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Detailed information for vg0606584760:

Variant ID: vg0606584760 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 6584760
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.01, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


GGGGTATTTATTGTCAAAATTAAATGTGCTAACCGCATAAAAAATGCCACTTGTTCGTGACTGAAGGAGGGATTTGAGTACTATCATTTTGAGATCCCAC[C/T]
ACGGAAGACACAATTTTACCCATCACACCCATGCACACCACATCCTCAATTACAAAATATAGAAAATTATATTTTAAAAAATATGTATCTTTATTTTCTT

Reverse complement sequence

AAGAAAATAAAGATACATATTTTTTAAAATATAATTTTCTATATTTTGTAATTGAGGATGTGGTGTGCATGGGTGTGATGGGTAAAATTGTGTCTTCCGT[G/A]
GTGGGATCTCAAAATGATAGTACTCAAATCCCTCCTTCAGTCACGAACAAGTGGCATTTTTTATGCGGTTAGCACATTTAATTTTGACAATAAATACCCC

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 91.50% 7.40% 1.06% 0.00% NA
All Indica  2759 85.80% 12.40% 1.74% 0.00% NA
All Japonica  1512 99.60% 0.30% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.20% 0.00% 1.85% 0.00% NA
Indica II  465 70.50% 27.30% 2.15% 0.00% NA
Indica III  913 86.40% 13.40% 0.22% 0.00% NA
Indica Intermediate  786 84.90% 12.00% 3.18% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.40% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 3.30% 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
vg0606584760 C -> T LOC_Os06g12240.1 intron_variant ; MODIFIER silent_mutation Average:73.865; most accessible tissue: Callus, score: 93.469 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0606584760 NA 7.60E-07 mr1928 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
vg0606584760 NA 1.15E-07 mr1951 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
vg0606584760 3.91E-06 NA mr1970 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
vg0606584760 NA 6.27E-09 mr1970 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
vg0606584760 NA 1.00E-07 mr1973 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
vg0606584760 NA 9.13E-07 mr1498_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
vg0606584760 NA 6.82E-06 mr1951_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
vg0606584760 NA 1.48E-06 mr1970_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
vg0606584760 NA 4.06E-07 mr1973_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