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Detailed information for vg0417573231:

Variant ID: vg0417573231 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 17573231
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


CTGTGGACCAAAAGTGACATGGTGATGAAGAAGTGGACTTGGAGAATGTCTCATTTCCAATCAACTTATGTGATCTTCCATACATTCCTTATTCTTGGTC[T/C]
CTTTGCCTTACCCAAATAACTACCTCTGTAAACGAGAACAAGAACAGAGAAAACAAAAGGTGCAGTAATGTTTGATTAAATATATATCATATAAATCATA

Reverse complement sequence

TATGATTTATATGATATATATTTAATCAAACATTACTGCACCTTTTGTTTTCTCTGTTCTTGTTCTCGTTTACAGAGGTAGTTATTTGGGTAAGGCAAAG[A/G]
GACCAAGAATAAGGAATGTATGGAAGATCACATAAGTTGATTGGAAATGAGACATTCTCCAAGTCCACTTCTTCATCACCATGTCACTTTTGGTCCACAG

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 97.30% 1.90% 0.83% 0.00% NA
All Indica  2759 95.50% 3.20% 1.34% 0.00% NA
All Japonica  1512 99.80% 0.10% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 81.30% 12.80% 5.88% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 98.30% 1.40% 0.25% 0.00% NA
Temperate Japonica  767 99.60% 0.10% 0.26% 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 98.90% 1.10% 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
vg0417573231 T -> C LOC_Os04g29560-LOC_Os04g29580 intergenic_region ; MODIFIER silent_mutation Average:31.754; most accessible tissue: Callus, score: 65.776 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0417573231 NA 2.50E-06 mr1291_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
vg0417573231 NA 4.35E-06 mr1478_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
vg0417573231 NA 7.05E-08 mr1502_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
vg0417573231 NA 5.99E-07 mr1517_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
vg0417573231 NA 4.48E-08 mr1543_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