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Detailed information for vg0823588721:

Variant ID: vg0823588721 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 23588721
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCTCCAAATTTTTTTCCTTAGTTAATGGCCTATATGCATGCATGCCTTATATTATGGAACATCTTAAAAAAGTGGTTGTGCCTTATATTATGGAATGGAG[G/A]
GAGTACTACTAGAACCAGAATAGGATAATAATTCTAAATTTATATCCATGTAATTTTGGCCCTTTTGTCAATCAGAATCATGGTCAGAACAAGCTTGTTT

Reverse complement sequence

AAACAAGCTTGTTCTGACCATGATTCTGATTGACAAAAGGGCCAAAATTACATGGATATAAATTTAGAATTATTATCCTATTCTGGTTCTAGTAGTACTC[C/T]
CTCCATTCCATAATATAAGGCACAACCACTTTTTTAAGATGTTCCATAATATAAGGCATGCATGCATATAGGCCATTAACTAAGGAAAAAAATTTGGAGG

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 94.70% 5.10% 0.19% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 84.30% 15.10% 0.60% 0.00% NA
Aus  269 98.10% 1.90% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 97.40% 2.10% 0.52% 0.00% NA
Tropical Japonica  504 60.50% 38.50% 0.99% 0.00% NA
Japonica Intermediate  241 92.50% 7.50% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0823588721 G -> A LOC_Os08g37340.1 upstream_gene_variant ; 1350.0bp to feature; MODIFIER silent_mutation Average:79.526; most accessible tissue: Callus, score: 94.535 N N N N
vg0823588721 G -> A LOC_Os08g37345.1 downstream_gene_variant ; 882.0bp to feature; MODIFIER silent_mutation Average:79.526; most accessible tissue: Callus, score: 94.535 N N N N
vg0823588721 G -> A LOC_Os08g37350.1 downstream_gene_variant ; 4971.0bp to feature; MODIFIER silent_mutation Average:79.526; most accessible tissue: Callus, score: 94.535 N N N N
vg0823588721 G -> A LOC_Os08g37340-LOC_Os08g37345 intergenic_region ; MODIFIER silent_mutation Average:79.526; most accessible tissue: Callus, score: 94.535 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0823588721 NA 1.94E-08 mr1248 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
vg0823588721 NA 9.96E-09 mr1248 Jap_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
vg0823588721 NA 3.35E-15 mr1410 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
vg0823588721 NA 1.90E-06 mr1510 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
vg0823588721 NA 5.41E-29 mr1699 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
vg0823588721 NA 9.68E-12 mr1769 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
vg0823588721 NA 1.51E-13 mr1769 Jap_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
vg0823588721 NA 2.22E-14 mr1410_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
vg0823588721 4.04E-06 NA mr1448_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
vg0823588721 NA 9.86E-06 mr1498_2 Jap_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
vg0823588721 NA 2.26E-06 mr1553_2 Jap_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
vg0823588721 NA 2.74E-13 mr1769_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
vg0823588721 NA 3.54E-13 mr1769_2 Jap_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