Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0809379318:

Variant ID: vg0809379318 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 9379318
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.96, C: 0.04, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:


CCACACGGCGGCGGTGGATCGCACGGTGGGGAGGCATGGGGGCGGCGGCTAGCCCTTCCGCACGGGAAAACTTTTTTCGGGCCGTTTGCAAAAAAAATAT[A/C]
TTTTGTAGTGGTGAATAAAGGGGGCTTATTTGTGTGTGTTGTGTTTAATGGTACATGTACATAGCAATTGAAAAATGGAAACCTAAACTCCGAGGTGATG

Reverse complement sequence

CATCACCTCGGAGTTTAGGTTTCCATTTTTCAATTGCTATGTACATGTACCATTAAACACAACACACACAAATAAGCCCCCTTTATTCACCACTACAAAA[T/G]
ATATTTTTTTTGCAAACGGCCCGAAAAAAGTTTTCCCGTGCGGAAGGGCTAGCCGCCGCCCCCATGCCTCCCCACCGTGCGATCCACCGCCGCCGTGTGG

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 86.40% 13.60% 0.02% 0.00% NA
All Indica  2759 94.90% 5.10% 0.00% 0.00% NA
All Japonica  1512 73.10% 26.80% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 85.60% 14.40% 0.00% 0.00% NA
Indica III  913 95.40% 4.60% 0.00% 0.00% NA
Indica Intermediate  786 95.90% 4.10% 0.00% 0.00% NA
Temperate Japonica  767 98.30% 1.70% 0.00% 0.00% NA
Tropical Japonica  504 34.70% 65.30% 0.00% 0.00% NA
Japonica Intermediate  241 73.40% 26.10% 0.41% 0.00% NA
VI/Aromatic  96 13.50% 86.50% 0.00% 0.00% NA
Intermediate  90 86.70% 13.30% 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
vg0809379318 A -> C LOC_Os08g15410.1 upstream_gene_variant ; 2320.0bp to feature; MODIFIER silent_mutation Average:69.014; most accessible tissue: Callus, score: 86.114 N N N N
vg0809379318 A -> C LOC_Os08g15420.1 upstream_gene_variant ; 4022.0bp to feature; MODIFIER silent_mutation Average:69.014; most accessible tissue: Callus, score: 86.114 N N N N
vg0809379318 A -> C LOC_Os08g15410-LOC_Os08g15420 intergenic_region ; MODIFIER silent_mutation Average:69.014; most accessible tissue: Callus, score: 86.114 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0809379318 NA 2.42E-07 mr1206 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
vg0809379318 NA 7.59E-06 mr1596 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
vg0809379318 2.06E-06 NA mr1676 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
vg0809379318 NA 9.02E-06 mr1689 Jap_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