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Detailed information for vg1117177660:

Variant ID: vg1117177660 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 17177660
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, A: 0.02, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


CCAGTTCGGTCGCCAACTTCGTTCAATGCCATTGCCAGGATCTATATATCAAACCGAATTAAACTCAAAACACAAGTTTTAATTATTAGTACTATGATCT[T/A]
AACATGGCAAGTAAGCTATCATGTTTAACTATCTTAACTAATTACACCGGCATCCGTGTATACATGTGACGTCCAACATAACCATCTGTGATGTACTAGC

Reverse complement sequence

GCTAGTACATCACAGATGGTTATGTTGGACGTCACATGTATACACGGATGCCGGTGTAATTAGTTAAGATAGTTAAACATGATAGCTTACTTGCCATGTT[A/T]
AGATCATAGTACTAATAATTAAAACTTGTGTTTTGAGTTTAATTCGGTTTGATATATAGATCCTGGCAATGGCATTGAACGAAGTTGGCGACCGAACTGG

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 80.60% 19.40% 0.06% 0.00% NA
All Indica  2759 74.20% 25.70% 0.11% 0.00% NA
All Japonica  1512 99.10% 0.90% 0.00% 0.00% NA
Aus  269 34.90% 65.10% 0.00% 0.00% NA
Indica I  595 98.30% 1.50% 0.17% 0.00% NA
Indica II  465 46.00% 54.00% 0.00% 0.00% NA
Indica III  913 76.30% 23.70% 0.00% 0.00% NA
Indica Intermediate  786 70.20% 29.50% 0.25% 0.00% NA
Temperate Japonica  767 99.20% 0.80% 0.00% 0.00% NA
Tropical Japonica  504 98.60% 1.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 83.30% 16.70% 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
vg1117177660 T -> A LOC_Os11g29610.1 downstream_gene_variant ; 2470.0bp to feature; MODIFIER silent_mutation Average:76.839; most accessible tissue: Callus, score: 89.426 N N N N
vg1117177660 T -> A LOC_Os11g29620.1 downstream_gene_variant ; 1690.0bp to feature; MODIFIER silent_mutation Average:76.839; most accessible tissue: Callus, score: 89.426 N N N N
vg1117177660 T -> A LOC_Os11g29630.1 downstream_gene_variant ; 2869.0bp to feature; MODIFIER silent_mutation Average:76.839; most accessible tissue: Callus, score: 89.426 N N N N
vg1117177660 T -> A LOC_Os11g29610-LOC_Os11g29620 intergenic_region ; MODIFIER silent_mutation Average:76.839; most accessible tissue: Callus, score: 89.426 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1117177660 NA 8.18E-06 mr1188 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
vg1117177660 NA 9.88E-12 mr1232 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
vg1117177660 2.45E-06 2.45E-06 mr1396 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
vg1117177660 NA 1.64E-07 mr1347_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
vg1117177660 NA 5.66E-06 mr1609_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