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Detailed information for vg0800426468:

Variant ID: vg0800426468 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 426468
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, A: 0.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


ATGTCCATACCTAGATGGACAGAATAAAATTTGTATCCACATTGTGATTGTACATGTTACACCCAAACCCAAATGTGTGGTATATTCCTTTTTTTTCTAT[C/A]
TTTTTGTTGAGTAGTATGTATTGATTTTTTTTTTTAAAAAAAAAGCGGCCGCGTTGCATTGCAAGTTGGAATCTAGGAAACAATTCCAATCAAGTTAAGG

Reverse complement sequence

CCTTAACTTGATTGGAATTGTTTCCTAGATTCCAACTTGCAATGCAACGCGGCCGCTTTTTTTTTAAAAAAAAAAATCAATACATACTACTCAACAAAAA[G/T]
ATAGAAAAAAAAGGAATATACCACACATTTGGGTTTGGGTGTAACATGTACAATCACAATGTGGATACAAATTTTATTCTGTCCATCTAGGTATGGACAT

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 89.70% 10.00% 0.30% 0.00% NA
All Indica  2759 82.70% 16.80% 0.51% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 62.20% 35.80% 2.02% 0.00% NA
Indica II  465 96.80% 3.00% 0.22% 0.00% NA
Indica III  913 86.90% 13.10% 0.00% 0.00% NA
Indica Intermediate  786 85.00% 14.90% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0800426468 C -> A LOC_Os08g01700-LOC_Os08g01710 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
vg0800426468 NA 1.12E-06 mr1148 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
vg0800426468 5.06E-06 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
vg0800426468 3.26E-06 8.91E-08 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
vg0800426468 NA 4.32E-06 mr1881 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
vg0800426468 NA 3.24E-06 mr1928 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
vg0800426468 NA 3.64E-07 mr1928 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
vg0800426468 7.01E-06 NA mr1746_2 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
vg0800426468 8.01E-07 1.80E-07 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