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Detailed information for vg0919491195:

Variant ID: vg0919491195 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 19491195
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


GCACGTATACGGATGTTCCATGTACACGTTAAGGAAATTCATCACGGAGTCCACAGATGGAAGGAGTACTACTCGGACAGAACTGGATCGTTACTGTATC[G/A]
TATGGGGTCCGACATCTCCAAGTTCTACTTGGAGACCAATTGACCTGCGGTATAAAAGGGACCCCTGGGAGGACCTAAGGCATGGAATCTTACCGCCAAC

Reverse complement sequence

GTTGGCGGTAAGATTCCATGCCTTAGGTCCTCCCAGGGGTCCCTTTTATACCGCAGGTCAATTGGTCTCCAAGTAGAACTTGGAGATGTCGGACCCCATA[C/T]
GATACAGTAACGATCCAGTTCTGTCCGAGTAGTACTCCTTCCATCTGTGGACTCCGTGATGAATTTCCTTAACGTGTACATGGAACATCCGTATACGTGC

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 87.20% 12.70% 0.11% 0.00% NA
All Indica  2759 78.30% 21.50% 0.18% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 68.70% 30.90% 0.34% 0.00% NA
Indica II  465 83.40% 16.30% 0.22% 0.00% NA
Indica III  913 84.30% 15.70% 0.00% 0.00% NA
Indica Intermediate  786 75.60% 24.20% 0.25% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 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 94.40% 5.60% 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
vg0919491195 G -> A LOC_Os09g32670.1 upstream_gene_variant ; 3098.0bp to feature; MODIFIER silent_mutation Average:59.679; most accessible tissue: Minghui63 panicle, score: 76.913 N N N N
vg0919491195 G -> A LOC_Os09g32670-LOC_Os09g32680 intergenic_region ; MODIFIER silent_mutation Average:59.679; most accessible tissue: Minghui63 panicle, score: 76.913 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0919491195 NA 1.54E-08 mr1707 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
vg0919491195 NA 4.89E-09 mr1728 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
vg0919491195 NA 7.96E-06 mr1027_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
vg0919491195 NA 1.25E-07 mr1348_2 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
vg0919491195 NA 5.66E-06 mr1348_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