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Detailed information for vg0506490603:

Variant ID: vg0506490603 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 6490603
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


GCGACTGCTCCGTGTCTGGCACCATCGACTTCATATACTGCAACTCGCAGGCAAGTATATAATTAAACTCTTCTTCTTCTGTTTCTTTTGATCCAACAAT[T/A]
AACACCACCACCACCACCACGACGACGACGACGAAGAATAAGCAAATATTTAGAAAAAAGCAAATGAAATGCATGCAGGTGGTGCTCCAGAACTGCTTGA

Reverse complement sequence

TCAAGCAGTTCTGGAGCACCACCTGCATGCATTTCATTTGCTTTTTTCTAAATATTTGCTTATTCTTCGTCGTCGTCGTCGTGGTGGTGGTGGTGGTGTT[A/T]
ATTGTTGGATCAAAAGAAACAGAAGAAGAAGAGTTTAATTATATACTTGCCTGCGAGTTGCAGTATATGAAGTCGATGGTGCCAGACACGGAGCAGTCGC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.80% 4.20% 1.02% 0.00% NA
All Indica  2759 91.40% 7.00% 1.63% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.10% 0.30% 3.53% 0.00% NA
Indica II  465 68.20% 28.20% 3.66% 0.00% NA
Indica III  913 97.70% 2.30% 0.00% 0.00% NA
Indica Intermediate  786 94.30% 4.80% 0.89% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.40% 0.20% 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% 4.40% 2.22% 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
vg0506490603 T -> A LOC_Os05g11460.1 upstream_gene_variant ; 4375.0bp to feature; MODIFIER silent_mutation Average:71.305; most accessible tissue: Zhenshan97 flag leaf, score: 84.585 N N N N
vg0506490603 T -> A LOC_Os05g11470.1 intron_variant ; MODIFIER silent_mutation Average:71.305; most accessible tissue: Zhenshan97 flag leaf, score: 84.585 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0506490603 NA 1.30E-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
vg0506490603 1.07E-06 NA mr1632 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
vg0506490603 8.34E-06 2.56E-07 mr1632 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
vg0506490603 NA 1.64E-11 mr1039_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
vg0506490603 NA 1.28E-06 mr1428_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
vg0506490603 9.29E-06 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
vg0506490603 NA 1.78E-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