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Detailed information for vg0905154807:

Variant ID: vg0905154807 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 5154807
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


CTGACACAAAAAGAAAGCAGGTCATCTATTTGCATCCTTGTTCACACGAACTCACGGGAAACTCTTTTAAACACTCGGGTGGACATTCACCCGTTTCTTA[C/T]
ATATCATCTAAATGGTTATGAAAAATTTTCAAAAAAATTGACATGATAGATTAATATGTAATATATCACTTCACAAACATGCAAGTTCAAATTCGACTTC

Reverse complement sequence

GAAGTCGAATTTGAACTTGCATGTTTGTGAAGTGATATATTACATATTAATCTATCATGTCAATTTTTTTGAAAATTTTTCATAACCATTTAGATGATAT[G/A]
TAAGAAACGGGTGAATGTCCACCCGAGTGTTTAAAAGAGTTTCCCGTGAGTTCGTGTGAACAAGGATGCAAATAGATGACCTGCTTTCTTTTTGTGTCAG

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 97.00% 1.60% 0.83% 0.57% NA
All Indica  2759 95.00% 2.60% 1.41% 0.98% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 95.60% 1.70% 2.69% 0.00% NA
Indica II  465 87.10% 6.00% 1.51% 5.38% NA
Indica III  913 99.70% 0.20% 0.11% 0.00% NA
Indica Intermediate  786 93.80% 4.10% 1.91% 0.25% NA
Temperate Japonica  767 99.90% 0.10% 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
vg0905154807 C -> DEL N N silent_mutation Average:72.23; most accessible tissue: Minghui63 panicle, score: 86.85 N N N N
vg0905154807 C -> T LOC_Os09g09540.1 upstream_gene_variant ; 577.0bp to feature; MODIFIER silent_mutation Average:72.23; most accessible tissue: Minghui63 panicle, score: 86.85 N N N N
vg0905154807 C -> T LOC_Os09g09560.1 upstream_gene_variant ; 4653.0bp to feature; MODIFIER silent_mutation Average:72.23; most accessible tissue: Minghui63 panicle, score: 86.85 N N N N
vg0905154807 C -> T LOC_Os09g09550.1 downstream_gene_variant ; 1529.0bp to feature; MODIFIER silent_mutation Average:72.23; most accessible tissue: Minghui63 panicle, score: 86.85 N N N N
vg0905154807 C -> T LOC_Os09g09540-LOC_Os09g09550 intergenic_region ; MODIFIER silent_mutation Average:72.23; most accessible tissue: Minghui63 panicle, score: 86.85 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0905154807 NA 5.00E-07 mr1221 Ind_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0905154807 NA 7.27E-07 mr1422 Ind_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