042692 G -> A LOC_Os06g43320.1 downstream_gene_variant ; 4336.0bp to feature; MODIFIER silent_mutation Average:51.947; most accessible tissue: Minghui63 panicle, score: 76.913 N N N N
vg0626042692 G -> A LOC_Os06g43320-LOC_Os06g43330 intergenic_region ; MODIFIER silent_mutation Average:51.947; most accessible tissue: Minghui63 panicle, score: 76.913 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0626042692 NA 7.74E-20 mr1301 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
vg0626042692 NA 2.01E-08 mr1338 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
vg0626042692 3.18E-06 NA mr1891 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
vg0626042692 NA 3.34E-22 mr1301_2 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
vg0626042692 NA 7.10E-16 mr1410_2 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
vg0626042692 NA 1.69E-10 mr1696_2 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
vg0626042692 NA 1.89E-07 mr1696_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