Search for Variation information by Variation ID:

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

Detailed information for vg0601155306:

Variant ID: vg0601155306 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 1155306
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.69, C: 0.31, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:


TCAAATTGTTTTTTATCATTGGATCTAGTTGGACATGATGGATATTAATATATCCAACGATCGAAAATGATTTGGTACCGCACGTATTAGTATTTGGGAT[C/A]
GATCAACCTGCTTAATTTACATCCCTATCTATGCCAAATAAATCTTCAAAATGCATGTTTTTATTCATAACGTGCTATAACGTTATTAGGTTCTGTGCAT

Reverse complement sequence

ATGCACAGAACCTAATAACGTTATAGCACGTTATGAATAAAAACATGCATTTTGAAGATTTATTTGGCATAGATAGGGATGTAAATTAAGCAGGTTGATC[G/T]
ATCCCAAATACTAATACGTGCGGTACCAAATCATTTTCGATCGTTGGATATATTAATATCCATCATGTCCAACTAGATCCAATGATAAAAAACAATTTGA

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 78.50% 21.30% 0.13% 0.00% NA
All Indica  2759 77.70% 22.10% 0.18% 0.00% NA
All Japonica  1512 86.80% 13.20% 0.00% 0.00% NA
Aus  269 57.60% 42.40% 0.00% 0.00% NA
Indica I  595 94.60% 5.40% 0.00% 0.00% NA
Indica II  465 85.40% 14.60% 0.00% 0.00% NA
Indica III  913 63.40% 36.40% 0.22% 0.00% NA
Indica Intermediate  786 76.80% 22.80% 0.38% 0.00% NA
Temperate Japonica  767 92.80% 7.20% 0.00% 0.00% NA
Tropical Japonica  504 73.20% 26.80% 0.00% 0.00% NA
Japonica Intermediate  241 95.90% 4.10% 0.00% 0.00% NA
VI/Aromatic  96 34.40% 65.60% 0.00% 0.00% NA
Intermediate  90 76.70% 22.20% 1.11% 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
vg0601155306 C -> A LOC_Os06g03120.1 downstream_gene_variant ; 178.0bp to feature; MODIFIER silent_mutation Average:58.032; most accessible tissue: Zhenshan97 flower, score: 78.677 N N N N
vg0601155306 C -> A LOC_Os06g03120-LOC_Os06g03130 intergenic_region ; MODIFIER silent_mutation Average:58.032; most accessible tissue: Zhenshan97 flower, score: 78.677 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0601155306 2.27E-06 NA mr1647 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