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Detailed information for vg0206403097:

Variant ID: vg0206403097 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 6403097
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:


CACAACCGGTCGTGTACACAATCATTTTTGCAGAATGTGGGTGACGTACGGTGTGTGACAATCAGAAAAATCTGACTTTTTTTTAAAGATGCGGACATCC[C/T]
TCTAAATATTTTTTCAAGAAATTGTGAGCGTGTTGGGGATTAAACATAGAACCTCGGAGTTGAAACTACACACCACTTACCGCTACACTATCAAATGCAT

Reverse complement sequence

ATGCATTTGATAGTGTAGCGGTAAGTGGTGTGTAGTTTCAACTCCGAGGTTCTATGTTTAATCCCCAACACGCTCACAATTTCTTGAAAAAATATTTAGA[G/A]
GGATGTCCGCATCTTTAAAAAAAAGTCAGATTTTTCTGATTGTCACACACCGTACGTCACCCACATTCTGCAAAAATGATTGTGTACACGACCGGTTGTG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.50% 1.80% 1.63% 0.00% NA
All Indica  2759 94.10% 3.20% 2.75% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 83.90% 9.10% 7.06% 0.00% NA
Indica II  465 97.40% 1.10% 1.51% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 93.00% 3.60% 3.44% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 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  90 100.00% 0.00% 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
vg0206403097 C -> T LOC_Os02g12300.1 upstream_gene_variant ; 911.0bp to feature; MODIFIER silent_mutation Average:52.009; most accessible tissue: Zhenshan97 panicle, score: 73.605 N N N N
vg0206403097 C -> T LOC_Os02g12310.1 upstream_gene_variant ; 921.0bp to feature; MODIFIER silent_mutation Average:52.009; most accessible tissue: Zhenshan97 panicle, score: 73.605 N N N N
vg0206403097 C -> T LOC_Os02g12290.1 downstream_gene_variant ; 3861.0bp to feature; MODIFIER silent_mutation Average:52.009; most accessible tissue: Zhenshan97 panicle, score: 73.605 N N N N
vg0206403097 C -> T LOC_Os02g12320.1 downstream_gene_variant ; 3756.0bp to feature; MODIFIER silent_mutation Average:52.009; most accessible tissue: Zhenshan97 panicle, score: 73.605 N N N N
vg0206403097 C -> T LOC_Os02g12300-LOC_Os02g12310 intergenic_region ; MODIFIER silent_mutation Average:52.009; most accessible tissue: Zhenshan97 panicle, score: 73.605 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0206403097 2.79E-07 NA Plant_height 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