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Detailed information for vg0224963772:

Variant ID: vg0224963772 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 24963772
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.82, T: 0.18, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


TAATAAAAATGAATGGTCAAATGTTACAAGTAAAAAGTCAAAGCGACATTTATTATAAGACAGGGGTAGTAGTTATCAATGTCACGCATCCCAATCCCTT[A/T]
AAAAAATATATATTAAGAGCCTGCGAAACTCATTTATAGGCTAAAATGAGCCGTGGACCCACTTATTTTGAGCCATAAGCATCCCTTAGCTCCAAGGCTC

Reverse complement sequence

GAGCCTTGGAGCTAAGGGATGCTTATGGCTCAAAATAAGTGGGTCCACGGCTCATTTTAGCCTATAAATGAGTTTCGCAGGCTCTTAATATATATTTTTT[T/A]
AAGGGATTGGGATGCGTGACATTGATAACTACTACCCCTGTCTTATAATAAATGTCGCTTTGACTTTTTACTTGTAACATTTGACCATTCATTTTTATTA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 76.80% 23.20% 0.00% 0.00% NA
All Indica  2759 93.90% 6.10% 0.00% 0.00% NA
All Japonica  1512 43.70% 56.30% 0.00% 0.00% NA
Aus  269 84.40% 15.60% 0.00% 0.00% NA
Indica I  595 95.30% 4.70% 0.00% 0.00% NA
Indica II  465 98.30% 1.70% 0.00% 0.00% NA
Indica III  913 92.90% 7.10% 0.00% 0.00% NA
Indica Intermediate  786 91.50% 8.50% 0.00% 0.00% NA
Temperate Japonica  767 61.80% 38.20% 0.00% 0.00% NA
Tropical Japonica  504 12.50% 87.50% 0.00% 0.00% NA
Japonica Intermediate  241 51.50% 48.50% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 62.20% 37.80% 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
vg0224963772 A -> T LOC_Os02g41610.1 downstream_gene_variant ; 3514.0bp to feature; MODIFIER silent_mutation Average:47.038; most accessible tissue: Callus, score: 75.123 N N N N
vg0224963772 A -> T LOC_Os02g41620.1 downstream_gene_variant ; 892.0bp to feature; MODIFIER silent_mutation Average:47.038; most accessible tissue: Callus, score: 75.123 N N N N
vg0224963772 A -> T LOC_Os02g41620-LOC_Os02g41630 intergenic_region ; MODIFIER silent_mutation Average:47.038; most accessible tissue: Callus, score: 75.123 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0224963772 1.83E-07 NA Spikelet_length 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
vg0224963772 3.09E-07 1.13E-13 Spikelet_length Jap_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
vg0224963772 NA 7.49E-09 mr1851_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