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Detailed information for vg0116741094:

Variant ID: vg0116741094 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 16741094
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


TAAGCCAACCAGAGGGGGGGGTGAATGGTTGATATACCCAAAAACCAAAACTTTTAGCGGAAATAAAAGTTACCCTCAAATTCGATGGATCGCGGTCTGA[C/T]
TGAAGGTGTTGCGCTGGTCGAACCGCCTGATGAATGTCGGTCTGACCGAGATCGAACTCCGGTCGAACCGCCGAGATGCCTGCTGCCGACTCCTATCGCC

Reverse complement sequence

GGCGATAGGAGTCGGCAGCAGGCATCTCGGCGGTTCGACCGGAGTTCGATCTCGGTCAGACCGACATTCATCAGGCGGTTCGACCAGCGCAACACCTTCA[G/A]
TCAGACCGCGATCCATCGAATTTGAGGGTAACTTTTATTTCCGCTAAAAGTTTTGGTTTTTGGGTATATCAACCATTCACCCCCCCCTCTGGTTGGCTTA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.80% 2.70% 2.50% 0.00% NA
All Indica  2759 91.20% 4.50% 4.28% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 76.80% 10.60% 12.61% 0.00% NA
Indica II  465 95.10% 2.60% 2.37% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 89.80% 6.10% 4.07% 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 98.90% 1.10% 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
vg0116741094 C -> T LOC_Os01g29880.1 upstream_gene_variant ; 180.0bp to feature; MODIFIER silent_mutation Average:41.213; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N
vg0116741094 C -> T LOC_Os01g29890.1 downstream_gene_variant ; 2087.0bp to feature; MODIFIER silent_mutation Average:41.213; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N
vg0116741094 C -> T LOC_Os01g29880-LOC_Os01g29890 intergenic_region ; MODIFIER silent_mutation Average:41.213; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0116741094 NA 7.17E-06 mr1038 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
vg0116741094 NA 5.96E-06 mr1038 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
vg0116741094 NA 6.08E-08 mr1389 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
vg0116741094 NA 3.32E-07 mr1389 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
vg0116741094 5.57E-06 8.58E-06 mr1725 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
vg0116741094 NA 1.91E-06 mr1038_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
vg0116741094 NA 1.30E-06 mr1389_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
vg0116741094 NA 4.15E-06 mr1389_2 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
vg0116741094 NA 5.98E-06 mr1968_2 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