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Detailed information for vg0419360666:

Variant ID: vg0419360666 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 19360666
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


TTTCTTTACATGTGGGCTAGCTTGTTAACTTTGTATGATCCCCTGATAGGAATAAGTCCACTTTGACTCCCACAATTACAAGTGCAATCTGATTCATATC[C/T]
CTTAACCAAAATAAAGATATTTTGACCCCTCAAAAATGACACCTCCAGTGGTTTTGAAGGTGGTTTTCGCTGACGTGTCGAATTGACTTGTCTCTGAGTG

Reverse complement sequence

CACTCAGAGACAAGTCAATTCGACACGTCAGCGAAAACCACCTTCAAAACCACTGGAGGTGTCATTTTTGAGGGGTCAAAATATCTTTATTTTGGTTAAG[G/A]
GATATGAATCAGATTGCACTTGTAATTGTGGGAGTCAAAGTGGACTTATTCCTATCAGGGGATCATACAAAGTTAACAAGCTAGCCCACATGTAAAGAAA

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 94.40% 4.10% 1.59% 0.00% NA
All Indica  2759 90.40% 6.90% 2.68% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 69.40% 21.20% 9.41% 0.00% NA
Indica II  465 95.70% 3.00% 1.29% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 92.10% 6.40% 1.53% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 2.20% 1.11% 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
vg0419360666 C -> T LOC_Os04g32300.1 downstream_gene_variant ; 3859.0bp to feature; MODIFIER silent_mutation Average:44.301; most accessible tissue: Zhenshan97 young leaf, score: 66.32 N N N N
vg0419360666 C -> T LOC_Os04g32300-LOC_Os04g32310 intergenic_region ; MODIFIER silent_mutation Average:44.301; most accessible tissue: Zhenshan97 young leaf, score: 66.32 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0419360666 NA 5.01E-08 mr1038 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
vg0419360666 NA 6.99E-08 mr1038 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
vg0419360666 6.81E-08 1.83E-11 mr1389 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
vg0419360666 7.06E-07 7.47E-10 mr1389 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
vg0419360666 3.43E-06 NA mr1644 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
vg0419360666 1.37E-10 4.65E-15 mr1038_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
vg0419360666 1.37E-09 1.73E-13 mr1038_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
vg0419360666 7.32E-08 NA mr1141_2 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
vg0419360666 5.75E-07 NA mr1141_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
vg0419360666 1.29E-08 1.05E-12 mr1389_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
vg0419360666 6.67E-08 5.99E-12 mr1389_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