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Detailed information for vg0123679747:

Variant ID: vg0123679747 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 23679747
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, T: 0.02, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


AGCTTTTATACATATTTTGATTAAATCTCAACCCTTATAGTCTAGATCTACTATGATCTAACGATATAGGTTTTTTCTTTTTCTCCGATTAATGTGAAAA[A/T]
TTCTAAACTTGTCCCATCCAACCAAAACCTTATCGTCTAGATCTACTATGATCTGACGATATAGATTTTTTCATTTTCTCCGATTAACGTGGAAATTTCT

Reverse complement sequence

AGAAATTTCCACGTTAATCGGAGAAAATGAAAAAATCTATATCGTCAGATCATAGTAGATCTAGACGATAAGGTTTTGGTTGGATGGGACAAGTTTAGAA[T/A]
TTTTCACATTAATCGGAGAAAAAGAAAAAACCTATATCGTTAGATCATAGTAGATCTAGACTATAAGGGTTGAGATTTAATCAAAATATGTATAAAAGCT

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 83.10% 16.40% 0.02% 0.49% NA
All Indica  2759 77.40% 21.80% 0.00% 0.83% NA
All Japonica  1512 91.50% 8.50% 0.00% 0.00% NA
Aus  269 91.80% 8.20% 0.00% 0.00% NA
Indica I  595 90.90% 9.10% 0.00% 0.00% NA
Indica II  465 66.70% 32.50% 0.00% 0.86% NA
Indica III  913 72.70% 25.60% 0.00% 1.64% NA
Indica Intermediate  786 78.90% 20.60% 0.00% 0.51% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 77.40% 22.60% 0.00% 0.00% NA
Japonica Intermediate  241 95.00% 5.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 73.30% 25.60% 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
vg0123679747 A -> T LOC_Os01g41810.1 upstream_gene_variant ; 3878.0bp to feature; MODIFIER silent_mutation Average:40.381; most accessible tissue: Callus, score: 70.04 N N N N
vg0123679747 A -> T LOC_Os01g41820.1 downstream_gene_variant ; 2635.0bp to feature; MODIFIER silent_mutation Average:40.381; most accessible tissue: Callus, score: 70.04 N N N N
vg0123679747 A -> T LOC_Os01g41810-LOC_Os01g41820 intergenic_region ; MODIFIER silent_mutation Average:40.381; most accessible tissue: Callus, score: 70.04 N N N N
vg0123679747 A -> DEL N N silent_mutation Average:40.381; most accessible tissue: Callus, score: 70.04 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0123679747 4.12E-06 4.12E-06 mr1473 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
vg0123679747 9.78E-07 9.78E-07 mr1664 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
vg0123679747 3.28E-06 3.28E-06 mr1834 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
vg0123679747 NA 9.70E-06 mr1561_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
vg0123679747 NA 2.07E-06 mr1795_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
vg0123679747 NA 8.57E-07 mr1875_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
vg0123679747 NA 1.12E-06 mr1908_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