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Detailed information for vg0505613072:

Variant ID: vg0505613072 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 5613072
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


TGCATTTGAACGTGTGCCTTGTCACAACATCGGTTTTTCTGCTATGGTAATTGCTAGCTTTGCATGTAGAGAAACCAACCATATAAGCATAACCATTGTA[G/T]
AAGTCAAAAGCTTCATTCTCATCAGCAAAAACTTTGTTGATTGACGGCGCATGTGCACTGTTAGCTTCCTGACCACCTCTCTGAACAGCTGCTACACTTT

Reverse complement sequence

AAAGTGTAGCAGCTGTTCAGAGAGGTGGTCAGGAAGCTAACAGTGCACATGCGCCGTCAATCAACAAAGTTTTTGCTGATGAGAATGAAGCTTTTGACTT[C/A]
TACAATGGTTATGCTTATATGGTTGGTTTCTCTACATGCAAAGCTAGCAATTACCATAGCAGAAAAACCGATGTTGTGACAAGGCACACGTTCAAATGCA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.70% 2.20% 1.08% 0.00% NA
All Indica  2759 94.50% 3.70% 1.81% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.70% 0.00% 1.34% 0.00% NA
Indica II  465 75.90% 18.30% 5.81% 0.00% NA
Indica III  913 99.50% 0.00% 0.55% 0.00% NA
Indica Intermediate  786 96.40% 2.30% 1.27% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 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 98.90% 0.00% 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
vg0505613072 G -> T LOC_Os05g10270.1 downstream_gene_variant ; 3438.0bp to feature; MODIFIER silent_mutation Average:17.38; most accessible tissue: Minghui63 flag leaf, score: 23.047 N N N N
vg0505613072 G -> T LOC_Os05g10270-LOC_Os05g10290 intergenic_region ; MODIFIER silent_mutation Average:17.38; most accessible tissue: Minghui63 flag leaf, score: 23.047 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0505613072 NA 1.42E-10 mr1039 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
vg0505613072 9.40E-15 NA mr1039_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
vg0505613072 2.77E-10 5.49E-12 mr1039_2 Ind_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
vg0505613072 NA 3.28E-06 mr1042_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
vg0505613072 NA 3.32E-06 mr1133_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
vg0505613072 2.46E-08 NA mr1632_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
vg0505613072 8.72E-06 9.64E-10 mr1632_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
vg0505613072 NA 1.79E-06 mr1726_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