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Detailed information for vg0806250261:

Variant ID: vg0806250261 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 6250261
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


TCGGATACTCCATCGGATACGCTCCGATACATATCCCATACGTATCCTCAATTTTTCTGATTTTCAAATAAATAAAGATAATTCGGATACTTCTTGGATA[C/A]
GGCTCTGCGCATCCTGGATAGTCCCAAGTCCCAACCCTAACAAATACTTCCTCCGTTTCACAATGTAAGACTTTCTAGCATTACCGACATTCATATAGAT

Reverse complement sequence

ATCTATATGAATGTCGGTAATGCTAGAAAGTCTTACATTGTGAAACGGAGGAAGTATTTGTTAGGGTTGGGACTTGGGACTATCCAGGATGCGCAGAGCC[G/T]
TATCCAAGAAGTATCCGAATTATCTTTATTTATTTGAAAATCAGAAAAATTGAGGATACGTATGGGATATGTATCGGAGCGTATCCGATGGAGTATCCGA

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 96.40% 3.30% 0.25% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 89.40% 9.90% 0.73% 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 99.80% 0.20% 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 99.60% 0.00% 0.39% 0.00% NA
Tropical Japonica  504 74.40% 24.20% 1.39% 0.00% NA
Japonica Intermediate  241 88.00% 11.60% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 5.60% 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
vg0806250261 C -> A LOC_Os08g10608.1 upstream_gene_variant ; 3114.0bp to feature; MODIFIER silent_mutation Average:66.18; most accessible tissue: Zhenshan97 panicle, score: 81.752 N N N N
vg0806250261 C -> A LOC_Os08g10612.1 upstream_gene_variant ; 1092.0bp to feature; MODIFIER silent_mutation Average:66.18; most accessible tissue: Zhenshan97 panicle, score: 81.752 N N N N
vg0806250261 C -> A LOC_Os08g10608-LOC_Os08g10612 intergenic_region ; MODIFIER silent_mutation Average:66.18; most accessible tissue: Zhenshan97 panicle, score: 81.752 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0806250261 1.39E-06 NA mr1301 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
vg0806250261 4.04E-07 4.04E-07 mr1848 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
vg0806250261 2.22E-06 NA mr1301_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
vg0806250261 2.37E-06 NA mr1993_2 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