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Detailed information for vg0102330722:

Variant ID: vg0102330722 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 2330722
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GATTAGCTCTAATCTTTAGCAGATTCTGGCTCTGTCACTGGTTAAAAGTACAGAGGATCTTGCTAACACCATTGTTCCAGTAACTTTTGAGTATAACAGT[A/G]
AAGTCCCGCACTGATGCTCCTCATTCTTGTCTAGATTTGCCCAGTCGGCCCAAACTGAAATTTCCCGATGTCTCTCATGCTTAATTACATAATAGTTACA

Reverse complement sequence

TGTAACTATTATGTAATTAAGCATGAGAGACATCGGGAAATTTCAGTTTGGGCCGACTGGGCAAATCTAGACAAGAATGAGGAGCATCAGTGCGGGACTT[T/C]
ACTGTTATACTCAAAAGTTACTGGAACAATGGTGTTAGCAAGATCCTCTGTACTTTTAACCAGTGACAGAGCCAGAATCTGCTAAAGATTAGAGCTAATC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.60% 1.00% 0.47% 0.00% NA
All Indica  2759 99.90% 0.00% 0.07% 0.00% NA
All Japonica  1512 96.80% 2.10% 1.12% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.00% 0.25% 0.00% NA
Temperate Japonica  767 95.80% 2.30% 1.83% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 93.40% 5.40% 1.24% 0.00% NA
VI/Aromatic  96 83.30% 15.60% 1.04% 0.00% NA
Intermediate  90 97.80% 0.00% 2.22% 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
vg0102330722 A -> G LOC_Os01g04970.1 downstream_gene_variant ; 1866.0bp to feature; MODIFIER silent_mutation Average:34.855; most accessible tissue: Callus, score: 83.454 N N N N
vg0102330722 A -> G LOC_Os01g04970-LOC_Os01g04980 intergenic_region ; MODIFIER silent_mutation Average:34.855; most accessible tissue: Callus, score: 83.454 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0102330722 1.76E-06 1.76E-06 mr1389 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
vg0102330722 1.37E-08 1.37E-08 mr1024_2 Jap_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
vg0102330722 1.41E-11 1.45E-10 mr1038_2 Jap_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
vg0102330722 3.24E-06 3.24E-06 mr1191_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
vg0102330722 3.01E-07 3.01E-07 mr1367_2 Jap_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
vg0102330722 NA 7.42E-08 mr1565_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
vg0102330722 NA 7.27E-06 mr1842_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