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Detailed information for vg0806359109:

Variant ID: vg0806359109 (JBrowse)Variation Type: INDEL
Chromosome: chr08Position: 6359109
Reference Allele: AAlternative Allele: C,ACTTCC
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:


CGCCGTCGATGCTTCCTGGACCTCTCCGACCCCTTTCAGCTGCACGGTGAGACACTGCATACCCCTGAACACCCCATGCATGCACCCATATAGCCCATTC[A/C,ACTTCC]
GAGCTGTAGCTCGACACGCATGCACATACCAAGAACCACCGCCGCTGTAGCTTGTTTTTCGCGAGCTACAGACCACCGCTGTAGCTGTAGCTTGTTCATC

Reverse complement sequence

GATGAACAAGCTACAGCTACAGCGGTGGTCTGTAGCTCGCGAAAAACAAGCTACAGCGGCGGTGGTTCTTGGTATGTGCATGCGTGTCGAGCTACAGCTC[T/G,GGAAGT]
GAATGGGCTATATGGGTGCATGCATGGGGTGTTCAGGGGTATGCAGTGTCTCACCGTGCAGCTGAAAGGGGTCGGAGAGGTCCAGGAAGCATCGACGGCG

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 78.10% 5.10% 3.51% 10.52% ACTTCC: 2.77%
All Indica  2759 67.70% 7.50% 5.04% 15.55% ACTTCC: 4.24%
All Japonica  1512 99.00% 0.10% 0.26% 0.66% NA
Aus  269 72.50% 0.40% 7.06% 14.87% ACTTCC: 5.20%
Indica I  595 66.90% 16.50% 2.86% 8.74% ACTTCC: 5.04%
Indica II  465 63.00% 1.90% 3.23% 27.10% ACTTCC: 4.73%
Indica III  913 67.70% 6.00% 7.89% 15.99% ACTTCC: 2.41%
Indica Intermediate  786 71.10% 5.60% 4.45% 13.36% ACTTCC: 5.47%
Temperate Japonica  767 99.50% 0.00% 0.13% 0.39% NA
Tropical Japonica  504 98.20% 0.00% 0.60% 1.19% NA
Japonica Intermediate  241 99.20% 0.40% 0.00% 0.41% NA
VI/Aromatic  96 51.00% 32.30% 1.04% 15.62% NA
Intermediate  90 90.00% 3.30% 3.33% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0806359109 A -> C LOC_Os08g10790.1 downstream_gene_variant ; 2944.0bp to feature; MODIFIER silent_mutation Average:18.007; most accessible tissue: Callus, score: 43.373 N N N N
vg0806359109 A -> C LOC_Os08g10800.1 intron_variant ; MODIFIER silent_mutation Average:18.007; most accessible tissue: Callus, score: 43.373 N N N N
vg0806359109 A -> DEL N N silent_mutation Average:18.007; most accessible tissue: Callus, score: 43.373 N N N N
vg0806359109 A -> ACTTCC LOC_Os08g10790.1 downstream_gene_variant ; 2945.0bp to feature; MODIFIER silent_mutation Average:18.007; most accessible tissue: Callus, score: 43.373 N N N N
vg0806359109 A -> ACTTCC LOC_Os08g10800.1 intron_variant ; MODIFIER silent_mutation Average:18.007; most accessible tissue: Callus, score: 43.373 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0806359109 9.95E-08 2.73E-11 mr1038 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
vg0806359109 2.26E-09 2.81E-13 mr1038 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
vg0806359109 5.45E-08 4.34E-12 mr1389 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
vg0806359109 2.47E-09 9.89E-13 mr1389 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
vg0806359109 6.20E-08 2.14E-13 mr1038_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
vg0806359109 1.99E-09 4.72E-14 mr1038_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
vg0806359109 NA 1.28E-06 mr1057_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
vg0806359109 1.23E-06 NA mr1141_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
vg0806359109 7.20E-07 NA mr1141_2 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
vg0806359109 NA 5.88E-06 mr1220_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
vg0806359109 NA 3.15E-06 mr1266_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
vg0806359109 NA 2.55E-07 mr1389_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
vg0806359109 NA 1.70E-09 mr1389_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
vg0806359109 7.54E-07 7.53E-07 mr1906_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
vg0806359109 NA 1.19E-07 mr1909_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
vg0806359109 NA 3.85E-06 mr1924_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
vg0806359109 NA 5.35E-06 mr1951_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
vg0806359109 NA 5.89E-06 mr1960_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