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Detailed information for vg0134092893:

Variant ID: vg0134092893 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 34092893
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATAACGGAATCCTATTTTCGAACGGGATGATCCTGTCGACGTTTGATGTCGTCATTCTGGTATTTGCATAGTATGGGGATCGTCGGTGCTAGGATATAC[G/A]
CGAGACTGAGGTAAAAGAGACGAAGACGGGGATTTTTATACAGGTTCAGGCTCCTGAGTGGTCAGGTAATGGCCCTACATCCTGTTGGCCGGAGCCGGAG

Reverse complement sequence

CTCCGGCTCCGGCCAACAGGATGTAGGGCCATTACCTGACCACTCAGGAGCCTGAACCTGTATAAAAATCCCCGTCTTCGTCTCTTTTACCTCAGTCTCG[C/T]
GTATATCCTAGCACCGACGATCCCCATACTATGCAAATACCAGAATGACGACATCAAACGTCGACAGGATCATCCCGTTCGAAAATAGGATTCCGTTATA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.80% 2.50% 3.68% 0.00% NA
All Indica  2759 89.50% 4.30% 6.23% 0.00% NA
All Japonica  1512 99.90% 0.00% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 64.20% 11.40% 24.37% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 96.60% 2.70% 0.66% 0.00% NA
Indica Intermediate  786 94.00% 3.30% 2.67% 0.00% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 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 98.90% 0.00% 1.11% 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
vg0134092893 G -> A LOC_Os01g58990.1 upstream_gene_variant ; 1716.0bp to feature; MODIFIER silent_mutation Average:39.934; most accessible tissue: Zhenshan97 root, score: 64.819 N N N N
vg0134092893 G -> A LOC_Os01g58970.1 downstream_gene_variant ; 1492.0bp to feature; MODIFIER silent_mutation Average:39.934; most accessible tissue: Zhenshan97 root, score: 64.819 N N N N
vg0134092893 G -> A LOC_Os01g58980.1 downstream_gene_variant ; 785.0bp to feature; MODIFIER silent_mutation Average:39.934; most accessible tissue: Zhenshan97 root, score: 64.819 N N N N
vg0134092893 G -> A LOC_Os01g58970-LOC_Os01g58980 intergenic_region ; MODIFIER silent_mutation Average:39.934; most accessible tissue: Zhenshan97 root, score: 64.819 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0134092893 NA 6.37E-06 mr1350 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
vg0134092893 NA 8.39E-08 mr1641 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
vg0134092893 NA 1.50E-08 mr1839 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
vg0134092893 4.07E-06 6.43E-07 mr1901 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
vg0134092893 NA 1.46E-07 mr1901 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
vg0134092893 NA 2.25E-07 mr1909 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
vg0134092893 NA 5.81E-07 mr1921 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
vg0134092893 9.23E-07 NA mr1011_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
vg0134092893 9.95E-07 1.01E-08 mr1011_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
vg0134092893 NA 5.41E-08 mr1013_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
vg0134092893 NA 2.07E-07 mr1015_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
vg0134092893 NA 1.58E-07 mr1031_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
vg0134092893 NA 7.87E-06 mr1543_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
vg0134092893 NA 1.89E-09 mr1641_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
vg0134092893 NA 3.51E-07 mr1683_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
vg0134092893 NA 5.49E-06 mr1706_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
vg0134092893 NA 5.96E-07 mr1759_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
vg0134092893 NA 7.16E-07 mr1759_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
vg0134092893 NA 8.68E-11 mr1794_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
vg0134092893 NA 7.42E-06 mr1832_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
vg0134092893 7.19E-06 7.18E-06 mr1832_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
vg0134092893 NA 3.41E-06 mr1833_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
vg0134092893 2.67E-06 2.67E-06 mr1833_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
vg0134092893 NA 6.13E-08 mr1838_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