Search for Variation information by Variation ID:

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

Detailed information for vg0604638246:

Variant ID: vg0604638246 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 4638246
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, G: 0.01, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


AAATGGCAGTCCATAAAGAGATGTTGAATAGTCTTATTCTTCATGCAAAAACAACGTCTCAAGCTACCATTCCAATTCCGCTTCGCCAAATTATTCTTAG[T/G]
TAACACAACCCTTTAGGCATACCTCATGAAAATCTTAATCTTAAATAGCATCTTAAGCTTCCAAATACACTTATTCCTCTCAATATAGCCATTATTCCAA

Reverse complement sequence

TTGGAATAATGGCTATATTGAGAGGAATAAGTGTATTTGGAAGCTTAAGATGCTATTTAAGATTAAGATTTTCATGAGGTATGCCTAAAGGGTTGTGTTA[A/C]
CTAAGAATAATTTGGCGAAGCGGAATTGGAATGGTAGCTTGAGACGTTGTTTTTGCATGAAGAATAAGACTATTCAACATCTCTTTATGGACTGCCATTT

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 97.60% 2.30% 0.15% 0.00% NA
All Indica  2759 98.80% 1.20% 0.00% 0.00% NA
All Japonica  1512 94.90% 4.60% 0.46% 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 98.10% 1.90% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 97.30% 2.70% 0.00% 0.00% NA
Temperate Japonica  767 97.40% 1.80% 0.78% 0.00% NA
Tropical Japonica  504 91.90% 8.10% 0.00% 0.00% NA
Japonica Intermediate  241 93.40% 6.20% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0604638246 T -> G LOC_Os06g09220.1 upstream_gene_variant ; 2777.0bp to feature; MODIFIER silent_mutation Average:31.6; most accessible tissue: Callus, score: 64.183 N N N N
vg0604638246 T -> G LOC_Os06g09230.2 downstream_gene_variant ; 2345.0bp to feature; MODIFIER silent_mutation Average:31.6; most accessible tissue: Callus, score: 64.183 N N N N
vg0604638246 T -> G LOC_Os06g09220-LOC_Os06g09230 intergenic_region ; MODIFIER silent_mutation Average:31.6; most accessible tissue: Callus, score: 64.183 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0604638246 8.40E-06 2.53E-06 mr1077 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
vg0604638246 NA 1.77E-06 mr1124_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
vg0604638246 NA 4.84E-06 mr1150_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
vg0604638246 1.24E-07 7.62E-12 mr1200_2 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
vg0604638246 7.43E-06 3.69E-07 mr1861_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