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Detailed information for vg0920091049:

Variant ID: vg0920091049 (JBrowse)Variation Type: INDEL
Chromosome: chr09Position: 20091049
Reference Allele: TAlternative Allele: A,TA
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.87, T: 0.13, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


AAGGGTGGATGGAACACCTTCAATAGAGAATCCTTCTTCGCGTTGAATTTCAATTAGAAAAATAGATTCATAAAAGACCATCATCTACATATATTTTTTT[T/A,TA]
AAAAAAGAACTTTTGTAAAACTTGACGTGCCATCATACTTGTAGTAAGATGCAATAAAGAAAATGACTCTAGAGGGTTTGCTTGAGTAAGTATCTGGCAG

Reverse complement sequence

CTGCCAGATACTTACTCAAGCAAACCCTCTAGAGTCATTTTCTTTATTGCATCTTACTACAAGTATGATGGCACGTCAAGTTTTACAAAAGTTCTTTTTT[A/T,TA]
AAAAAAATATATGTAGATGATGGTCTTTTATGAATCTATTTTTCTAATTGAAATTCAACGCGAAGAAGGATTCTCTATTGAAGGTGTTCCATCCACCCTT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 63.70% 36.00% 0.11% 0.00% TA: 0.23%
All Indica  2759 94.00% 5.40% 0.18% 0.00% TA: 0.36%
All Japonica  1512 10.40% 89.60% 0.00% 0.00% TA: 0.07%
Aus  269 72.50% 27.50% 0.00% 0.00% NA
Indica I  595 95.50% 3.90% 0.34% 0.00% TA: 0.34%
Indica II  465 93.30% 5.60% 0.22% 0.00% TA: 0.86%
Indica III  913 96.90% 2.70% 0.00% 0.00% TA: 0.33%
Indica Intermediate  786 89.90% 9.70% 0.25% 0.00% TA: 0.13%
Temperate Japonica  767 12.10% 87.70% 0.00% 0.00% TA: 0.13%
Tropical Japonica  504 1.80% 98.20% 0.00% 0.00% NA
Japonica Intermediate  241 22.80% 77.20% 0.00% 0.00% NA
VI/Aromatic  96 29.20% 70.80% 0.00% 0.00% NA
Intermediate  90 38.90% 61.10% 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
vg0920091049 T -> TA LOC_Os09g34040.1 upstream_gene_variant ; 457.0bp to feature; MODIFIER silent_mutation Average:64.441; most accessible tissue: Callus, score: 87.5 N N N N
vg0920091049 T -> TA LOC_Os09g34050.1 upstream_gene_variant ; 313.0bp to feature; MODIFIER silent_mutation Average:64.441; most accessible tissue: Callus, score: 87.5 N N N N
vg0920091049 T -> TA LOC_Os09g34060.1 downstream_gene_variant ; 3072.0bp to feature; MODIFIER silent_mutation Average:64.441; most accessible tissue: Callus, score: 87.5 N N N N
vg0920091049 T -> TA LOC_Os09g34040-LOC_Os09g34050 intergenic_region ; MODIFIER silent_mutation Average:64.441; most accessible tissue: Callus, score: 87.5 N N N N
vg0920091049 T -> A LOC_Os09g34040.1 upstream_gene_variant ; 456.0bp to feature; MODIFIER silent_mutation Average:64.441; most accessible tissue: Callus, score: 87.5 N N N N
vg0920091049 T -> A LOC_Os09g34050.1 upstream_gene_variant ; 314.0bp to feature; MODIFIER silent_mutation Average:64.441; most accessible tissue: Callus, score: 87.5 N N N N
vg0920091049 T -> A LOC_Os09g34060.1 downstream_gene_variant ; 3073.0bp to feature; MODIFIER silent_mutation Average:64.441; most accessible tissue: Callus, score: 87.5 N N N N
vg0920091049 T -> A LOC_Os09g34040-LOC_Os09g34050 intergenic_region ; MODIFIER silent_mutation Average:64.441; most accessible tissue: Callus, score: 87.5 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0920091049 NA 6.25E-09 mr1050 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
vg0920091049 NA 4.90E-08 mr1220 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
vg0920091049 NA 5.57E-11 mr1272 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
vg0920091049 NA 9.47E-18 mr1324 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
vg0920091049 NA 6.48E-12 mr1325 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
vg0920091049 NA 1.49E-13 mr1326 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
vg0920091049 NA 5.39E-15 mr1335 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
vg0920091049 NA 4.60E-20 mr1518 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
vg0920091049 NA 2.87E-07 mr1518 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
vg0920091049 NA 6.33E-07 mr1532 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
vg0920091049 NA 8.97E-08 mr1660 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
vg0920091049 NA 9.48E-24 mr1676 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
vg0920091049 NA 1.83E-07 mr1676 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
vg0920091049 NA 1.20E-06 mr1677 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
vg0920091049 NA 2.12E-06 mr1681 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
vg0920091049 9.10E-07 NA mr1879 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
vg0920091049 NA 7.48E-15 mr1950 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
vg0920091049 NA 6.74E-09 mr1986 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
vg0920091049 NA 7.72E-06 mr1064_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
vg0920091049 2.82E-06 NA mr1071_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
vg0920091049 7.77E-06 NA mr1080_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
vg0920091049 1.62E-06 8.84E-08 mr1100_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
vg0920091049 2.96E-08 3.15E-09 mr1203_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
vg0920091049 NA 6.64E-07 mr1623_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
vg0920091049 8.42E-07 9.28E-26 mr1676_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
vg0920091049 2.73E-11 2.64E-14 mr1676_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