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Detailed information for vg0401056244:

Variant ID: vg0401056244 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 1056244
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.76, C: 0.25, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


TCTCTGAAAGCGAACTACCTTCCGTGCCAGCTCTCTCTGTCATTTCACATGTCATGTTCAGCCTTCTGAGGTCTCACTTACAACTTATTCAATCAAGATA[T/C]
CTTTATCTATACTACTATAAAAGACAAAATGTTTTACAAATAAGCTCCTGATATTTTTATGTAATAGTCTAATGTTTGTTTGAATAAAGTGAGTAACTTA

Reverse complement sequence

TAAGTTACTCACTTTATTCAAACAAACATTAGACTATTACATAAAAATATCAGGAGCTTATTTGTAAAACATTTTGTCTTTTATAGTAGTATAGATAAAG[A/G]
TATCTTGATTGAATAAGTTGTAAGTGAGACCTCAGAAGGCTGAACATGACATGTGAAATGACAGAGAGAGCTGGCACGGAAGGTAGTTCGCTTTCAGAGA

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 52.70% 47.10% 0.19% 0.00% NA
All Indica  2759 75.20% 24.60% 0.22% 0.00% NA
All Japonica  1512 7.20% 92.70% 0.13% 0.00% NA
Aus  269 93.30% 6.70% 0.00% 0.00% NA
Indica I  595 93.10% 6.90% 0.00% 0.00% NA
Indica II  465 68.20% 31.20% 0.65% 0.00% NA
Indica III  913 71.90% 28.10% 0.00% 0.00% NA
Indica Intermediate  786 69.70% 29.90% 0.38% 0.00% NA
Temperate Japonica  767 6.10% 93.60% 0.26% 0.00% NA
Tropical Japonica  504 10.50% 89.50% 0.00% 0.00% NA
Japonica Intermediate  241 3.70% 96.30% 0.00% 0.00% NA
VI/Aromatic  96 14.60% 84.40% 1.04% 0.00% NA
Intermediate  90 45.60% 54.40% 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
vg0401056244 T -> C LOC_Os04g02730.1 downstream_gene_variant ; 2240.0bp to feature; MODIFIER silent_mutation Average:64.493; most accessible tissue: Callus, score: 84.651 N N N N
vg0401056244 T -> C LOC_Os04g02754.1 intron_variant ; MODIFIER silent_mutation Average:64.493; most accessible tissue: Callus, score: 84.651 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0401056244 NA 7.07E-07 mr1298_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
vg0401056244 NA 4.34E-06 mr1318_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
vg0401056244 7.39E-07 7.39E-07 mr1377_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
vg0401056244 NA 4.79E-07 mr1545_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
vg0401056244 NA 4.03E-06 mr1702_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
vg0401056244 8.64E-06 4.58E-08 mr1713_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
vg0401056244 NA 9.16E-07 mr1731_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
vg0401056244 NA 2.08E-06 mr1735_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
vg0401056244 NA 5.34E-06 mr1788_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
vg0401056244 NA 9.36E-06 mr1924_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