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Detailed information for vg0504656439:

Variant ID: vg0504656439 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 4656439
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGTATTTTAAACCGCTAACAACTCGAATATAAATTTATCTATTTCGTGCATTCGTTTCGGTTTATCGGTCATAGCTCAACCGATCATGATCATCTTATA[G/A]
GCCGCAAAGAAAAAAAAGCTTTCTAAACTGACCACTGTTTTTTTTTAAATAAATGAGAATAAAAATTGTTCCTATTTGAACAAAACTATTTCCACTCCCT

Reverse complement sequence

AGGGAGTGGAAATAGTTTTGTTCAAATAGGAACAATTTTTATTCTCATTTATTTAAAAAAAAACAGTGGTCAGTTTAGAAAGCTTTTTTTTCTTTGCGGC[C/T]
TATAAGATGATCATGATCGGTTGAGCTATGACCGATAAACCGAAACGAATGCACGAAATAGATAAATTTATATTCGAGTTGTTAGCGGTTTAAAATACAA

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 73.80% 26.10% 0.13% 0.00% NA
All Indica  2759 98.90% 1.10% 0.00% 0.00% NA
All Japonica  1512 24.70% 75.00% 0.33% 0.00% NA
Aus  269 97.80% 2.20% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 97.60% 2.40% 0.00% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 98.30% 1.70% 0.00% 0.00% NA
Temperate Japonica  767 6.90% 93.10% 0.00% 0.00% NA
Tropical Japonica  504 50.40% 48.80% 0.79% 0.00% NA
Japonica Intermediate  241 27.40% 72.20% 0.41% 0.00% NA
VI/Aromatic  96 76.00% 24.00% 0.00% 0.00% NA
Intermediate  90 56.70% 42.20% 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
vg0504656439 G -> A LOC_Os05g08540.1 downstream_gene_variant ; 4223.0bp to feature; MODIFIER silent_mutation Average:51.768; most accessible tissue: Callus, score: 88.865 N N N N
vg0504656439 G -> A LOC_Os05g08530.1 intron_variant ; MODIFIER silent_mutation Average:51.768; most accessible tissue: Callus, score: 88.865 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0504656439 1.90E-08 6.96E-38 Grain_thickness 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
vg0504656439 NA 3.90E-09 mr1693 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
vg0504656439 NA 8.15E-23 mr1679_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
vg0504656439 NA 5.47E-15 mr1790_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