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Detailed information for vg0725004532:

Variant ID: vg0725004532 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 25004532
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


CCAAATACTAGTAACAAAAAGTAGGTAAGTTGGTATTTGTCATTTGGGAGTCCATAGCAGCAAATTTGGCTAAAAAGCACCGGCCCCGTGCATGAGAGAG[G/A]
CAGCAGCAATTAATAGCAAAACTTTACCATACATCTAAACACTAACTTATAAAATTGCAATGCCAAATCTTTTGCCACCAAAACTTTTGCTAAAAAAATT

Reverse complement sequence

AATTTTTTTAGCAAAAGTTTTGGTGGCAAAAGATTTGGCATTGCAATTTTATAAGTTAGTGTTTAGATGTATGGTAAAGTTTTGCTATTAATTGCTGCTG[C/T]
CTCTCTCATGCACGGGGCCGGTGCTTTTTAGCCAAATTTGCTGCTATGGACTCCCAAATGACAAATACCAACTTACCTACTTTTTGTTACTAGTATTTGG

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 94.40% 4.80% 0.76% 0.00% NA
All Indica  2759 98.60% 1.30% 0.11% 0.00% NA
All Japonica  1512 85.80% 12.10% 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 94.60% 5.20% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 98.30% 1.40% 0.25% 0.00% NA
Temperate Japonica  767 96.20% 1.20% 2.61% 0.00% NA
Tropical Japonica  504 66.90% 31.20% 1.98% 0.00% NA
Japonica Intermediate  241 92.10% 7.10% 0.83% 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
vg0725004532 G -> A LOC_Os07g41720.1 upstream_gene_variant ; 3314.0bp to feature; MODIFIER silent_mutation Average:74.593; most accessible tissue: Callus, score: 96.982 N N N N
vg0725004532 G -> A LOC_Os07g41730.2 upstream_gene_variant ; 2691.0bp to feature; MODIFIER silent_mutation Average:74.593; most accessible tissue: Callus, score: 96.982 N N N N
vg0725004532 G -> A LOC_Os07g41720.2 upstream_gene_variant ; 3312.0bp to feature; MODIFIER silent_mutation Average:74.593; most accessible tissue: Callus, score: 96.982 N N N N
vg0725004532 G -> A LOC_Os07g41730.1 upstream_gene_variant ; 2691.0bp to feature; MODIFIER silent_mutation Average:74.593; most accessible tissue: Callus, score: 96.982 N N N N
vg0725004532 G -> A LOC_Os07g41720-LOC_Os07g41730 intergenic_region ; MODIFIER silent_mutation Average:74.593; most accessible tissue: Callus, score: 96.982 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0725004532 NA 4.85E-07 mr1125 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
vg0725004532 NA 2.41E-11 mr1136 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
vg0725004532 NA 1.87E-07 mr1188 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
vg0725004532 8.63E-06 NA mr1103_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
vg0725004532 NA 9.52E-06 mr1112_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
vg0725004532 5.10E-06 7.94E-11 mr1125_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
vg0725004532 NA 6.74E-11 mr1136_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
vg0725004532 NA 2.73E-07 mr1155_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
vg0725004532 NA 1.58E-07 mr1188_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
vg0725004532 3.78E-06 NA mr1226_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
vg0725004532 2.48E-06 8.70E-08 mr1246_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
vg0725004532 NA 8.54E-07 mr1404_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
vg0725004532 9.69E-07 9.20E-08 mr1620_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
vg0725004532 NA 1.83E-06 mr1718_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