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Detailed information for vg0207991663:

Variant ID: vg0207991663 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 7991663
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 31. )

Flanking Sequence (100 bp) in Reference Genome:


CATCGTCATTGATACAATGACGAAAGTTCTCCTGCCATTGATGAATGACGAGACAAATTCGTCATAACAAATTGAACCCACGCGTATGATGACATGTGAT[G/A]
TTGCAGATGACAAGGCAGGTGATGTGGCAAATGACGTGCCAATTCACATTCGGCCCATATAGCATGGGCTTTTTTATTTTCAATTACAATCAGCCCAATT

Reverse complement sequence

AATTGGGCTGATTGTAATTGAAAATAAAAAAGCCCATGCTATATGGGCCGAATGTGAATTGGCACGTCATTTGCCACATCACCTGCCTTGTCATCTGCAA[C/T]
ATCACATGTCATCATACGCGTGGGTTCAATTTGTTATGACGAATTTGTCTCGTCATTCATCAATGGCAGGAGAACTTTCGTCATTGTATCAATGACGATG

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 93.10% 3.70% 3.26% 0.00% NA
All Indica  2759 88.60% 6.00% 5.44% 0.00% NA
All Japonica  1512 99.50% 0.30% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 69.40% 14.60% 15.97% 0.00% NA
Indica II  465 94.60% 2.40% 3.01% 0.00% NA
Indica III  913 99.00% 0.90% 0.11% 0.00% NA
Indica Intermediate  786 87.40% 7.50% 5.09% 0.00% NA
Temperate Japonica  767 99.20% 0.70% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 4.40% 2.22% 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
vg0207991663 G -> A LOC_Os02g14490.1 downstream_gene_variant ; 3033.0bp to feature; MODIFIER silent_mutation Average:55.747; most accessible tissue: Callus, score: 91.114 N N N N
vg0207991663 G -> A LOC_Os02g14500.1 downstream_gene_variant ; 218.0bp to feature; MODIFIER silent_mutation Average:55.747; most accessible tissue: Callus, score: 91.114 N N N N
vg0207991663 G -> A LOC_Os02g14490-LOC_Os02g14500 intergenic_region ; MODIFIER silent_mutation Average:55.747; most accessible tissue: Callus, score: 91.114 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0207991663 3.94E-08 NA mr1570 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
vg0207991663 4.36E-08 3.16E-07 mr1570 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
vg0207991663 8.72E-06 6.97E-06 mr1570_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