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Detailed information for vg0827572715:

Variant ID: vg0827572715 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 27572715
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTAGGCCTGGTTTAGTTGCCAACCTTTTCTTTAAACTTTCGACTTTTCTATCACATTAAAAATTTTCTACATATACAAACTTTTAACTTTTCCGTCACAT[C/T]
GTTCCAATTTCAATTAAACTTTTAATTTTGACGTGAACTAAACACACCTGTAGAATCGATCAGATTTAGCAATGCACCGACGGAAAGTCTCAAACCTTAA

Reverse complement sequence

TTAAGGTTTGAGACTTTCCGTCGGTGCATTGCTAAATCTGATCGATTCTACAGGTGTGTTTAGTTCACGTCAAAATTAAAAGTTTAATTGAAATTGGAAC[G/A]
ATGTGACGGAAAAGTTAAAAGTTTGTATATGTAGAAAATTTTTAATGTGATAGAAAAGTCGAAAGTTTAAAGAAAAGGTTGGCAACTAAACCAGGCCTAG

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 93.30% 5.00% 1.69% 0.00% NA
All Indica  2759 88.80% 8.30% 2.83% 0.00% NA
All Japonica  1512 99.80% 0.10% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 95.50% 2.70% 1.85% 0.00% NA
Indica II  465 92.30% 6.20% 1.51% 0.00% NA
Indica III  913 88.70% 10.30% 0.99% 0.00% NA
Indica Intermediate  786 81.90% 11.60% 6.49% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 4.40% 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
vg0827572715 C -> T LOC_Os08g43580.1 upstream_gene_variant ; 4085.0bp to feature; MODIFIER silent_mutation Average:33.685; most accessible tissue: Callus, score: 66.87 N N N N
vg0827572715 C -> T LOC_Os08g43600.1 upstream_gene_variant ; 3422.0bp to feature; MODIFIER silent_mutation Average:33.685; most accessible tissue: Callus, score: 66.87 N N N N
vg0827572715 C -> T LOC_Os08g43580.2 upstream_gene_variant ; 4091.0bp to feature; MODIFIER silent_mutation Average:33.685; most accessible tissue: Callus, score: 66.87 N N N N
vg0827572715 C -> T LOC_Os08g43590.1 downstream_gene_variant ; 731.0bp to feature; MODIFIER silent_mutation Average:33.685; most accessible tissue: Callus, score: 66.87 N N N N
vg0827572715 C -> T LOC_Os08g43590-LOC_Os08g43600 intergenic_region ; MODIFIER silent_mutation Average:33.685; most accessible tissue: Callus, score: 66.87 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0827572715 4.64E-06 NA mr1502 Ind_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
vg0827572715 NA 8.63E-06 mr1751_2 Ind_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