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Detailed information for vg0401819705:

Variant ID: vg0401819705 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 1819705
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 127. )

Flanking Sequence (100 bp) in Reference Genome:


ATGGGGGTAAGATAATACAAAAGAGTTACGTTGATCTCTGTGTTTACAAACAGACGTCATCTATGACGTATGCAGCCAAATCTCGAAATCTTATGCATAA[C/T]
TAAAATAAAAATATGCAAAAAAAATATTAAGATTTAGTATGTAAAAACATACTAGTAGACGATTTTCATGAAAAATAACATCGTGTAGTTATATTCTAAT

Reverse complement sequence

ATTAGAATATAACTACACGATGTTATTTTTCATGAAAATCGTCTACTAGTATGTTTTTACATACTAAATCTTAATATTTTTTTTGCATATTTTTATTTTA[G/A]
TTATGCATAAGATTTCGAGATTTGGCTGCATACGTCATAGATGACGTCTGTTTGTAAACACAGAGATCAACGTAACTCTTTTGTATTATCTTACCCCCAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 83.80% 15.50% 0.68% 0.00% NA
All Indica  2759 73.00% 25.90% 1.12% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 34.60% 61.70% 3.70% 0.00% NA
Indica II  465 79.80% 19.40% 0.86% 0.00% NA
Indica III  913 90.00% 10.00% 0.00% 0.00% NA
Indica Intermediate  786 78.10% 21.20% 0.64% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 85.60% 13.30% 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
vg0401819705 C -> T LOC_Os04g03980.1 upstream_gene_variant ; 3632.0bp to feature; MODIFIER silent_mutation Average:54.3; most accessible tissue: Callus, score: 85.855 N N N N
vg0401819705 C -> T LOC_Os04g03980-LOC_Os04g03990 intergenic_region ; MODIFIER silent_mutation Average:54.3; most accessible tissue: Callus, score: 85.855 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0401819705 NA 3.73E-06 mr1201 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
vg0401819705 NA 7.07E-07 mr1274 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
vg0401819705 NA 2.05E-08 mr1565 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
vg0401819705 NA 5.93E-07 mr1728 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
vg0401819705 NA 9.22E-06 mr1201_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
vg0401819705 NA 2.04E-06 mr1201_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
vg0401819705 2.11E-06 7.23E-12 mr1565_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