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Detailed information for vg0822545105:

Variant ID: vg0822545105 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 22545105
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCGAGTCAAGGGGGGTAATTCATCCAGTATAAAAAATTGAGGGTGAAAGATGTCTGGTTTCGTGATTAAGGGGATAATTTGTATTGCAACTGTATGCATG[G/A]
GGTAATTTAGACTTTTTCCATTAAAGAACACAACCTTATACCTTTTCCTAACTTCTACTCTATCCTTTTCCACACGCACGTTTTAAAGAAAACACTATTT

Reverse complement sequence

AAATAGTGTTTTCTTTAAAACGTGCGTGTGGAAAAGGATAGAGTAGAAGTTAGGAAAAGGTATAAGGTTGTGTTCTTTAATGGAAAAAGTCTAAATTACC[C/T]
CATGCATACAGTTGCAATACAAATTATCCCCTTAATCACGAAACCAGACATCTTTCACCCTCAATTTTTTATACTGGATGAATTACCCCCCTTGACTCGC

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 97.80% 1.40% 0.80% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 93.40% 4.20% 2.45% 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 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 87.70% 7.70% 4.56% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 1.70% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 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
vg0822545105 G -> A LOC_Os08g35730.1 upstream_gene_variant ; 853.0bp to feature; MODIFIER silent_mutation Average:38.449; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N
vg0822545105 G -> A LOC_Os08g35740.1 upstream_gene_variant ; 2079.0bp to feature; MODIFIER silent_mutation Average:38.449; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N
vg0822545105 G -> A LOC_Os08g35740.2 upstream_gene_variant ; 2079.0bp to feature; MODIFIER silent_mutation Average:38.449; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N
vg0822545105 G -> A LOC_Os08g35720.1 downstream_gene_variant ; 3792.0bp to feature; MODIFIER silent_mutation Average:38.449; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N
vg0822545105 G -> A LOC_Os08g35730-LOC_Os08g35740 intergenic_region ; MODIFIER silent_mutation Average:38.449; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0822545105 8.94E-07 5.79E-10 mr1648 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
vg0822545105 3.89E-06 1.19E-08 mr1697 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