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Detailed information for vg0123633011:

Variant ID: vg0123633011 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 23633011
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.78, G: 0.23, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:


GCATTTTGAAGAAATTGAGGAAATATACCTGAAAGTTCATTGTGGTTCAAGGCAAGACTGAGCATACTAGAACCAAATTTATCTGCAGAGTTTGTATTGG[T/G]
CATATCTGACTGTTTCCAGCATTGCATTTGTTCAAGATCTCCTGTTATTTTGTTTCCTGACAGGTCCAAACGTTTCAAACCAGTCAATTGGCACATGGAT

Reverse complement sequence

ATCCATGTGCCAATTGACTGGTTTGAAACGTTTGGACCTGTCAGGAAACAAAATAACAGGAGATCTTGAACAAATGCAATGCTGGAAACAGTCAGATATG[A/C]
CCAATACAAACTCTGCAGATAAATTTGGTTCTAGTATGCTCAGTCTTGCCTTGAACCACAATGAACTTTCAGGTATATTTCCTCAATTTCTTCAAAATGC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 48.30% 39.90% 1.14% 10.62% NA
All Indica  2759 47.20% 51.00% 0.98% 0.91% NA
All Japonica  1512 57.00% 13.60% 0.93% 28.51% NA
Aus  269 11.50% 88.10% 0.37% 0.00% NA
Indica I  595 9.60% 88.70% 1.68% 0.00% NA
Indica II  465 41.30% 57.00% 0.22% 1.51% NA
Indica III  913 75.40% 22.50% 1.31% 0.88% NA
Indica Intermediate  786 46.30% 51.90% 0.51% 1.27% NA
Temperate Japonica  767 70.10% 1.00% 0.52% 28.29% NA
Tropical Japonica  504 34.90% 27.20% 0.99% 36.90% NA
Japonica Intermediate  241 61.40% 24.90% 2.07% 11.62% NA
VI/Aromatic  96 36.50% 15.60% 9.38% 38.54% NA
Intermediate  90 58.90% 27.80% 3.33% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0123633011 T -> G LOC_Os01g41750.1 missense_variant ; p.Thr789Pro; MODERATE nonsynonymous_codon ; T789P Average:44.792; most accessible tissue: Callus, score: 79.982 unknown unknown TOLERATED 0.31
vg0123633011 T -> DEL LOC_Os01g41750.1 N frameshift_variant Average:44.792; most accessible tissue: Callus, score: 79.982 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0123633011 NA 5.47E-06 mr1100 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
vg0123633011 NA 7.07E-07 mr1164 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
vg0123633011 4.77E-06 4.77E-06 mr1773 Jap_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
vg0123633011 NA 8.33E-08 mr1100_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
vg0123633011 NA 4.20E-09 mr1380_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
vg0123633011 NA 9.30E-06 mr1561_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
vg0123633011 NA 1.26E-09 mr1561_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
vg0123633011 NA 4.88E-07 mr1795_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
vg0123633011 NA 1.28E-07 mr1875_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
vg0123633011 NA 6.70E-09 mr1908_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
vg0123633011 NA 1.87E-08 mr1996_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