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Detailed information for vg0116735143:

Variant ID: vg0116735143 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 16735143
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGGTGTTTGGAAAAATAAAAACAAAAGTGGTAAAAAGCACACTTCGTACAAACGTACACATTGTGCTCAAAAATCCAAAAGAAAACTTCTCCCCCTTTTT[A/T]
AAAGAAAGAAATTCCCAAAAACATGCTTTTCTCAAAAACTCTCAAAAATCCAAAAGAAAACTTCTTCCCCTTTTTAAAAGAAAGAAATTCCCAATTGAAC

Reverse complement sequence

GTTCAATTGGGAATTTCTTTCTTTTAAAAAGGGGAAGAAGTTTTCTTTTGGATTTTTGAGAGTTTTTGAGAAAAGCATGTTTTTGGGAATTTCTTTCTTT[T/A]
AAAAAGGGGGAGAAGTTTTCTTTTGGATTTTTGAGCACAATGTGTACGTTTGTACGAAGTGTGCTTTTTACCACTTTTGTTTTTATTTTTCCAAACACCA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.10% 0.70% 0.21% 0.00% NA
All Indica  2759 98.80% 0.90% 0.25% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 96.70% 2.20% 1.12% 0.00% NA
Indica I  595 96.80% 2.50% 0.67% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 98.70% 1.00% 0.25% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0116735143 A -> T LOC_Os01g29860.1 upstream_gene_variant ; 4234.0bp to feature; MODIFIER silent_mutation Average:20.671; most accessible tissue: Zhenshan97 panicle, score: 32.308 N N N N
vg0116735143 A -> T LOC_Os01g29870.1 downstream_gene_variant ; 1424.0bp to feature; MODIFIER silent_mutation Average:20.671; most accessible tissue: Zhenshan97 panicle, score: 32.308 N N N N
vg0116735143 A -> T LOC_Os01g29880.1 downstream_gene_variant ; 3918.0bp to feature; MODIFIER silent_mutation Average:20.671; most accessible tissue: Zhenshan97 panicle, score: 32.308 N N N N
vg0116735143 A -> T LOC_Os01g29870-LOC_Os01g29880 intergenic_region ; MODIFIER silent_mutation Average:20.671; most accessible tissue: Zhenshan97 panicle, score: 32.308 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0116735143 NA 1.33E-06 mr1042 Ind_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
vg0116735143 NA 8.24E-07 mr1043 Ind_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
vg0116735143 NA 5.82E-08 mr1739 Ind_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