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Detailed information for vg0103188289:

Variant ID: vg0103188289 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 3188289
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.72, T: 0.27, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


TTTACATGCGTAATCTGTAATTTATTTTGTTATTAGTCTACGTTTAATACTTCAAATGTGTGTTTGTATACTTCAAACTTAGGCTGTGTTTAGTTCACGC[T/C]
AAAATTGAAAGTTTGGTTGAAATTGGAACGATGTGACGGAAAAGTTTAAAGTTTGTGTGTGTAGAAAAGTTTTGATGTGATGAAAAAGTTGAAAGTTTGA

Reverse complement sequence

TCAAACTTTCAACTTTTTCATCACATCAAAACTTTTCTACACACACAAACTTTAAACTTTTCCGTCACATCGTTCCAATTTCAACCAAACTTTCAATTTT[A/G]
GCGTGAACTAAACACAGCCTAAGTTTGAAGTATACAAACACACATTTGAAGTATTAAACGTAGACTAATAACAAAATAAATTACAGATTACGCATGTAAA

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 26.40% 14.80% 0.72% 58.06% NA
All Indica  2759 4.30% 7.40% 0.91% 87.35% NA
All Japonica  1512 72.20% 12.00% 0.40% 15.34% NA
Aus  269 3.30% 89.60% 0.00% 7.06% NA
Indica I  595 1.50% 4.00% 0.84% 93.61% NA
Indica II  465 2.80% 7.50% 1.29% 88.39% NA
Indica III  913 6.80% 10.00% 0.77% 82.48% NA
Indica Intermediate  786 4.50% 7.00% 0.89% 87.66% NA
Temperate Japonica  767 65.40% 17.30% 0.65% 16.56% NA
Tropical Japonica  504 81.50% 3.00% 0.00% 15.48% NA
Japonica Intermediate  241 74.30% 14.10% 0.41% 11.20% NA
VI/Aromatic  96 1.00% 52.10% 0.00% 46.88% NA
Intermediate  90 31.10% 23.30% 3.33% 42.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0103188289 T -> DEL N N silent_mutation Average:11.591; most accessible tissue: Callus, score: 59.674 N N N N
vg0103188289 T -> C LOC_Os01g06730.1 downstream_gene_variant ; 2943.0bp to feature; MODIFIER silent_mutation Average:11.591; most accessible tissue: Callus, score: 59.674 N N N N
vg0103188289 T -> C LOC_Os01g06740.1 downstream_gene_variant ; 468.0bp to feature; MODIFIER silent_mutation Average:11.591; most accessible tissue: Callus, score: 59.674 N N N N
vg0103188289 T -> C LOC_Os01g06730-LOC_Os01g06740 intergenic_region ; MODIFIER silent_mutation Average:11.591; most accessible tissue: Callus, score: 59.674 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0103188289 NA 4.83E-09 mr1005 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
vg0103188289 NA 5.04E-06 mr1101 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
vg0103188289 8.74E-06 8.74E-06 mr1317 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
vg0103188289 8.77E-06 8.77E-06 mr1589 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
vg0103188289 2.79E-06 3.20E-07 mr1897 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
vg0103188289 NA 1.98E-08 mr1321_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
vg0103188289 NA 2.75E-07 mr1749_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