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Detailed information for vg0605295746:

Variant ID: vg0605295746 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 5295746
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


AGATCATCCCAATTTTGTCCAGAGAAAGCTTTGCTTATTACTTTCTAGTAGATAGATTCAGTGTTATCTTCTAGACTTGTATCACTTCAGTATTTGCATT[C/T]
TTTTTTTGTTGTCTGAATAGATTAGATATTGTAGATGAAAAGTACATACAATTGATAATGTTCATTGCAGGATTGGAAAGAAGAAAGAAGATTGCGGTCC

Reverse complement sequence

GGACCGCAATCTTCTTTCTTCTTTCCAATCCTGCAATGAACATTATCAATTGTATGTACTTTTCATCTACAATATCTAATCTATTCAGACAACAAAAAAA[G/A]
AATGCAAATACTGAAGTGATACAAGTCTAGAAGATAACACTGAATCTATCTACTAGAAAGTAATAAGCAAAGCTTTCTCTGGACAAAATTGGGATGATCT

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 89.40% 10.60% 0.00% 0.00% NA
All Indica  2759 82.00% 18.00% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 66.40% 33.60% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 79.60% 20.40% 0.00% 0.00% NA
Indica Intermediate  786 86.30% 13.70% 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  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0605295746 C -> T LOC_Os06g10310.1 upstream_gene_variant ; 4390.0bp to feature; MODIFIER silent_mutation Average:36.675; most accessible tissue: Callus, score: 76.484 N N N N
vg0605295746 C -> T LOC_Os06g10290.1 downstream_gene_variant ; 2286.0bp to feature; MODIFIER silent_mutation Average:36.675; most accessible tissue: Callus, score: 76.484 N N N N
vg0605295746 C -> T LOC_Os06g10300.1 intron_variant ; MODIFIER silent_mutation Average:36.675; most accessible tissue: Callus, score: 76.484 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0605295746 2.12E-22 2.59E-40 mr1201 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
vg0605295746 4.68E-21 3.67E-43 mr1201 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
vg0605295746 1.11E-18 1.89E-31 mr1219 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
vg0605295746 7.34E-20 1.75E-39 mr1219 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
vg0605295746 1.93E-21 1.99E-40 mr1274 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
vg0605295746 5.00E-21 7.17E-38 mr1274 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
vg0605295746 1.79E-20 4.76E-37 mr1201_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
vg0605295746 1.39E-20 1.99E-38 mr1201_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
vg0605295746 4.46E-18 4.90E-29 mr1219_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
vg0605295746 1.18E-19 4.55E-36 mr1219_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
vg0605295746 3.82E-19 8.43E-37 mr1274_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
vg0605295746 9.67E-20 4.39E-38 mr1274_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