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Detailed information for vg0432418113:

Variant ID: vg0432418113 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 32418113
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, C: 0.08, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:


GCTGTGTCAGCACTGACCAGTGTTGTTAACGATGACATTAAACCACTCAACAGGTCTAGTGGCTCTGAACTGAAGACTCAATGGCAACCAGATTCTAAGA[C/T]
TGATGCTTCCGTTCTGAAGATCTCTAAAGTCGAGACAAGCCTGCAGTTTGATGACAAAGCTAGGGATGGTTATGATGGAGATGAACATGAATGCACAGCC

Reverse complement sequence

GGCTGTGCATTCATGTTCATCTCCATCATAACCATCCCTAGCTTTGTCATCAAACTGCAGGCTTGTCTCGACTTTAGAGATCTTCAGAACGGAAGCATCA[G/A]
TCTTAGAATCTGGTTGCCATTGAGTCTTCAGTTCAGAGCCACTAGACCTGTTGAGTGGTTTAATGTCATCGTTAACAACACTGGTCAGTGCTGACACAGC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 59.60% 40.20% 0.04% 0.21% NA
All Indica  2759 75.60% 24.10% 0.00% 0.29% NA
All Japonica  1512 25.60% 74.20% 0.07% 0.13% NA
Aus  269 80.70% 19.30% 0.00% 0.00% NA
Indica I  595 83.70% 15.80% 0.00% 0.50% NA
Indica II  465 59.60% 40.00% 0.00% 0.43% NA
Indica III  913 85.90% 14.00% 0.00% 0.11% NA
Indica Intermediate  786 67.20% 32.60% 0.00% 0.25% NA
Temperate Japonica  767 23.30% 76.70% 0.00% 0.00% NA
Tropical Japonica  504 30.40% 69.00% 0.20% 0.40% NA
Japonica Intermediate  241 22.80% 77.20% 0.00% 0.00% NA
VI/Aromatic  96 78.10% 21.90% 0.00% 0.00% NA
Intermediate  90 54.40% 44.40% 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
vg0432418113 C -> DEL N N silent_mutation Average:51.028; most accessible tissue: Zhenshan97 young leaf, score: 66.83 N N N N
vg0432418113 C -> T LOC_Os04g54500.1 upstream_gene_variant ; 250.0bp to feature; MODIFIER silent_mutation Average:51.028; most accessible tissue: Zhenshan97 young leaf, score: 66.83 N N N N
vg0432418113 C -> T LOC_Os04g54490.1 downstream_gene_variant ; 2500.0bp to feature; MODIFIER silent_mutation Average:51.028; most accessible tissue: Zhenshan97 young leaf, score: 66.83 N N N N
vg0432418113 C -> T LOC_Os04g54490-LOC_Os04g54500 intergenic_region ; MODIFIER silent_mutation Average:51.028; most accessible tissue: Zhenshan97 young leaf, score: 66.83 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0432418113 5.84E-07 6.62E-12 mr1741_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
vg0432418113 NA 1.71E-09 mr1785_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
vg0432418113 2.09E-06 NA mr1800_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