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Detailed information for vg0401256484:

Variant ID: vg0401256484 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 1256484
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.93, G: 0.06, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


TCCCAGTTGTATACTCTGCTGGGAACGATGGACCCGTTGCTCAGACAGTGGAGAACTCATCACCATGGCTGTTAACGGTTGCTGCAGCCACCATGGATCG[A/G]
TCCTTCCCTGTGGTTATCACCTTGGGCGATAATCATAAGTTTGTGGTATATATATATTATGTGCAGTTCATTCATTCTGACTTAAATTGGATATATATCC

Reverse complement sequence

GGATATATATCCAATTTAAGTCAGAATGAATGAACTGCACATAATATATATATACCACAAACTTATGATTATCGCCCAAGGTGATAACCACAGGGAAGGA[T/C]
CGATCCATGGTGGCTGCAGCAACCGTTAACAGCCATGGTGATGAGTTCTCCACTGTCTGAGCAACGGGTCCATCGTTCCCAGCAGAGTATACAACTGGGA

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 84.20% 15.70% 0.11% 0.00% NA
All Indica  2759 89.90% 10.00% 0.11% 0.00% NA
All Japonica  1512 70.40% 29.50% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.50% 1.30% 0.17% 0.00% NA
Indica II  465 79.80% 20.20% 0.00% 0.00% NA
Indica III  913 85.70% 14.20% 0.11% 0.00% NA
Indica Intermediate  786 94.30% 5.60% 0.13% 0.00% NA
Temperate Japonica  767 60.60% 39.20% 0.13% 0.00% NA
Tropical Japonica  504 78.20% 21.80% 0.00% 0.00% NA
Japonica Intermediate  241 85.50% 14.50% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 82.20% 16.70% 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
vg0401256484 A -> G LOC_Os04g03050.1 synonymous_variant ; p.Arg341Arg; LOW synonymous_codon Average:60.308; most accessible tissue: Callus, score: 81.069 N N N N
vg0401256484 A -> G LOC_Os04g03050.1 synonymous_variant ; p.Arg341Arg; LOW nonsynonymous_codon ; R341Q Average:60.308; most accessible tissue: Callus, score: 81.069 benign 0.93 DELETERIOUS 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0401256484 NA 6.45E-10 Heading_date Jap_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
vg0401256484 2.07E-06 NA mr1565_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