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Detailed information for vg0809946687:

Variant ID: vg0809946687 (JBrowse)Variation Type: INDEL
Chromosome: chr08Position: 9946687
Reference Allele: CAlternative Allele: T,CAAGGTG
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


CTGGGGTATAAGCCAAACGTCTTCTCCTTCGCAACTTGTCTTCAACTGAGGTTTGATTGATTATTGCAAGGTGAGTACATGGAATACTCCGCAAGCCACA[C/T,CAAGGTG]
AGCAAATAAGTAAGTGCACAAGGATACCAAAGGATGGCATAATATAGGGCTCATTTGCAAAAGCAGCATTTAGCAAACATTTGAGAATTGTAAAACAGTA

Reverse complement sequence

TACTGTTTTACAATTCTCAAATGTTTGCTAAATGCTGCTTTTGCAAATGAGCCCTATATTATGCCATCCTTTGGTATCCTTGTGCACTTACTTATTTGCT[G/A,CACCTTG]
TGTGGCTTGCGGAGTATTCCATGTACTCACCTTGCAATAATCAATCAAACCTCAGTTGAAGACAAGTTGCGAAGGAGAAGACGTTTGGCTTATACCCCAG

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 85.70% 14.20% 0.11% 0.00% NA
All Indica  2759 80.70% 19.10% 0.18% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 50.60% 49.40% 0.00% 0.00% NA
Indica I  595 63.40% 36.10% 0.50% 0.00% NA
Indica II  465 96.30% 3.70% 0.00% 0.00% NA
Indica III  913 80.40% 19.50% 0.11% 0.00% NA
Indica Intermediate  786 84.90% 15.00% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0809946687 C -> CAAGGTG LOC_Os08g16290.1 intron_variant ; MODIFIER N Average:45.346; most accessible tissue: Minghui63 young leaf, score: 58.21 N N N N
vg0809946687 C -> T LOC_Os08g16290.1 intron_variant ; MODIFIER silent_mutation Average:45.346; most accessible tissue: Minghui63 young leaf, score: 58.21 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0809946687 NA 5.96E-07 mr1072 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
vg0809946687 NA 9.95E-07 mr1124 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
vg0809946687 NA 2.76E-12 mr1222 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
vg0809946687 NA 3.91E-06 mr1222 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
vg0809946687 NA 1.30E-07 mr1861 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
vg0809946687 NA 3.52E-07 mr1962 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
vg0809946687 NA 1.96E-10 mr1222_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
vg0809946687 NA 4.86E-06 mr1222_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