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Detailed information for vg0600222950:

Variant ID: vg0600222950 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 222950
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.58, C: 0.42, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:


TACCGTTCATATGTAGAGTTGAAACTTACTCCAACTTCAAGAAAGGTCAAGCTGCAGCTAAAACTATGCCAAACGGCCCCCTAAGCATATCGACTCCACC[A/C]
TTTTCTCTTCAGCTTAAGCTAAAATTTAAATTTCAAAACTTAATTTTATATCTTTTTTAAAAAAACATAGTATAAACTTATACGCTCTTATAAATATACA

Reverse complement sequence

TGTATATTTATAAGAGCGTATAAGTTTATACTATGTTTTTTTAAAAAAGATATAAAATTAAGTTTTGAAATTTAAATTTTAGCTTAAGCTGAAGAGAAAA[T/G]
GGTGGAGTCGATATGCTTAGGGGGCCGTTTGGCATAGTTTTAGCTGCAGCTTGACCTTTCTTGAAGTTGGAGTAAGTTTCAACTCTACATATGAACGGTA

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 65.40% 34.60% 0.06% 0.00% NA
All Indica  2759 95.20% 4.80% 0.04% 0.00% NA
All Japonica  1512 5.00% 94.90% 0.07% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.70% 0.20% 0.17% 0.00% NA
Indica II  465 92.90% 7.10% 0.00% 0.00% NA
Indica III  913 95.10% 4.90% 0.00% 0.00% NA
Indica Intermediate  786 93.30% 6.70% 0.00% 0.00% NA
Temperate Japonica  767 0.10% 99.90% 0.00% 0.00% NA
Tropical Japonica  504 13.10% 86.70% 0.20% 0.00% NA
Japonica Intermediate  241 3.70% 96.30% 0.00% 0.00% NA
VI/Aromatic  96 77.10% 22.90% 0.00% 0.00% NA
Intermediate  90 51.10% 47.80% 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
vg0600222950 A -> C LOC_Os06g01360.1 upstream_gene_variant ; 4656.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0600222950 A -> C LOC_Os06g01370.1 upstream_gene_variant ; 1833.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0600222950 A -> C LOC_Os06g01390.1 upstream_gene_variant ; 4751.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0600222950 A -> C LOC_Os06g01360.2 upstream_gene_variant ; 4656.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0600222950 A -> C LOC_Os06g01370-LOC_Os06g01390 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0600222950 4.61E-06 4.36E-06 mr1677 Jap_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