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Detailed information for vg0432880276:

Variant ID: vg0432880276 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 32880276
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


TTGGATCAAGTCAGATACTAAGCCTTCTACTACTACTTAGGTACTTAGGAGAGAAAATGCTATATTTCATAGATTGGACTCTCTTACTGTGTTTTTCTCA[G/A]
GGCAGTTCCCGAGCCGGGTTCCCTGGATCCATTCTGACCTAATTGGATGAATGAAGAAGGGGGCGAGCAGATACGACGGCCTCTTTTTAGCCGAATAAAG

Reverse complement sequence

CTTTATTCGGCTAAAAAGAGGCCGTCGTATCTGCTCGCCCCCTTCTTCATTCATCCAATTAGGTCAGAATGGATCCAGGGAACCCGGCTCGGGAACTGCC[C/T]
TGAGAAAAACACAGTAAGAGAGTCCAATCTATGAAATATAGCATTTTCTCTCCTAAGTACCTAAGTAGTAGTAGAAGGCTTAGTATCTGACTTGATCCAA

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 66.30% 33.50% 0.17% 0.00% NA
All Indica  2759 96.80% 3.20% 0.04% 0.00% NA
All Japonica  1512 13.30% 86.60% 0.13% 0.00% NA
Aus  269 55.40% 44.20% 0.37% 0.00% NA
Indica I  595 93.90% 6.10% 0.00% 0.00% NA
Indica II  465 97.60% 2.40% 0.00% 0.00% NA
Indica III  913 99.10% 0.90% 0.00% 0.00% NA
Indica Intermediate  786 95.80% 4.10% 0.13% 0.00% NA
Temperate Japonica  767 0.70% 99.30% 0.00% 0.00% NA
Tropical Japonica  504 36.30% 63.70% 0.00% 0.00% NA
Japonica Intermediate  241 5.40% 93.80% 0.83% 0.00% NA
VI/Aromatic  96 65.60% 33.30% 1.04% 0.00% NA
Intermediate  90 54.40% 42.20% 3.33% 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
vg0432880276 G -> A LOC_Os04g55300-LOC_Os04g55310 intergenic_region ; MODIFIER silent_mutation Average:16.357; most accessible tissue: Callus, score: 43.831 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0432880276 7.41E-06 7.41E-06 mr1145 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
vg0432880276 NA 1.40E-07 mr1364 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
vg0432880276 NA 1.12E-06 mr1408 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
vg0432880276 NA 3.52E-07 mr1443 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
vg0432880276 NA 2.43E-08 mr1929 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
vg0432880276 4.63E-06 8.84E-07 mr1126_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
vg0432880276 2.38E-07 3.75E-09 mr1498_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