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Detailed information for vg1217954689:

Variant ID: vg1217954689 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 17954689
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.85, A: 0.15, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


TGGATTTTGCACATTCACTTCCATCTATGTGACTGTTTGTCTAGGAGGGGCAGTTATCATGCATGAAAGATTCCAAAGGTAGCGCAAAGCTTTATGGTAA[A/C]
AATAGGAATAATGATATGATGGAAAGAAGACCATGAGGTATGAAAAGAATAGGAACAACAAAAATATGACGCGGGGTAGGAATGACGCCATATGCAGCAT

Reverse complement sequence

ATGCTGCATATGGCGTCATTCCTACCCCGCGTCATATTTTTGTTGTTCCTATTCTTTTCATACCTCATGGTCTTCTTTCCATCATATCATTATTCCTATT[T/G]
TTACCATAAAGCTTTGCGCTACCTTTGGAATCTTTCATGCATGATAACTGCCCCTCCTAGACAAACAGTCACATAGATGGAAGTGAATGTGCAAAATCCA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 71.80% 28.20% 0.06% 0.00% NA
All Indica  2759 78.80% 21.20% 0.07% 0.00% NA
All Japonica  1512 52.70% 47.20% 0.07% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 68.40% 31.40% 0.17% 0.00% NA
Indica II  465 78.10% 21.70% 0.22% 0.00% NA
Indica III  913 88.10% 11.90% 0.00% 0.00% NA
Indica Intermediate  786 76.20% 23.80% 0.00% 0.00% NA
Temperate Japonica  767 29.90% 70.10% 0.00% 0.00% NA
Tropical Japonica  504 77.80% 22.00% 0.20% 0.00% NA
Japonica Intermediate  241 73.00% 27.00% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 67.80% 32.20% 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
vg1217954689 A -> C LOC_Os12g30020.1 upstream_gene_variant ; 1092.0bp to feature; MODIFIER silent_mutation Average:49.058; most accessible tissue: Callus, score: 75.72 N N N N
vg1217954689 A -> C LOC_Os12g30020.2 upstream_gene_variant ; 1092.0bp to feature; MODIFIER silent_mutation Average:49.058; most accessible tissue: Callus, score: 75.72 N N N N
vg1217954689 A -> C LOC_Os12g30000-LOC_Os12g30020 intergenic_region ; MODIFIER silent_mutation Average:49.058; most accessible tissue: Callus, score: 75.72 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1217954689 NA 1.95E-07 mr1088 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
vg1217954689 NA 1.12E-07 mr1104 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
vg1217954689 NA 1.61E-06 mr1107 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
vg1217954689 NA 1.42E-07 mr1193 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
vg1217954689 NA 1.11E-07 mr1246 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
vg1217954689 NA 1.87E-07 mr1280 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
vg1217954689 NA 5.89E-06 mr1518 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
vg1217954689 NA 1.27E-06 mr1577 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
vg1217954689 NA 3.04E-06 mr1620 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
vg1217954689 NA 4.29E-06 mr1631 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
vg1217954689 1.58E-06 2.73E-07 mr1645 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
vg1217954689 NA 5.76E-07 mr1788 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
vg1217954689 NA 6.13E-06 mr1805 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
vg1217954689 NA 2.30E-06 mr1015_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
vg1217954689 NA 1.30E-07 mr1180_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