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Detailed information for vg0612806445:

Variant ID: vg0612806445 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 12806445
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCAGCACAGACTTCAAGATGTAATCAAGATGTAATGTATGTATGCTATGTGGGACCAGGTATTAATAGTATAGTAAGTAACTATTGTATGAATTGGCTAT[C/T]
ATATTGGCTATAGATGATTTAGAACTAGTAGAGGGCTATACTATTAAACTTGCTCTTAGAACCGAACCTCCGTCCCAAAATATAAGCATTTTTGACTTCG

Reverse complement sequence

CGAAGTCAAAAATGCTTATATTTTGGGACGGAGGTTCGGTTCTAAGAGCAAGTTTAATAGTATAGCCCTCTACTAGTTCTAAATCATCTATAGCCAATAT[G/A]
ATAGCCAATTCATACAATAGTTACTTACTATACTATTAATACCTGGTCCCACATAGCATACATACATTACATCTTGATTACATCTTGAAGTCTGTGCTGC

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 95.40% 4.60% 0.00% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 45.70% 54.30% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.00% 1.00% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 44.80% 55.20% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0612806445 C -> T LOC_Os06g22080.1 upstream_gene_variant ; 3121.0bp to feature; MODIFIER silent_mutation Average:45.414; most accessible tissue: Zhenshan97 root, score: 76.749 N N N N
vg0612806445 C -> T LOC_Os06g22080.3 upstream_gene_variant ; 3205.0bp to feature; MODIFIER silent_mutation Average:45.414; most accessible tissue: Zhenshan97 root, score: 76.749 N N N N
vg0612806445 C -> T LOC_Os06g22070.1 downstream_gene_variant ; 2401.0bp to feature; MODIFIER silent_mutation Average:45.414; most accessible tissue: Zhenshan97 root, score: 76.749 N N N N
vg0612806445 C -> T LOC_Os06g22070-LOC_Os06g22080 intergenic_region ; MODIFIER silent_mutation Average:45.414; most accessible tissue: Zhenshan97 root, score: 76.749 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0612806445 NA 3.61E-09 mr1585 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
vg0612806445 NA 3.02E-06 mr1633 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
vg0612806445 2.33E-06 NA mr1987_2 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