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Detailed information for vg1123433680:

Variant ID: vg1123433680 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 23433680
Reference Allele: CAlternative Allele: A,T
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:


ATGCTTGCAACCACCTTGAGTTTGGAGTTATTTGATCCACCTGTTGATAAAAAGAATGGAATTGTTTATTGATCCAAATTAAGGGGGCAATATAGATTGC[C/A,T]
ATGTTGATTTCTATATTACCTGTATTTATATTGTTTCCTTCACAAGAAATCAAGTGTTGGCCACAATTCAAATGGTTACCTATATAACTGGAATTACAAT

Reverse complement sequence

ATTGTAATTCCAGTTATATAGGTAACCATTTGAATTGTGGCCAACACTTGATTTCTTGTGAAGGAAACAATATAAATACAGGTAATATAGAAATCAACAT[G/T,A]
GCAATCTATATTGCCCCCTTAATTTGGATCAATAAACAATTCCATTCTTTTTATCAACAGGTGGATCAAATAACTCCAAACTCAAGGTGGTTGCAAGCAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 83.40% 16.60% 0.00% 0.00% NA
All Indica  2759 90.50% 9.50% 0.00% 0.00% NA
All Japonica  1512 75.70% 24.30% 0.00% 0.00% NA
Aus  269 74.70% 25.30% 0.00% 0.00% NA
Indica I  595 99.20% 0.80% 0.00% 0.00% NA
Indica II  465 94.40% 5.60% 0.00% 0.00% NA
Indica III  913 79.70% 20.30% 0.00% 0.00% NA
Indica Intermediate  786 94.30% 5.70% 0.00% 0.00% NA
Temperate Japonica  767 69.10% 30.90% 0.00% 0.00% NA
Tropical Japonica  504 86.10% 13.90% 0.00% 0.00% NA
Japonica Intermediate  241 74.70% 25.30% 0.00% 0.00% NA
VI/Aromatic  96 29.20% 70.80% 0.00% 0.00% NA
Intermediate  90 76.70% 23.30% 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
vg1123433680 C -> T LOC_Os11g39360.1 downstream_gene_variant ; 3755.0bp to feature; MODIFIER N Average:48.354; most accessible tissue: Callus, score: 71.389 N N N N
vg1123433680 C -> T LOC_Os11g39360.2 downstream_gene_variant ; 3754.0bp to feature; MODIFIER N Average:48.354; most accessible tissue: Callus, score: 71.389 N N N N
vg1123433680 C -> T LOC_Os11g39370.1 intron_variant ; MODIFIER N Average:48.354; most accessible tissue: Callus, score: 71.389 N N N N
vg1123433680 C -> T LOC_Os11g39370.2 intron_variant ; MODIFIER N Average:48.354; most accessible tissue: Callus, score: 71.389 N N N N
vg1123433680 C -> A LOC_Os11g39360.1 downstream_gene_variant ; 3755.0bp to feature; MODIFIER silent_mutation Average:48.354; most accessible tissue: Callus, score: 71.389 N N N N
vg1123433680 C -> A LOC_Os11g39360.2 downstream_gene_variant ; 3754.0bp to feature; MODIFIER silent_mutation Average:48.354; most accessible tissue: Callus, score: 71.389 N N N N
vg1123433680 C -> A LOC_Os11g39370.1 intron_variant ; MODIFIER silent_mutation Average:48.354; most accessible tissue: Callus, score: 71.389 N N N N
vg1123433680 C -> A LOC_Os11g39370.2 intron_variant ; MODIFIER silent_mutation Average:48.354; most accessible tissue: Callus, score: 71.389 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1123433680 1.42E-10 8.50E-07 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