Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0809143046:

Variant ID: vg0809143046 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 9143046
Reference Allele: AAlternative Allele: C,T
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACTAATTTGAGCGGGTGGATTTATGACCATCTCAAGGCAGAGAAAAAGAATAGGTGAGTAAAATCTAGCAGCAAGTGATTTCTCCAACTCTTTGATCAAA[A/C,T]
TAATAGCTTATCCTACAATATTGCTATAGATAGTGAGAAGAAACAGTTAGACAATGATAACCATGATGATATTCATGTTTATGAAGACTTGGGCCACGTA

Reverse complement sequence

TACGTGGCCCAAGTCTTCATAAACATGAATATCATCATGGTTATCATTGTCTAACTGTTTCTTCTCACTATCTATAGCAATATTGTAGGATAAGCTATTA[T/G,A]
TTTGATCAAAGAGTTGGAGAAATCACTTGCTGCTAGATTTTACTCACCTATTCTTTTTCTCTGCCTTGAGATGGTCATAAATCCACCCGCTCAAATTAGT

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 82.70% 11.50% 5.71% 0.06% T: 0.06%
All Indica  2759 90.80% 1.00% 8.05% 0.07% T: 0.11%
All Japonica  1512 64.60% 33.00% 2.45% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 87.20% 1.80% 10.92% 0.00% NA
Indica II  465 91.00% 1.10% 7.74% 0.00% T: 0.22%
Indica III  913 93.20% 0.30% 6.02% 0.22% T: 0.22%
Indica Intermediate  786 90.60% 1.00% 8.40% 0.00% NA
Temperate Japonica  767 42.20% 56.70% 1.04% 0.00% NA
Tropical Japonica  504 95.20% 1.40% 3.37% 0.00% NA
Japonica Intermediate  241 71.40% 23.70% 4.98% 0.00% NA
VI/Aromatic  96 88.50% 2.10% 8.33% 1.04% NA
Intermediate  90 81.10% 15.60% 3.33% 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
vg0809143046 A -> C LOC_Os08g15090-LOC_Os08g15100 intergenic_region ; MODIFIER silent_mutation Average:31.747; most accessible tissue: Callus, score: 60.666 N N N N
vg0809143046 A -> T LOC_Os08g15090-LOC_Os08g15100 intergenic_region ; MODIFIER silent_mutation Average:31.747; most accessible tissue: Callus, score: 60.666 N N N N
vg0809143046 A -> DEL N N silent_mutation Average:31.747; most accessible tissue: Callus, score: 60.666 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0809143046 NA 1.89E-13 Heading_date All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0809143046 NA 2.49E-11 Heading_date Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0809143046 NA 4.34E-15 Spikelet_length All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0809143046 NA 3.96E-07 mr1606 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
vg0809143046 NA 4.69E-06 mr1043_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
vg0809143046 NA 8.21E-06 mr1588_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
vg0809143046 NA 3.67E-06 mr1693_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
vg0809143046 NA 8.45E-06 mr1912_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
vg0809143046 1.81E-08 1.81E-08 mr1919_2 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
vg0809143046 NA 3.25E-07 mr1919_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