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Detailed information for vg1200288458:

Variant ID: vg1200288458 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 288458
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


CAGTTAAGGGTTTGAGTGAAACCTGAATCACACAAGACTGATAATTCAAGGCATAGTCCATTGTTCAGTTGTGATCTGGTGTAGCTCTTTTCTAAGGTGG[A/C]
AGTTCAACTTAACAGTCTCCATCGAAACACTGGTATAACTAACAGGTTCAGTTTTGAGAACATTTCTTGTGAGCCATGAAATTTGGTGGGAATTGTTGGA

Reverse complement sequence

TCCAACAATTCCCACCAAATTTCATGGCTCACAAGAAATGTTCTCAAAACTGAACCTGTTAGTTATACCAGTGTTTCGATGGAGACTGTTAAGTTGAACT[T/G]
CCACCTTAGAAAAGAGCTACACCAGATCACAACTGAACAATGGACTATGCCTTGAATTATCAGTCTTGTGTGATTCAGGTTTCACTCAAACCCTTAACTG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.20% 5.80% 0.06% 0.00% NA
All Indica  2759 90.30% 9.60% 0.11% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 90.60% 9.40% 0.00% 0.00% NA
Indica II  465 97.60% 2.40% 0.00% 0.00% NA
Indica III  913 87.00% 12.90% 0.11% 0.00% NA
Indica Intermediate  786 89.60% 10.20% 0.25% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 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
vg1200288458 A -> C LOC_Os12g01470.1 downstream_gene_variant ; 451.0bp to feature; MODIFIER silent_mutation Average:26.466; most accessible tissue: Minghui63 root, score: 40.262 N N N N
vg1200288458 A -> C LOC_Os12g01480.1 downstream_gene_variant ; 1142.0bp to feature; MODIFIER silent_mutation Average:26.466; most accessible tissue: Minghui63 root, score: 40.262 N N N N
vg1200288458 A -> C LOC_Os12g01470-LOC_Os12g01480 intergenic_region ; MODIFIER silent_mutation Average:26.466; most accessible tissue: Minghui63 root, score: 40.262 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1200288458 1.33E-08 8.01E-12 Awn_length 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