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Detailed information for vg0626068609:

Variant ID: vg0626068609 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 26068609
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:


AAAGGACTTGCACTTGTGCGGCATCCAAGGCCTCCATATTAGGGTGTCGAAATTTGACGATGTTGTACCCAGGAGCTGCACCTTATAAGCTGTGGTGGCC[G/A]
TGTATTCGCCATGGTTGTTTAGCTTCCAGGTGATCTGGTCTTCATGTTCCGTGAAGTGTACATTCTGAACGGCGCTCCAAATGGTGATGAGCTGGTCAAT

Reverse complement sequence

ATTGACCAGCTCATCACCATTTGGAGCGCCGTTCAGAATGTACACTTCACGGAACATGAAGACCAGATCACCTGGAAGCTAAACAACCATGGCGAATACA[C/T]
GGCCACCACAGCTTATAAGGTGCAGCTCCTGGGTACAACATCGTCAAATTTCGACACCCTAATATGGAGGCCTTGGATGCCGCACAAGTGCAAGTCCTTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.20% 5.70% 0.04% 0.00% NA
All Indica  2759 98.40% 1.60% 0.00% 0.00% NA
All Japonica  1512 88.00% 11.80% 0.13% 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 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 95.80% 4.20% 0.00% 0.00% NA
Temperate Japonica  767 97.80% 2.20% 0.00% 0.00% NA
Tropical Japonica  504 79.80% 20.00% 0.20% 0.00% NA
Japonica Intermediate  241 74.30% 25.30% 0.41% 0.00% NA
VI/Aromatic  96 66.70% 33.30% 0.00% 0.00% NA
Intermediate  90 83.30% 16.70% 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
vg0626068609 G -> A LOC_Os06g43360.1 upstream_gene_variant ; 383.0bp to feature; MODIFIER silent_mutation Average:54.621; most accessible tissue: Zhenshan97 panicle, score: 79.799 N N N N
vg0626068609 G -> A LOC_Os06g43370.1 upstream_gene_variant ; 3769.0bp to feature; MODIFIER silent_mutation Average:54.621; most accessible tissue: Zhenshan97 panicle, score: 79.799 N N N N
vg0626068609 G -> A LOC_Os06g43350.1 downstream_gene_variant ; 3252.0bp to feature; MODIFIER silent_mutation Average:54.621; most accessible tissue: Zhenshan97 panicle, score: 79.799 N N N N
vg0626068609 G -> A LOC_Os06g43350-LOC_Os06g43360 intergenic_region ; MODIFIER silent_mutation Average:54.621; most accessible tissue: Zhenshan97 panicle, score: 79.799 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0626068609 NA 4.12E-06 mr1278_2 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
vg0626068609 NA 9.03E-06 mr1833_2 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
vg0626068609 2.43E-06 2.43E-06 mr1983_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