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Detailed information for vg1105850139:

Variant ID: vg1105850139 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 5850139
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.66, A: 0.33, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:


TGTGAGTCTAAATGCTCTTGTATTTTTTTGGCTGTGTATATTATTTGTGGATATAGAGGCCGGATTAATGAAAATCCATTATTTAAAAAAATGTGTTGCT[A/G]
GGACCAGGCTTTTCGTGACGAATTTCAGTAATCATCAGGTAATACAATCCTTATGCCCAGTGAGTGTTTAAACACAACTCTTGCTCTGGCAGTCCCAAAT

Reverse complement sequence

ATTTGGGACTGCCAGAGCAAGAGTTGTGTTTAAACACTCACTGGGCATAAGGATTGTATTACCTGATGATTACTGAAATTCGTCACGAAAAGCCTGGTCC[T/C]
AGCAACACATTTTTTTAAATAATGGATTTTCATTAATCCGGCCTCTATATCCACAAATAATATACACAGCCAAAAAAATACAAGAGCATTTAGACTCACA

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 45.90% 9.70% 1.78% 42.68% NA
All Indica  2759 18.50% 10.60% 2.72% 68.18% NA
All Japonica  1512 92.20% 2.40% 0.33% 5.09% NA
Aus  269 48.00% 42.80% 0.74% 8.55% NA
Indica I  595 7.40% 9.10% 1.18% 82.35% NA
Indica II  465 8.80% 5.20% 3.44% 82.58% NA
Indica III  913 26.60% 11.00% 3.29% 59.15% NA
Indica Intermediate  786 23.30% 14.50% 2.80% 59.41% NA
Temperate Japonica  767 91.40% 1.60% 0.65% 6.39% NA
Tropical Japonica  504 97.40% 1.00% 0.00% 1.59% NA
Japonica Intermediate  241 83.80% 7.90% 0.00% 8.30% NA
VI/Aromatic  96 91.70% 5.20% 0.00% 3.12% NA
Intermediate  90 50.00% 11.10% 2.22% 36.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1105850139 A -> DEL N N silent_mutation Average:12.878; most accessible tissue: Callus, score: 49.436 N N N N
vg1105850139 A -> G LOC_Os11g10670.1 downstream_gene_variant ; 1914.0bp to feature; MODIFIER silent_mutation Average:12.878; most accessible tissue: Callus, score: 49.436 N N N N
vg1105850139 A -> G LOC_Os11g10650-LOC_Os11g10670 intergenic_region ; MODIFIER silent_mutation Average:12.878; most accessible tissue: Callus, score: 49.436 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1105850139 NA 3.81E-06 mr1229 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
vg1105850139 NA 2.12E-06 mr1286 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
vg1105850139 NA 2.02E-06 mr1419 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
vg1105850139 1.56E-06 1.56E-06 mr1419 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
vg1105850139 NA 4.58E-07 mr1569 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
vg1105850139 5.60E-06 5.60E-06 mr1774 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
vg1105850139 NA 5.83E-07 mr1863 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
vg1105850139 9.52E-06 9.52E-06 mr1863 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