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Detailed information for vg0226921378:

Variant ID: vg0226921378 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 26921378
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAAAAGTGCAGTTAACCCATCCTATAAAAAAGTGTTTCGTTACACCTGGTAAGTCTGAAGATCGAAGGGAACACCAAACTGCAATAATCTAACGTAAGCA[G/T]
GCAATTGCTCACAAACAACTCAATCCAAATTGAGACTTTTAGGTCAGTAACTGCCACACGTAAGATCGAAACAAAACCAAACATAAAAAATATGCTATGT

Reverse complement sequence

ACATAGCATATTTTTTATGTTTGGTTTTGTTTCGATCTTACGTGTGGCAGTTACTGACCTAAAAGTCTCAATTTGGATTGAGTTGTTTGTGAGCAATTGC[C/A]
TGCTTACGTTAGATTATTGCAGTTTGGTGTTCCCTTCGATCTTCAGACTTACCAGGTGTAACGAAACACTTTTTTATAGGATGGGTTAACTGCACTTTTG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.70% 0.70% 0.68% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 95.80% 2.10% 2.12% 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  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 91.90% 4.00% 4.04% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 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
vg0226921378 G -> T LOC_Os02g44460.1 downstream_gene_variant ; 2874.0bp to feature; MODIFIER silent_mutation Average:45.265; most accessible tissue: Zhenshan97 root, score: 78.34 N N N N
vg0226921378 G -> T LOC_Os02g44480.1 downstream_gene_variant ; 1134.0bp to feature; MODIFIER silent_mutation Average:45.265; most accessible tissue: Zhenshan97 root, score: 78.34 N N N N
vg0226921378 G -> T LOC_Os02g44490.1 downstream_gene_variant ; 3339.0bp to feature; MODIFIER silent_mutation Average:45.265; most accessible tissue: Zhenshan97 root, score: 78.34 N N N N
vg0226921378 G -> T LOC_Os02g44470.1 intron_variant ; MODIFIER silent_mutation Average:45.265; most accessible tissue: Zhenshan97 root, score: 78.34 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0226921378 4.25E-06 4.25E-06 mr1445 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
vg0226921378 NA 3.83E-07 mr1383_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