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Detailed information for vg0800122371:

Variant ID: vg0800122371 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 122371
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.96, G: 0.03, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


CTATTTTGAACCGTGATTTTTAGTCTCGGTTCCCATTCGAATTGGGACAAATATGATTTTTGCCATCCAAACAAAGATCAGCTCTCTAGCAGTAACTATT[A/G]
AACGGTACATTTTACATGAAAACTTTTTATACATAAGTTGTTTTAAAAAATCTAATAAATTTATTCATCAAAACTTTATATATTACTACTTAATTAATTA

Reverse complement sequence

TAATTAATTAAGTAGTAATATATAAAGTTTTGATGAATAAATTTATTAGATTTTTTAAAACAACTTATGTATAAAAAGTTTTCATGTAAAATGTACCGTT[T/C]
AATAGTTACTGCTAGAGAGCTGATCTTTGTTTGGATGGCAAAAATCATATTTGTCCCAATTCGAATGGGAACCGAGACTAAAAATCACGGTTCAAAATAG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 74.50% 25.30% 0.15% 0.00% NA
All Indica  2759 66.60% 33.20% 0.22% 0.00% NA
All Japonica  1512 98.90% 1.00% 0.07% 0.00% NA
Aus  269 13.40% 86.60% 0.00% 0.00% NA
Indica I  595 87.40% 12.60% 0.00% 0.00% NA
Indica II  465 30.80% 69.20% 0.00% 0.00% NA
Indica III  913 75.60% 24.00% 0.44% 0.00% NA
Indica Intermediate  786 61.60% 38.20% 0.25% 0.00% NA
Temperate Japonica  767 98.60% 1.40% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.40% 0.20% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 67.80% 32.20% 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
vg0800122371 A -> G LOC_Os08g01180.1 upstream_gene_variant ; 1250.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0800122371 A -> G LOC_Os08g01180-LOC_Os08g01190 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0800122371 NA 2.14E-06 mr1542 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
vg0800122371 NA 7.24E-06 mr1564 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
vg0800122371 NA 5.81E-06 mr1633 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
vg0800122371 NA 3.31E-07 mr1659 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
vg0800122371 3.36E-07 NA mr1746 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
vg0800122371 7.87E-07 8.66E-09 mr1746 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
vg0800122371 6.02E-10 NA mr1746_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
vg0800122371 5.23E-09 4.14E-11 mr1746_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