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Detailed information for vg0505358756:

Variant ID: vg0505358756 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 5358756
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


TACGCTTGTTTGTTTGTAGAGGGGAGCTTCCAGATGTGATTTTTACTGCCAAATAGATCTAACGATCTAAAATAATGGGTCCACCAATTTAAATGAAAAT[C/T]
AATGGTCGGATTTATTTTTTTTTATTAGAATGCCACTTGGCGACTCGATAGCGTTTATAGGAAGTTTAATGGACTTTTAGTATATAATAGATTATAGCTC

Reverse complement sequence

GAGCTATAATCTATTATATACTAAAAGTCCATTAAACTTCCTATAAACGCTATCGAGTCGCCAAGTGGCATTCTAATAAAAAAAAATAAATCCGACCATT[G/A]
ATTTTCATTTAAATTGGTGGACCCATTATTTTAGATCGTTAGATCTATTTGGCAGTAAAAATCACATCTGGAAGCTCCCCTCTACAAACAAACAAGCGTA

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 66.90% 31.00% 0.42% 1.71% NA
All Indica  2759 53.90% 45.90% 0.22% 0.04% NA
All Japonica  1512 88.70% 5.30% 0.73% 5.29% NA
Aus  269 76.20% 22.70% 1.12% 0.00% NA
Indica I  595 17.80% 81.50% 0.67% 0.00% NA
Indica II  465 85.20% 14.80% 0.00% 0.00% NA
Indica III  913 59.80% 40.00% 0.11% 0.11% NA
Indica Intermediate  786 55.70% 44.10% 0.13% 0.00% NA
Temperate Japonica  767 97.10% 1.80% 0.78% 0.26% NA
Tropical Japonica  504 73.20% 11.90% 0.79% 14.09% NA
Japonica Intermediate  241 94.20% 2.50% 0.41% 2.90% NA
VI/Aromatic  96 60.40% 39.60% 0.00% 0.00% NA
Intermediate  90 80.00% 20.00% 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
vg0505358756 C -> T LOC_Os05g09510-LOC_Os05g09520 intergenic_region ; MODIFIER silent_mutation Average:22.13; most accessible tissue: Callus, score: 36.907 N N N N
vg0505358756 C -> DEL N N silent_mutation Average:22.13; most accessible tissue: Callus, score: 36.907 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0505358756 7.73E-08 NA Grain_length All YES 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
vg0505358756 1.23E-06 4.42E-26 Grain_length 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
vg0505358756 3.93E-06 NA Grain_thickness 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
vg0505358756 2.45E-09 4.31E-17 Grain_thickness 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
vg0505358756 2.99E-13 NA Grain_width 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
vg0505358756 8.92E-22 6.57E-46 Grain_width 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
vg0505358756 NA 3.95E-08 mr1183 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
vg0505358756 NA 4.03E-08 mr1503 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
vg0505358756 NA 1.73E-07 mr1183_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
vg0505358756 NA 5.18E-06 mr1319_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
vg0505358756 NA 1.20E-07 mr1330_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