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Detailed information for vg1107793749:

Variant ID: vg1107793749 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 7793749
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


ATGAACAGAAATTTATGTTCTTACAGTTTGCAGTATATACTTGTATAATTTCCTCCTTCATATAAAGAAAAAGAAACAATATCTGAGATCTGTATCTGTA[T/A]
ATATCTGCAGGATTTTATTGAGGAGAAATTAGACTCACAGGAGAAAGTTAACTGGATCCAATATCACCTCAACAGGGGCTTCACAGGTTCTGTACTCTTG

Reverse complement sequence

CAAGAGTACAGAACCTGTGAAGCCCCTGTTGAGGTGATATTGGATCCAGTTAACTTTCTCCTGTGAGTCTAATTTCTCCTCAATAAAATCCTGCAGATAT[A/T]
TACAGATACAGATCTCAGATATTGTTTCTTTTTCTTTATATGAAGGAGGAAATTATACAAGTATATACTGCAAACTGTAAGAACATAAATTTCTGTTCAT

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 96.70% 1.50% 1.76% 0.00% NA
All Indica  2759 94.40% 2.60% 2.97% 0.00% NA
All Japonica  1512 99.90% 0.00% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 78.80% 9.90% 11.26% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 96.80% 1.40% 1.78% 0.00% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 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  90 100.00% 0.00% 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
vg1107793749 T -> A LOC_Os11g14030.1 upstream_gene_variant ; 3624.0bp to feature; MODIFIER silent_mutation Average:50.095; most accessible tissue: Callus, score: 75.603 N N N N
vg1107793749 T -> A LOC_Os11g14050.1 upstream_gene_variant ; 2798.0bp to feature; MODIFIER silent_mutation Average:50.095; most accessible tissue: Callus, score: 75.603 N N N N
vg1107793749 T -> A LOC_Os11g14050.2 upstream_gene_variant ; 2798.0bp to feature; MODIFIER silent_mutation Average:50.095; most accessible tissue: Callus, score: 75.603 N N N N
vg1107793749 T -> A LOC_Os11g14040.1 intron_variant ; MODIFIER silent_mutation Average:50.095; most accessible tissue: Callus, score: 75.603 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1107793749 4.17E-06 4.06E-17 mr1038 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
vg1107793749 NA 3.61E-18 mr1389 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
vg1107793749 7.76E-09 6.91E-23 mr1038_2 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
vg1107793749 3.32E-09 1.29E-23 mr1389_2 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
vg1107793749 NA 1.20E-08 mr1627_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