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Detailed information for vg1105076187:

Variant ID: vg1105076187 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 5076187
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTTGGACCATAAGATCAACATGTTGGACCGTAGGATCAACACCAAACATATTATGTAACCAACGTAGCACATCATACATAATCAATTGTTCTGGTGAATT[A/C]
AAACTAATAGCGACATATGCATAGACGGTTAAAACTGCCCCATTGTCACAATACTACACAAGAGCATCATCGTAATAAACCCTGATTAACACATCACCGG

Reverse complement sequence

CCGGTGATGTGTTAATCAGGGTTTATTACGATGATGCTCTTGTGTAGTATTGTGACAATGGGGCAGTTTTAACCGTCTATGCATATGTCGCTATTAGTTT[T/G]
AATTCACCAGAACAATTGATTATGTATGATGTGCTACGTTGGTTACATAATATGTTTGGTGTTGATCCTACGGTCCAACATGTTGATCTTATGGTCCAAC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 74.50% 25.40% 0.08% 0.02% NA
All Indica  2759 89.20% 10.70% 0.11% 0.00% NA
All Japonica  1512 62.40% 37.50% 0.00% 0.07% NA
Aus  269 21.60% 78.40% 0.00% 0.00% NA
Indica I  595 68.90% 31.10% 0.00% 0.00% NA
Indica II  465 98.70% 1.10% 0.22% 0.00% NA
Indica III  913 97.50% 2.50% 0.00% 0.00% NA
Indica Intermediate  786 89.30% 10.40% 0.25% 0.00% NA
Temperate Japonica  767 56.60% 43.40% 0.00% 0.00% NA
Tropical Japonica  504 82.70% 17.30% 0.00% 0.00% NA
Japonica Intermediate  241 38.60% 61.00% 0.00% 0.41% NA
VI/Aromatic  96 3.10% 96.90% 0.00% 0.00% NA
Intermediate  90 62.20% 36.70% 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
vg1105076187 A -> DEL N N silent_mutation Average:43.635; most accessible tissue: Callus, score: 72.31 N N N N
vg1105076187 A -> C LOC_Os11g09460.1 upstream_gene_variant ; 1376.0bp to feature; MODIFIER silent_mutation Average:43.635; most accessible tissue: Callus, score: 72.31 N N N N
vg1105076187 A -> C LOC_Os11g09470.1 downstream_gene_variant ; 150.0bp to feature; MODIFIER silent_mutation Average:43.635; most accessible tissue: Callus, score: 72.31 N N N N
vg1105076187 A -> C LOC_Os11g09474.1 downstream_gene_variant ; 4075.0bp to feature; MODIFIER silent_mutation Average:43.635; most accessible tissue: Callus, score: 72.31 N N N N
vg1105076187 A -> C LOC_Os11g09460-LOC_Os11g09470 intergenic_region ; MODIFIER silent_mutation Average:43.635; most accessible tissue: Callus, score: 72.31 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1105076187 NA 8.37E-06 mr1347 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
vg1105076187 4.03E-06 6.64E-06 mr1457 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
vg1105076187 NA 9.54E-08 mr1347_2 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