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Detailed information for vg1102381224:

Variant ID: vg1102381224 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 2381224
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


CCCTTTTTGTAATATACGAAAAGAGACTTGCAGAACGAACATAACAGGCAAGACATAATAATTCTGTTTTGCTAACCTTTGGGTTATGGCAAAAAGGTGT[A/G]
ATCACCTGAAACCAATGCGTCAGGATTCATGTAAATTCAAAAAAAAAAGAAACTTAGCAAAAAAAAAACTTTATTCTGAACAACCAAAATTCAGCAGCAA

Reverse complement sequence

TTGCTGCTGAATTTTGGTTGTTCAGAATAAAGTTTTTTTTTTGCTAAGTTTCTTTTTTTTTTGAATTTACATGAATCCTGACGCATTGGTTTCAGGTGAT[T/C]
ACACCTTTTTGCCATAACCCAAAGGTTAGCAAAACAGAATTATTATGTCTTGCCTGTTATGTTCGTTCTGCAAGTCTCTTTTCGTATATTACAAAAAGGG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.90% 3.90% 1.25% 0.00% NA
All Indica  2759 99.70% 0.20% 0.14% 0.00% NA
All Japonica  1512 86.10% 11.00% 2.84% 0.00% NA
Aus  269 98.10% 0.00% 1.86% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.30% 0.51% 0.00% NA
Temperate Japonica  767 96.30% 0.90% 2.74% 0.00% NA
Tropical Japonica  504 72.00% 24.80% 3.17% 0.00% NA
Japonica Intermediate  241 83.00% 14.50% 2.49% 0.00% NA
VI/Aromatic  96 93.80% 0.00% 6.25% 0.00% NA
Intermediate  90 86.70% 12.20% 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
vg1102381224 A -> G LOC_Os11g05350.1 upstream_gene_variant ; 4742.0bp to feature; MODIFIER silent_mutation Average:64.839; most accessible tissue: Callus, score: 85.303 N N N N
vg1102381224 A -> G LOC_Os11g05360.1 downstream_gene_variant ; 811.0bp to feature; MODIFIER silent_mutation Average:64.839; most accessible tissue: Callus, score: 85.303 N N N N
vg1102381224 A -> G LOC_Os11g05370.1 downstream_gene_variant ; 960.0bp to feature; MODIFIER silent_mutation Average:64.839; most accessible tissue: Callus, score: 85.303 N N N N
vg1102381224 A -> G LOC_Os11g05360-LOC_Os11g05370 intergenic_region ; MODIFIER silent_mutation Average:64.839; most accessible tissue: Callus, score: 85.303 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1102381224 4.48E-07 4.47E-07 mr1228 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
vg1102381224 NA 3.39E-10 mr1980 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
vg1102381224 NA 7.12E-06 mr1224_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
vg1102381224 NA 3.60E-08 mr1246_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
vg1102381224 NA 8.89E-06 mr1620_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