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Detailed information for vg0505359598:

Variant ID: vg0505359598 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 5359598
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.79, A: 0.21, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:


GAACCCGTCACGTTCAAAGATGAACATGTACATTCATGCATTTGCAAAAAGGTGAACCTACCCATCGGACAAGGTGGGTCGATCGACCCAGCTATAGCCC[G/A]
TGTCACCCCCACACCCCACATAGACACCTCTAGCCCTCCTAGCAGCATATCCTGTCAACCCACCAGCCTGATAAGTCAACAACTGCCCATCATCAACGTT

Reverse complement sequence

AACGTTGATGATGGGCAGTTGTTGACTTATCAGGCTGGTGGGTTGACAGGATATGCTGCTAGGAGGGCTAGAGGTGTCTATGTGGGGTGTGGGGGTGACA[C/T]
GGGCTATAGCTGGGTCGATCGACCCACCTTGTCCGATGGGTAGGTTCACCTTTTTGCAAATGCATGAATGTACATGTTCATCTTTGAACGTGACGGGTTC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 64.80% 33.30% 0.13% 1.78% NA
All Indica  2759 52.50% 47.30% 0.14% 0.07% NA
All Japonica  1512 84.60% 9.90% 0.13% 5.42% NA
Aus  269 77.70% 22.30% 0.00% 0.00% NA
Indica I  595 17.00% 82.50% 0.50% 0.00% NA
Indica II  465 86.20% 13.80% 0.00% 0.00% NA
Indica III  913 58.80% 41.00% 0.00% 0.22% NA
Indica Intermediate  786 52.20% 47.70% 0.13% 0.00% NA
Temperate Japonica  767 91.80% 8.00% 0.13% 0.13% NA
Tropical Japonica  504 71.80% 13.30% 0.00% 14.88% NA
Japonica Intermediate  241 88.40% 8.70% 0.41% 2.49% NA
VI/Aromatic  96 60.40% 39.60% 0.00% 0.00% NA
Intermediate  90 76.70% 23.30% 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
vg0505359598 G -> DEL N N silent_mutation Average:65.977; most accessible tissue: Callus, score: 92.455 N N N N
vg0505359598 G -> A LOC_Os05g09510-LOC_Os05g09520 intergenic_region ; MODIFIER silent_mutation Average:65.977; most accessible tissue: Callus, score: 92.455 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0505359598 7.68E-08 1.00E-29 Grain_length Ind_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
vg0505359598 3.66E-10 7.34E-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
vg0505359598 1.10E-10 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
vg0505359598 1.16E-29 4.55E-54 Grain_width Ind_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
vg0505359598 NA 2.94E-06 mr1113 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
vg0505359598 NA 1.35E-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
vg0505359598 NA 2.66E-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
vg0505359598 NA 5.29E-10 mr1860 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
vg0505359598 NA 3.71E-07 mr1942 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
vg0505359598 NA 8.58E-06 mr1159_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
vg0505359598 NA 1.37E-08 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
vg0505359598 NA 1.19E-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
vg0505359598 NA 6.86E-09 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
vg0505359598 NA 9.31E-07 mr1838_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
vg0505359598 NA 8.40E-06 mr1959_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