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Detailed information for vg0313045453:

Variant ID: vg0313045453 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 13045453
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.03, others allele: 0.00, population size: 182. )

Flanking Sequence (100 bp) in Reference Genome:


TAGGAATAGAAAAATCGTAGGAATATGATAGGAATGTATGTGTAAAACGGAGGATTGGAAAACACAGGAATTCTGTAGATAGGATTGGTAAACATGTGTT[T/C]
GGATAGGCAGAGGAAAAACATAGGAAATAGAAAAAATGAGGTAGGAGTGGATGGAAATTTTCCTTTGTTTCTCTATTGTTTCCACAGGAAAGGAATTTTT

Reverse complement sequence

AAAAATTCCTTTCCTGTGGAAACAATAGAGAAACAAAGGAAAATTTCCATCCACTCCTACCTCATTTTTTCTATTTCCTATGTTTTTCCTCTGCCTATCC[A/G]
AACACATGTTTACCAATCCTATCTACAGAATTCCTGTGTTTTCCAATCCTCCGTTTTACACATACATTCCTATCATATTCCTACGATTTTTCTATTCCTA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.60% 12.30% 0.06% 0.00% NA
All Indica  2759 84.80% 15.20% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 45.70% 53.90% 0.37% 0.00% NA
Indica I  595 91.10% 8.90% 0.00% 0.00% NA
Indica II  465 91.80% 8.20% 0.00% 0.00% NA
Indica III  913 77.10% 22.90% 0.00% 0.00% NA
Indica Intermediate  786 84.70% 15.30% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 87.80% 10.00% 2.22% 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
vg0313045453 T -> C LOC_Os03g22620.1 5_prime_UTR_variant ; 2565.0bp to feature; MODIFIER silent_mutation Average:32.979; most accessible tissue: Callus, score: 51.351 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0313045453 NA 1.01E-06 mr1004 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
vg0313045453 NA 2.88E-06 mr1208_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
vg0313045453 NA 8.14E-07 mr1762_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
vg0313045453 NA 7.06E-06 mr1762_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
vg0313045453 4.08E-06 NA mr1800_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