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Detailed information for vg0707836859:

Variant ID: vg0707836859 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 7836859
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


CCTCCTTTTCAATACTTAGGTAGGGGCAGGTAATTGGGAGGGAATTCCTCCTGTACTTTGTCTAAGAAAATCTCAGCCATCCGTTTTTATTAATGATCTA[A/G]
TCTCCAACTAAACTCCCTATCAATTTCCATCACCTCTACCAAACAAGATATTGGGATTAAAAATCAAATTACCATCTTAATCTCATAATCAATTCCCTCG

Reverse complement sequence

CGAGGGAATTGATTATGAGATTAAGATGGTAATTTGATTTTTAATCCCAATATCTTGTTTGGTAGAGGTGATGGAAATTGATAGGGAGTTTAGTTGGAGA[T/C]
TAGATCATTAATAAAAACGGATGGCTGAGATTTTCTTAGACAAAGTACAGGAGGAATTCCCTCCCAATTACCTGCCCCTACCTAAGTATTGAAAAGGAGG

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 91.80% 6.10% 2.16% 0.00% NA
All Indica  2759 86.10% 10.20% 3.66% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 56.50% 30.80% 12.77% 0.00% NA
Indica II  465 94.40% 4.70% 0.86% 0.00% NA
Indica III  913 98.70% 1.20% 0.11% 0.00% NA
Indica Intermediate  786 89.10% 8.40% 2.54% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 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 93.30% 5.60% 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
vg0707836859 A -> G LOC_Os07g13660.1 upstream_gene_variant ; 1905.0bp to feature; MODIFIER silent_mutation Average:48.556; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N
vg0707836859 A -> G LOC_Os07g13634.1 downstream_gene_variant ; 4548.0bp to feature; MODIFIER silent_mutation Average:48.556; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N
vg0707836859 A -> G LOC_Os07g13634-LOC_Os07g13660 intergenic_region ; MODIFIER silent_mutation Average:48.556; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0707836859 NA 4.55E-11 Heading_date Ind_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
vg0707836859 NA 1.81E-06 mr1547 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
vg0707836859 4.68E-06 NA mr1371_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
vg0707836859 3.48E-06 NA mr1371_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
vg0707836859 NA 1.18E-10 mr1709_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