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Detailed information for vg0139660797:

Variant ID: vg0139660797 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 39660797
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


TATGAATAGTTGAAATGTATCATGTTCCTTTCTAGGAAACGAGAACCATGTGTTACCTATTTGCACTTCTTTCTTTACTGTCTTCAACTCTTCATTAGCA[G/C]
CGGCTATGACTGTAGACTTAGTGTCTTAATTAAGTATATACCTGAAATTATATGCATTTGAGAGAGTTCAGTACTTGAGTTGGTTAAGTTCTACTCTTGT

Reverse complement sequence

ACAAGAGTAGAACTTAACCAACTCAAGTACTGAACTCTCTCAAATGCATATAATTTCAGGTATATACTTAATTAAGACACTAAGTCTACAGTCATAGCCG[C/G]
TGCTAATGAAGAGTTGAAGACAGTAAAGAAAGAAGTGCAAATAGGTAACACATGGTTCTCGTTTCCTAGAAAGGAACATGATACATTTCAACTATTCATA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.90% 0.40% 0.74% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 96.60% 1.10% 2.31% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 93.40% 2.10% 4.56% 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
vg0139660797 G -> C LOC_Os01g68230.1 upstream_gene_variant ; 3153.0bp to feature; MODIFIER silent_mutation Average:54.012; most accessible tissue: Callus, score: 91.645 N N N N
vg0139660797 G -> C LOC_Os01g68230.2 upstream_gene_variant ; 2811.0bp to feature; MODIFIER silent_mutation Average:54.012; most accessible tissue: Callus, score: 91.645 N N N N
vg0139660797 G -> C LOC_Os01g68240.1 downstream_gene_variant ; 164.0bp to feature; MODIFIER silent_mutation Average:54.012; most accessible tissue: Callus, score: 91.645 N N N N
vg0139660797 G -> C LOC_Os01g68240-LOC_Os01g68260 intergenic_region ; MODIFIER silent_mutation Average:54.012; most accessible tissue: Callus, score: 91.645 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0139660797 3.07E-06 8.86E-06 mr1672_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