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Detailed information for vg0706085714:

Variant ID: vg0706085714 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 6085714
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CATCCGCTAAACATAGATTAATATATCTCATTAGATTCGTCTCGGAAAATAGCCTAAGGGTTATGAAATTGGTTTTATCAGTAATCTACGTTTAATACTT[C/T]
TAAATAGCAAGATTCCGGATGGCTATTTAATAGCCCAGAGGATCCAAATAAGGCCATAGTAATGTCACTCAGGGTATATAAGGGATAATACAATCAACTA

Reverse complement sequence

TAGTTGATTGTATTATCCCTTATATACCCTGAGTGACATTACTATGGCCTTATTTGGATCCTCTGGGCTATTAAATAGCCATCCGGAATCTTGCTATTTA[G/A]
AAGTATTAAACGTAGATTACTGATAAAACCAATTTCATAACCCTTAGGCTATTTTCCGAGACGAATCTAATGAGATATATTAATCTATGTTTAGCGGATG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.90% 1.00% 0.11% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 96.60% 3.00% 0.33% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 93.40% 6.00% 0.65% 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
vg0706085714 C -> T LOC_Os07g11040.1 upstream_gene_variant ; 3585.0bp to feature; MODIFIER silent_mutation Average:37.531; most accessible tissue: Zhenshan97 panicle, score: 54.901 N N N N
vg0706085714 C -> T LOC_Os07g11050.1 upstream_gene_variant ; 4278.0bp to feature; MODIFIER silent_mutation Average:37.531; most accessible tissue: Zhenshan97 panicle, score: 54.901 N N N N
vg0706085714 C -> T LOC_Os07g11040-LOC_Os07g11050 intergenic_region ; MODIFIER silent_mutation Average:37.531; most accessible tissue: Zhenshan97 panicle, score: 54.901 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0706085714 NA 3.36E-06 Yield 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
vg0706085714 NA 1.64E-07 mr1712 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
vg0706085714 NA 1.79E-06 mr1946 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
vg0706085714 NA 2.95E-06 mr1161_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