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Detailed information for vg1213914027:

Variant ID: vg1213914027 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 13914027
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.86, T: 0.13, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


TCAGGATGGCGTTTAACGACGATGAGAAGCCTGCTACTACTCCAATTCCGAATGGAGGTATCGTCTTAATTCCATCAGCCTTCCATTGATGCATTACATA[C/T]
TGGAATACATACCGTTTGCCGCAATTTCGAAATGATCCTGCATTGAGGCGGATTCAATACATGTATATATGATGTGCAGGGAGCAAACAGGGCCTCGTGA

Reverse complement sequence

TCACGAGGCCCTGTTTGCTCCCTGCACATCATATATACATGTATTGAATCCGCCTCAATGCAGGATCATTTCGAAATTGCGGCAAACGGTATGTATTCCA[G/A]
TATGTAATGCATCAATGGAAGGCTGATGGAATTAAGACGATACCTCCATTCGGAATTGGAGTAGTAGCAGGCTTCTCATCGTCGTTAAACGCCATCCTGA

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 50.00% 49.80% 0.15% 0.00% NA
All Indica  2759 50.30% 49.50% 0.11% 0.00% NA
All Japonica  1512 60.30% 39.70% 0.07% 0.00% NA
Aus  269 3.00% 97.00% 0.00% 0.00% NA
Indica I  595 44.20% 55.80% 0.00% 0.00% NA
Indica II  465 56.60% 43.40% 0.00% 0.00% NA
Indica III  913 46.80% 53.10% 0.11% 0.00% NA
Indica Intermediate  786 55.50% 44.30% 0.25% 0.00% NA
Temperate Japonica  767 88.30% 11.70% 0.00% 0.00% NA
Tropical Japonica  504 16.90% 82.90% 0.20% 0.00% NA
Japonica Intermediate  241 61.80% 38.20% 0.00% 0.00% NA
VI/Aromatic  96 5.20% 94.80% 0.00% 0.00% NA
Intermediate  90 57.80% 38.90% 3.33% 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
vg1213914027 C -> T LOC_Os12g24400.1 upstream_gene_variant ; 3384.0bp to feature; MODIFIER silent_mutation Average:75.171; most accessible tissue: Callus, score: 90.748 N N N N
vg1213914027 C -> T LOC_Os12g24390.1 intron_variant ; MODIFIER silent_mutation Average:75.171; most accessible tissue: Callus, score: 90.748 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1213914027 NA 1.76E-07 mr1190 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
vg1213914027 NA 1.39E-06 mr1207 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
vg1213914027 NA 3.52E-06 mr1209 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
vg1213914027 NA 2.44E-06 mr1308 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
vg1213914027 NA 2.47E-06 mr1460 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
vg1213914027 NA 6.37E-06 mr1606 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
vg1213914027 NA 2.44E-06 mr1633 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
vg1213914027 NA 9.68E-06 mr1700 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
vg1213914027 NA 5.54E-08 mr1706 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
vg1213914027 NA 1.10E-08 mr1866 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