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Detailed information for vg0123634452:

Variant ID: vg0123634452 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 23634452
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 74. )

Flanking Sequence (100 bp) in Reference Genome:


TGTTGCCATCCATTAGCAATACTTGCAAATTACACATATTCTCTAAGGTCTTCGGAAACAAACCAACAATAGAACTGTAACTTAGATCTAAGACACGTAG[G/A]
GCAGACATGTTACCCAATCTATCAGGGATAGGTTCTGCAGGTGCAAACCATGCATATTCTGAGAGATAAAGCTCCTCGAGGCTAGTGAGATCCCAAAACC

Reverse complement sequence

GGTTTTGGGATCTCACTAGCCTCGAGGAGCTTTATCTCTCAGAATATGCATGGTTTGCACCTGCAGAACCTATCCCTGATAGATTGGGTAACATGTCTGC[C/T]
CTACGTGTCTTAGATCTAAGTTACAGTTCTATTGTTGGTTTGTTTCCGAAGACCTTAGAGAATATGTGTAATTTGCAAGTATTGCTAATGGATGGCAACA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 57.20% 30.80% 0.61% 11.36% NA
All Indica  2759 63.60% 35.50% 0.22% 0.65% NA
All Japonica  1512 36.60% 28.80% 1.19% 33.33% NA
Aus  269 98.10% 0.70% 1.12% 0.00% NA
Indica I  595 96.00% 4.00% 0.00% 0.00% NA
Indica II  465 60.40% 37.80% 0.22% 1.51% NA
Indica III  913 46.90% 52.70% 0.22% 0.22% NA
Indica Intermediate  786 60.40% 38.00% 0.38% 1.15% NA
Temperate Japonica  767 27.10% 43.90% 0.78% 28.16% NA
Tropical Japonica  504 41.70% 6.90% 1.59% 49.80% NA
Japonica Intermediate  241 56.40% 26.60% 1.66% 15.35% NA
VI/Aromatic  96 96.90% 0.00% 0.00% 3.12% NA
Intermediate  90 42.20% 42.20% 2.22% 13.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0123634452 G -> A LOC_Os01g41750.1 synonymous_variant ; p.Ala308Ala; LOW synonymous_codon Average:56.863; most accessible tissue: Callus, score: 87.243 N N N N
vg0123634452 G -> DEL LOC_Os01g41750.1 N frameshift_variant Average:56.863; most accessible tissue: Callus, score: 87.243 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0123634452 NA 9.42E-06 mr1072 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
vg0123634452 NA 3.57E-07 mr1861 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
vg0123634452 NA 8.88E-08 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
vg0123634452 NA 6.38E-08 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
vg0123634452 NA 8.70E-06 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
vg0123634452 NA 8.77E-07 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
vg0123634452 NA 2.46E-06 mr1977_2 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
vg0123634452 NA 6.24E-07 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