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Detailed information for vg0434528476:

Variant ID: vg0434528476 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 34528476
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.95, G: 0.05, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


GTTTGCTGTCAAATTTTAGTAAGTATATAAGAAATCCTACCAAAATTTTGTTAAGTTGCTAAAATTTTAGCAGGGTTAAAATTTGGTAAGGTTGAAAATG[G/A]
CATAAAATGAACCGGCCCTATAATAATCTTCACTGGAAGGTCTCGGATGGTAGTTACTCTCAACCTGAAGCCCAAAAGAAAAAAAAATAATAAAAAGAAA

Reverse complement sequence

TTTCTTTTTATTATTTTTTTTTCTTTTGGGCTTCAGGTTGAGAGTAACTACCATCCGAGACCTTCCAGTGAAGATTATTATAGGGCCGGTTCATTTTATG[C/T]
CATTTTCAACCTTACCAAATTTTAACCCTGCTAAAATTTTAGCAACTTAACAAAATTTTGGTAGGATTTCTTATATACTTACTAAAATTTGACAGCAAAC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.40% 36.90% 0.61% 0.00% NA
All Indica  2759 96.30% 3.60% 0.11% 0.00% NA
All Japonica  1512 15.70% 82.60% 1.72% 0.00% NA
Aus  269 1.10% 98.90% 0.00% 0.00% NA
Indica I  595 97.80% 2.20% 0.00% 0.00% NA
Indica II  465 97.40% 2.40% 0.22% 0.00% NA
Indica III  913 98.60% 1.30% 0.11% 0.00% NA
Indica Intermediate  786 91.70% 8.10% 0.13% 0.00% NA
Temperate Japonica  767 9.40% 88.00% 2.61% 0.00% NA
Tropical Japonica  504 7.30% 92.30% 0.40% 0.00% NA
Japonica Intermediate  241 53.10% 45.20% 1.66% 0.00% NA
VI/Aromatic  96 12.50% 87.50% 0.00% 0.00% NA
Intermediate  90 47.80% 52.20% 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
vg0434528476 G -> A LOC_Os04g57950.1 downstream_gene_variant ; 4897.0bp to feature; MODIFIER silent_mutation Average:36.483; most accessible tissue: Callus, score: 84.114 N N N N
vg0434528476 G -> A LOC_Os04g57950-LOC_Os04g57970 intergenic_region ; MODIFIER silent_mutation Average:36.483; most accessible tissue: Callus, score: 84.114 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0434528476 NA 1.04E-06 mr1321 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
vg0434528476 6.89E-07 NA mr1565_2 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
vg0434528476 NA 4.57E-11 mr1781_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
vg0434528476 NA 1.41E-09 mr1940_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
vg0434528476 NA 2.74E-26 mr1943_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