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Detailed information for vg0607699285:

Variant ID: vg0607699285 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 7699285
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:


AACTACAGTATCCCATGGATTCGCTTCAGAAGTCCCACGATTTGTGCCTGAAGCGCAAGCTTGTTGATGATTGCCTGTCGAAAGACTTCAAGTATCGCCG[C/T]
GTCGAAGAGGATAATGTATCTTCCAATGTGGAGAGCAGGCCCTTACCCGGTTCACCTTCTCAGAGTTGCTGCATTCAACCTAATCTGGCTAAAGATTGTG

Reverse complement sequence

CACAATCTTTAGCCAGATTAGGTTGAATGCAGCAACTCTGAGAAGGTGAACCGGGTAAGGGCCTGCTCTCCACATTGGAAGATACATTATCCTCTTCGAC[G/A]
CGGCGATACTTGAAGTCTTTCGACAGGCAATCATCAACAAGCTTGCGCTTCAGGCACAAATCGTGGGACTTCTGAAGCGAATCCATGGGATACTGTAGTT

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 94.90% 3.70% 1.38% 0.00% NA
All Indica  2759 91.40% 6.20% 2.36% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 71.30% 20.50% 8.24% 0.00% NA
Indica II  465 98.10% 0.60% 1.29% 0.00% NA
Indica III  913 99.10% 0.80% 0.11% 0.00% NA
Indica Intermediate  786 93.80% 5.10% 1.15% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 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 95.60% 4.40% 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
vg0607699285 C -> T LOC_Os06g13860.1 synonymous_variant ; p.Arg29Arg; LOW synonymous_codon Average:74.391; most accessible tissue: Callus, score: 87.863 N N N N
vg0607699285 C -> T LOC_Os06g13860.2 synonymous_variant ; p.Arg29Arg; LOW synonymous_codon Average:74.391; most accessible tissue: Callus, score: 87.863 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0607699285 NA 5.94E-12 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
vg0607699285 NA 1.97E-11 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
vg0607699285 NA 1.87E-07 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
vg0607699285 NA 9.46E-09 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
vg0607699285 NA 4.16E-10 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
vg0607699285 NA 9.58E-09 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
vg0607699285 4.26E-07 7.74E-15 mr1201_2 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
vg0607699285 7.90E-07 6.37E-14 mr1201_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
vg0607699285 NA 2.46E-08 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
vg0607699285 NA 5.26E-10 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
vg0607699285 NA 1.60E-13 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
vg0607699285 NA 1.89E-13 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