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Detailed information for vg0109280202:

Variant ID: vg0109280202 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 9280202
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


TCGGTCCTGACAAATCAAGCTTGAGCTTATCTACCGACTCCTTCCGCGTCGTTCAACATGTATTGCATTTTTGATGCTCCTTCTCTCGCTGGTACTCTAC[T/A]
TGTGTTTCAGACTCAGTTATCTTTTGGCCATCATATGTTGGATCGACATTGTCGATCCATAAAGTGAATGCGCACCTCCTTGGATTGCCATAAGAAACAA

Reverse complement sequence

TTGTTTCTTATGGCAATCCAAGGAGGTGCGCATTCACTTTATGGATCGACAATGTCGATCCAACATATGATGGCCAAAAGATAACTGAGTCTGAAACACA[A/T]
GTAGAGTACCAGCGAGAGAAGGAGCATCAAAAATGCAATACATGTTGAACGACGCGGAAGGAGTCGGTAGATAAGCTCAAGCTTGATTTGTCAGGACCGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.30% 4.70% 0.02% 0.00% NA
All Indica  2759 93.70% 6.30% 0.04% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 84.40% 15.60% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 86.70% 13.10% 0.22% 0.00% NA
Indica III  913 92.60% 7.40% 0.00% 0.00% NA
Indica Intermediate  786 94.40% 5.60% 0.00% 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 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0109280202 T -> A LOC_Os01g16354.1 upstream_gene_variant ; 1170.0bp to feature; MODIFIER silent_mutation Average:36.799; most accessible tissue: Callus, score: 59.124 N N N N
vg0109280202 T -> A LOC_Os01g16354-LOC_Os01g16360 intergenic_region ; MODIFIER silent_mutation Average:36.799; most accessible tissue: Callus, score: 59.124 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0109280202 NA 3.82E-07 mr1310_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
vg0109280202 NA 1.23E-08 mr1769_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
vg0109280202 4.41E-06 2.44E-07 mr1790_2 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
vg0109280202 NA 2.82E-07 mr1951_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