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Detailed information for vg0201211730:

Variant ID: vg0201211730 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 1211730
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, G: 0.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


TTTCGGCTAGCTCCACAAGGTGATAGACGATCTGGGTTCGAAACCTCATCTCTTCTAATTATTTGATATTAGTTTCTTCCATAATATTAGCTTTTTAAGT[A/G]
TGCAAGCAGAGCAACGAGCCTACGAGAGGCAGAGTTAGCTAGTATCACTTGGAATAGGCTTCCAATTGCCATCATCTCAATCTTGGAATTCAAGCTCATG

Reverse complement sequence

CATGAGCTTGAATTCCAAGATTGAGATGATGGCAATTGGAAGCCTATTCCAAGTGATACTAGCTAACTCTGCCTCTCGTAGGCTCGTTGCTCTGCTTGCA[T/C]
ACTTAAAAAGCTAATATTATGGAAGAAACTAATATCAAATAATTAGAAGAGATGAGGTTTCGAACCCAGATCGTCTATCACCTTGTGGAGCTAGCCGAAA

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 88.30% 11.70% 0.00% 0.00% NA
All Indica  2759 81.00% 19.00% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 90.70% 9.30% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 90.30% 9.70% 0.00% 0.00% NA
Indica III  913 59.70% 40.30% 0.00% 0.00% NA
Indica Intermediate  786 85.90% 14.10% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 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 97.80% 2.20% 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
vg0201211730 A -> G LOC_Os02g03070.1 upstream_gene_variant ; 2265.0bp to feature; MODIFIER silent_mutation Average:76.543; most accessible tissue: Callus, score: 92.457 N N N N
vg0201211730 A -> G LOC_Os02g03070.2 upstream_gene_variant ; 2277.0bp to feature; MODIFIER silent_mutation Average:76.543; most accessible tissue: Callus, score: 92.457 N N N N
vg0201211730 A -> G LOC_Os02g03070.3 upstream_gene_variant ; 2277.0bp to feature; MODIFIER silent_mutation Average:76.543; most accessible tissue: Callus, score: 92.457 N N N N
vg0201211730 A -> G LOC_Os02g03060.1 downstream_gene_variant ; 504.0bp to feature; MODIFIER silent_mutation Average:76.543; most accessible tissue: Callus, score: 92.457 N N N N
vg0201211730 A -> G LOC_Os02g03060.2 downstream_gene_variant ; 504.0bp to feature; MODIFIER silent_mutation Average:76.543; most accessible tissue: Callus, score: 92.457 N N N N
vg0201211730 A -> G LOC_Os02g03060-LOC_Os02g03070 intergenic_region ; MODIFIER silent_mutation Average:76.543; most accessible tissue: Callus, score: 92.457 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0201211730 NA 5.19E-09 Grain_thickness Ind_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
vg0201211730 NA 7.48E-09 Grain_weight Ind_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