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Detailed information for vg0140047043:

Variant ID: vg0140047043 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 40047043
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


CTCACCCAGAGTCCCCGGCCGAACCGGCAAAGGGGGGCCAGCGCGGTCTCCCGGTGAGGAGCCCCACGCTCCGTCACGGTGTCAGTATCATGAGCCTCTC[G/A]
CCGTTGAGCTCTTGAGATTCGGCGCGGCGGAGGAAATGTCGAGGTGAACCCAACTATCATATCATTCGCAGTTGAGGCATTCAATTGCCGTCGAGGTAGC

Reverse complement sequence

GCTACCTCGACGGCAATTGAATGCCTCAACTGCGAATGATATGATAGTTGGGTTCACCTCGACATTTCCTCCGCCGCGCCGAATCTCAAGAGCTCAACGG[C/T]
GAGAGGCTCATGATACTGACACCGTGACGGAGCGTGGGGCTCCTCACCGGGAGACCGCGCTGGCCCCCCTTTGCCGGTTCGGCCGGGGACTCTGGGTGAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.90% 4.80% 0.30% 0.00% NA
All Indica  2759 99.70% 0.20% 0.07% 0.00% NA
All Japonica  1512 84.90% 14.40% 0.73% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.40% 0.13% 0.00% NA
Temperate Japonica  767 78.00% 20.60% 1.43% 0.00% NA
Tropical Japonica  504 98.60% 1.40% 0.00% 0.00% NA
Japonica Intermediate  241 78.00% 22.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 3.30% 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
vg0140047043 G -> A LOC_Os01g68920.1 downstream_gene_variant ; 2791.0bp to feature; MODIFIER silent_mutation Average:47.911; most accessible tissue: Callus, score: 82.025 N N N N
vg0140047043 G -> A LOC_Os01g68920-LOC_Os01g68930 intergenic_region ; MODIFIER silent_mutation Average:47.911; most accessible tissue: Callus, score: 82.025 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0140047043 NA 5.21E-06 mr1154 Jap_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
vg0140047043 5.27E-06 4.25E-08 mr1092_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
vg0140047043 NA 1.84E-06 mr1154_2 Jap_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