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Detailed information for vg0404416226:

Variant ID: vg0404416226 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 4416226
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.76, G: 0.24, others allele: 0.00, population size: 46. )

Flanking Sequence (100 bp) in Reference Genome:


TTTGAATACCGTTTGCTAGGACAATACATTTTTCATACCAACACTTCAAATTTGATTATAATCTGAGTAAAAAGCAGTACTTGTACAATAGTTTGTTCGT[A/G]
AGATGAGCACACAATGTTCATTACCTGCTGTGATCGCTACTTTCTGCGATCTGCTGTTGCGGGTCCACCAAATTTGGTTTTGCCATCCATGTGGACTCAG

Reverse complement sequence

CTGAGTCCACATGGATGGCAAAACCAAATTTGGTGGACCCGCAACAGCAGATCGCAGAAAGTAGCGATCACAGCAGGTAATGAACATTGTGTGCTCATCT[T/C]
ACGAACAAACTATTGTACAAGTACTGCTTTTTACTCAGATTATAATCAAATTTGAAGTGTTGGTATGAAAAATGTATTGTCCTAGCAAACGGTATTCAAA

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 79.10% 20.80% 0.11% 0.00% NA
All Indica  2759 95.80% 4.10% 0.14% 0.00% NA
All Japonica  1512 44.60% 55.40% 0.07% 0.00% NA
Aus  269 92.60% 7.40% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 90.80% 8.80% 0.43% 0.00% NA
Indica III  913 96.70% 3.30% 0.00% 0.00% NA
Indica Intermediate  786 94.80% 5.00% 0.25% 0.00% NA
Temperate Japonica  767 9.60% 90.40% 0.00% 0.00% NA
Tropical Japonica  504 91.50% 8.50% 0.00% 0.00% NA
Japonica Intermediate  241 57.70% 41.90% 0.41% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 85.60% 14.40% 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
vg0404416226 A -> G LOC_Os04g08280.1 downstream_gene_variant ; 2950.0bp to feature; MODIFIER silent_mutation Average:36.977; most accessible tissue: Callus, score: 58.272 N N N N
vg0404416226 A -> G LOC_Os04g08260-LOC_Os04g08280 intergenic_region ; MODIFIER silent_mutation Average:36.977; most accessible tissue: Callus, score: 58.272 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0404416226 NA 4.40E-07 mr1401 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
vg0404416226 NA 1.50E-06 mr1627 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
vg0404416226 NA 1.31E-11 mr1667 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
vg0404416226 3.84E-06 NA mr1933 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
vg0404416226 NA 1.83E-06 mr1763_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
vg0404416226 NA 1.68E-15 mr1800_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
vg0404416226 NA 1.66E-06 mr1860_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