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Detailed information for vg0827252347:

Variant ID: vg0827252347 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 27252347
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAATAATCTAATCTACAACTAAACTCCCTATCAATTTCCACCACCTCTACCAAACAAACAAGAGACTGGGATGAAAAATCAAATTCCCATCTTAATCTTA[A/C]
CATCAATTCCCTCGTGTAAACTCCCAATCCCCTTCTCTCGAGTTATTAAACAAGCCGTAAGATTATGTGTTGATGGAGTATAGCTAGCTAGCTGCCTGCA

Reverse complement sequence

TGCAGGCAGCTAGCTAGCTATACTCCATCAACACATAATCTTACGGCTTGTTTAATAACTCGAGAGAAGGGGATTGGGAGTTTACACGAGGGAATTGATG[T/G]
TAAGATTAAGATGGGAATTTGATTTTTCATCCCAGTCTCTTGTTTGTTTGGTAGAGGTGGTGGAAATTGATAGGGAGTTTAGTTGTAGATTAGATTATTA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.50% 6.50% 1.54% 1.44% NA
All Indica  2759 92.80% 2.20% 2.57% 2.43% NA
All Japonica  1512 90.40% 9.50% 0.13% 0.00% NA
Aus  269 66.20% 33.50% 0.00% 0.37% NA
Indica I  595 99.70% 0.00% 0.00% 0.34% NA
Indica II  465 75.10% 3.00% 11.40% 10.54% NA
Indica III  913 96.90% 2.00% 0.22% 0.88% NA
Indica Intermediate  786 93.10% 3.80% 2.04% 1.02% NA
Temperate Japonica  767 96.20% 3.70% 0.13% 0.00% NA
Tropical Japonica  504 95.00% 5.00% 0.00% 0.00% NA
Japonica Intermediate  241 62.20% 37.30% 0.41% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0827252347 A -> C LOC_Os08g43110.1 upstream_gene_variant ; 3145.0bp to feature; MODIFIER silent_mutation Average:31.663; most accessible tissue: Zhenshan97 flower, score: 54.935 N N N N
vg0827252347 A -> C LOC_Os08g43100-LOC_Os08g43110 intergenic_region ; MODIFIER silent_mutation Average:31.663; most accessible tissue: Zhenshan97 flower, score: 54.935 N N N N
vg0827252347 A -> DEL N N silent_mutation Average:31.663; most accessible tissue: Zhenshan97 flower, score: 54.935 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0827252347 NA 7.99E-07 mr1691 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
vg0827252347 NA 3.78E-09 mr1693 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
vg0827252347 1.28E-06 1.65E-11 mr1720 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
vg0827252347 NA 6.09E-06 mr1720 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